Starting phenix.real_space_refine on Mon Sep 14 03:06:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7py1_13707/09_2026/7py1_13707.cif Found real_map, /net/cci-nas-00/data/ceres_data/7py1_13707/09_2026/7py1_13707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7py1_13707/09_2026/7py1_13707.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7py1_13707/09_2026/7py1_13707.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7py1_13707/09_2026/7py1_13707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7py1_13707/09_2026/7py1_13707.map" model { file = "/net/cci-nas-00/data/ceres_data/7py1_13707/09_2026/7py1_13707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7py1_13707/09_2026/7py1_13707.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.036 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 75 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 16966 2.51 5 N 4863 2.21 5 O 5422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27442 Number of models: 1 Model: "" Number of chains: 10 Chain: "N" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 620 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain breaks: 1 Chain: "T" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 690 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "R" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 235 Classifications: {'RNAv2': 11} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "A" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1706 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 1 Chain: "B" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Chain: "C" Number of atoms: 10548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10548 Classifications: {'peptide': 1337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1280} Chain breaks: 1 Chain: "D" Number of atoms: 10388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10388 Classifications: {'peptide': 1335} Link IDs: {'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 Chain: "E" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "G" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 987 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} 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 15931 SG CYS D 70 23.808 56.226 95.610 1.00117.23 S ATOM 15945 SG CYS D 72 24.017 53.800 98.142 1.00121.27 S ATOM 21765 SG CYS D 814 44.027 122.965 90.186 1.00 81.42 S ATOM 22330 SG CYS D 888 45.127 118.500 90.716 1.00 69.27 S ATOM 22381 SG CYS D 895 43.791 120.121 87.625 1.00 59.88 S ATOM 22402 SG CYS D 898 46.845 121.099 88.703 1.00 57.14 S Time building chain proxies: 5.51, per 1000 atoms: 0.20 Number of scatterers: 27442 At special positions: 0 Unit cell: (135.3, 167.2, 169.4, 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 113 16.00 P 75 15.00 Mg 1 11.99 O 5422 8.00 N 4863 7.00 C 16966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " Number of angles added : 6 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6102 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 52 sheets defined 36.0% alpha, 14.6% beta 32 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 4.280A pdb=" N ASN A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 212 through 230 removed outlier: 3.834A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.926A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.951A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 229 removed outlier: 3.712A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 10 removed outlier: 3.709A pdb=" N LYS C 9 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG C 10 " --> pdb=" O GLU C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.985A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 163 through 167 removed outlier: 4.177A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.916A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.631A pdb=" N ARG C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 345 through 353 Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.787A pdb=" N ARG C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 387 Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.515A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.632A pdb=" N GLU C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 607 through 614' Processing helix chain 'C' and resid 663 through 668 removed outlier: 4.014A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 Processing helix chain 'C' and resid 704 through 712 removed outlier: 4.006A pdb=" N VAL C 708 " --> pdb=" O MET C 704 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 712 " --> pdb=" O VAL C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 826 Processing helix chain 'C' and resid 942 through 977 removed outlier: 3.547A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN C 965 " --> pdb=" O SER C 961 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 992 removed outlier: 3.882A pdb=" N LYS C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.552A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.728A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 4.042A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 4.265A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1175 Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.750A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.547A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1293 Processing helix chain 'C' and resid 1299 through 1309 removed outlier: 3.648A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.814A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.614A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 4.028A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.614A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.955A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 284 removed outlier: 3.794A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 369 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 408 through 415 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 452 through 458 removed outlier: 4.086A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 505 through 514 removed outlier: 3.565A pdb=" N THR D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.875A pdb=" N GLU D 534 " --> pdb=" O PRO D 530 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 removed outlier: 4.223A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 4.090A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.838A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 634 Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.566A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.921A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.535A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.135A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.609A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.584A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.753A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 1068 through 1073 removed outlier: 3.545A pdb=" N ASP D1073 " --> pdb=" O ALA D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.501A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D1234 " --> pdb=" O THR D1230 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.568A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 removed outlier: 3.814A pdb=" N ASN D1295 " --> pdb=" O GLU D1291 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1319 through 1324 Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1347 through 1354 removed outlier: 3.634A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1361 through 1373 removed outlier: 4.589A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 15 through 33 removed outlier: 3.544A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.659A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 73 Processing helix chain 'G' and resid 18 through 34 Processing helix chain 'G' and resid 77 through 86 removed outlier: 3.609A pdb=" N VAL G 86 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 4.384A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 13 through 18 removed outlier: 4.384A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N LEU A 198 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ALA A 189 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LYS A 200 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL A 187 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL A 202 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N TYR A 185 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLU A 204 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ILE A 183 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU A 206 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.591A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A 143 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 60 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.750A pdb=" N ARG A 91 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU A 122 " --> pdb=" O ARG A 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 111 removed outlier: 4.090A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 13 removed outlier: 3.707A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N HIS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 13 removed outlier: 3.707A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET B 205 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU B 188 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU B 204 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 104 removed outlier: 3.998A pdb=" N VAL B 98 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL B 146 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 100 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL B 59 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 171 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AB1, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.816A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 152 through 153 removed outlier: 4.013A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 175 " --> pdb=" O VAL B 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.769A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 60 removed outlier: 4.958A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 100 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 102 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS C 118 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 143 through 145 removed outlier: 3.650A pdb=" N VAL C 144 " --> pdb=" O GLN C 513 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 451 through 453 removed outlier: 6.126A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 158 removed outlier: 4.308A pdb=" N ASN C 173 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 228 through 231 removed outlier: 3.526A pdb=" N THR C 335 " --> pdb=" O VAL C 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 239 through 240 removed outlier: 3.512A pdb=" N MET C 239 " --> pdb=" O ILE C 285 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 256 through 257 removed outlier: 3.827A pdb=" N ALA C 257 " --> pdb=" O LYS C 260 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.019A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 301 through 302 removed outlier: 6.696A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.846A pdb=" N THR C 589 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU C 606 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS C 593 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.502A pdb=" N MET C 653 " --> pdb=" O ARG C 592 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 634 through 636 Processing sheet with id=AC7, first strand: chain 'C' and resid 716 through 717 removed outlier: 7.146A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 750 through 752 removed outlier: 3.598A pdb=" N ILE C 732 " --> pdb=" O TYR C 751 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.518A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AD2, first strand: chain 'C' and resid 1076 through 1080 removed outlier: 7.484A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE C 804 " --> pdb=" O THR C1226 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 830 through 841 removed outlier: 6.322A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 882 through 884 removed outlier: 3.674A pdb=" N LEU C 883 " --> pdb=" O LEU C 918 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 887 through 888 removed outlier: 3.561A pdb=" N LYS C 914 " --> pdb=" O THR C 888 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.505A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL D 468 " --> pdb=" O GLY D 351 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET D 466 " --> pdb=" O SER D 353 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN D 424 " --> pdb=" O ALA D 467 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 421 " --> pdb=" O PHE D 437 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.505A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1335 through 1339 removed outlier: 3.675A pdb=" N ILE D 20 " --> pdb=" O ASP D1342 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP D1342 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 104 through 112 removed outlier: 3.518A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.319A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AE2, first strand: chain 'D' and resid 366 through 368 removed outlier: 6.568A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'D' and resid 526 through 527 removed outlier: 4.048A pdb=" N ARG D 551 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D 550 " --> pdb=" O LYS D 570 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS D 566 " --> pdb=" O GLU D 554 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE5, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.638A pdb=" N VAL D 882 " --> pdb=" O ILE D 820 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 825 through 826 removed outlier: 7.342A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 949 through 951 removed outlier: 3.764A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 991 through 995 removed outlier: 4.177A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1024 through 1026 Processing sheet with id=AF1, first strand: chain 'D' and resid 1034 through 1038 removed outlier: 3.579A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU D1078 " --> pdb=" O TYR D1099 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1046 through 1048 Processing sheet with id=AF3, first strand: chain 'D' and resid 1155 through 1156 removed outlier: 6.657A pdb=" N ILE D1155 " --> pdb=" O ILE D1210 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1175 through 1178 Processing sheet with id=AF5, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 3.595A pdb=" N VAL D1280 " --> pdb=" O ALA D1264 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 68 through 71 removed outlier: 4.503A pdb=" N GLY G 91 " --> pdb=" O GLN G 13 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 47 through 48 929 hydrogen bonds defined for protein. 2601 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 85 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 7.38 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8931 1.34 - 1.46: 3861 1.46 - 1.58: 14872 1.58 - 1.70: 146 1.70 - 1.82: 198 Bond restraints: 28008 Sorted by residual: bond pdb=" C3' DC N 35 " pdb=" C2' DC N 35 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DG N 26 " pdb=" C2' DG N 26 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DC N 13 " pdb=" C2' DC N 13 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DT N 20 " pdb=" C2' DT N 20 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DT T 2 " pdb=" C2' DT T 2 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 ... (remaining 28003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 37275 1.81 - 3.63: 771 3.63 - 5.44: 70 5.44 - 7.26: 21 7.26 - 9.07: 4 Bond angle restraints: 38141 Sorted by residual: angle pdb=" C3' U R 4 " pdb=" O3' U R 4 " pdb=" P C R 5 " ideal model delta sigma weight residual 119.70 125.24 -5.54 1.20e+00 6.94e-01 2.13e+01 angle pdb=" CA TYR C1018 " pdb=" CB TYR C1018 " pdb=" CG TYR C1018 " ideal model delta sigma weight residual 113.90 122.12 -8.22 1.80e+00 3.09e-01 2.08e+01 angle pdb=" N3 DT T 12 " pdb=" C4 DT T 12 " pdb=" O4 DT T 12 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT T 13 " pdb=" C4 DT T 13 " pdb=" O4 DT T 13 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT T 32 " pdb=" C4 DT T 32 " pdb=" O4 DT T 32 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 ... (remaining 38136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 16463 35.17 - 70.34: 517 70.34 - 105.51: 36 105.51 - 140.68: 1 140.68 - 175.85: 4 Dihedral angle restraints: 17021 sinusoidal: 7536 harmonic: 9485 Sorted by residual: dihedral pdb=" C4' C R 5 " pdb=" C3' C R 5 " pdb=" C2' C R 5 " pdb=" C1' C R 5 " ideal model delta sinusoidal sigma weight residual 36.34 -35.50 71.85 1 3.10e+00 1.04e-01 6.88e+02 dihedral pdb=" C4' U R 4 " pdb=" C3' U R 4 " pdb=" C2' U R 4 " pdb=" C1' U R 4 " ideal model delta sinusoidal sigma weight residual 36.34 -30.90 67.25 1 3.10e+00 1.04e-01 6.13e+02 dihedral pdb=" O4' C R 5 " pdb=" C4' C R 5 " pdb=" C3' C R 5 " pdb=" C2' C R 5 " ideal model delta sinusoidal sigma weight residual -35.15 23.92 -59.07 1 4.00e+00 6.25e-02 2.92e+02 ... (remaining 17018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3876 0.070 - 0.140: 457 0.140 - 0.211: 3 0.211 - 0.281: 13 0.281 - 0.351: 2 Chirality restraints: 4351 Sorted by residual: chirality pdb=" P C R 5 " pdb=" OP1 C R 5 " pdb=" OP2 C R 5 " pdb=" O5' C R 5 " both_signs ideal model delta sigma weight residual True 2.17 -2.52 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" C2' U R 4 " pdb=" C3' U R 4 " pdb=" O2' U R 4 " pdb=" C1' U R 4 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C2' C R 5 " pdb=" C3' C R 5 " pdb=" O2' C R 5 " pdb=" C1' C R 5 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 4348 not shown) Planarity restraints: 4731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 177 " 0.057 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO C 178 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 178 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 178 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 287 " 0.038 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO D 288 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 288 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 288 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 125 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO A 126 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " -0.029 5.00e-02 4.00e+02 ... (remaining 4728 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 737 2.70 - 3.25: 26800 3.25 - 3.80: 41539 3.80 - 4.35: 50526 4.35 - 4.90: 83440 Nonbonded interactions: 203042 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.154 2.170 nonbonded pdb=" O3' G R 14 " pdb="MG MG D1501 " model vdw 2.177 2.170 nonbonded pdb=" N CYS D 72 " pdb="ZN ZN D1502 " model vdw 2.187 2.310 nonbonded pdb=" O VAL C 884 " pdb=" OG SER C 917 " model vdw 2.222 3.040 nonbonded pdb=" O GLN C1013 " pdb=" NE2 GLN C1017 " model vdw 2.230 3.120 ... (remaining 203037 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 7 through 158 or resid 170 through 232)) selection = (chain 'B' and resid 7 through 232) } 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 31.930 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 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 : 0.003 0.187 28014 Z= 0.205 Angle : 0.640 39.083 38147 Z= 0.361 Chirality : 0.044 0.351 4351 Planarity : 0.004 0.087 4731 Dihedral : 16.416 175.852 10919 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.16 % Rotamer: Outliers : 0.04 % Allowed : 0.11 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.14), residues: 3285 helix: 1.17 (0.17), residues: 1052 sheet: -0.26 (0.29), residues: 324 loop : -1.38 (0.13), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 275 TYR 0.032 0.001 TYR C1018 PHE 0.019 0.001 PHE D1325 TRP 0.026 0.001 TRP C 997 HIS 0.011 0.001 HIS G 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.19 (28008) covalent geometry : angle 0.59209 / 0.36 (38141) hydrogen bonds : bond 0.18438 / 20.78 ( 1001) hydrogen bonds : angle 6.25348 / 6.92 ( 2771) metal coordination : bond 0.13078 / 10.41 ( 6) metal coordination : angle 19.48317 / 34.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 722 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.6645 (mt-10) cc_final: 0.6439 (mt-10) REVERT: A 143 ARG cc_start: 0.6920 (mpp80) cc_final: 0.5948 (mtm-85) REVERT: A 204 GLU cc_start: 0.7368 (pp20) cc_final: 0.7132 (pp20) REVERT: B 58 GLU cc_start: 0.7414 (pt0) cc_final: 0.7059 (pt0) REVERT: B 80 GLU cc_start: 0.7382 (tp30) cc_final: 0.7180 (tp30) REVERT: B 110 VAL cc_start: 0.7785 (t) cc_final: 0.7535 (t) REVERT: B 123 ILE cc_start: 0.8471 (mp) cc_final: 0.7643 (mp) REVERT: B 185 TYR cc_start: 0.8564 (p90) cc_final: 0.8236 (p90) REVERT: B 200 LYS cc_start: 0.8446 (tttm) cc_final: 0.7998 (tttm) REVERT: B 227 GLN cc_start: 0.7552 (tp40) cc_final: 0.7057 (tp40) REVERT: C 14 ASP cc_start: 0.7047 (t0) cc_final: 0.6702 (t0) REVERT: C 84 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7675 (mt-10) REVERT: C 101 ARG cc_start: 0.7792 (ttm-80) cc_final: 0.7510 (ttm-80) REVERT: C 122 VAL cc_start: 0.8375 (m) cc_final: 0.7815 (p) REVERT: C 124 MET cc_start: 0.7047 (ptm) cc_final: 0.6508 (ppp) REVERT: C 158 ASP cc_start: 0.7173 (m-30) cc_final: 0.6943 (m-30) REVERT: C 160 ASP cc_start: 0.6726 (t70) cc_final: 0.6223 (t0) REVERT: C 179 TYR cc_start: 0.7173 (t80) cc_final: 0.6856 (t80) REVERT: C 180 ARG cc_start: 0.7828 (ttp-170) cc_final: 0.7430 (ttp-170) REVERT: C 196 VAL cc_start: 0.7785 (t) cc_final: 0.7544 (p) REVERT: C 208 ILE cc_start: 0.7250 (pt) cc_final: 0.7044 (mp) REVERT: C 316 GLU cc_start: 0.7168 (tt0) cc_final: 0.6962 (tt0) REVERT: C 337 PHE cc_start: 0.6914 (t80) cc_final: 0.6483 (t80) REVERT: C 386 GLU cc_start: 0.7517 (tp30) cc_final: 0.7269 (tp30) REVERT: C 429 MET cc_start: 0.7262 (tpp) cc_final: 0.6858 (tpt) REVERT: C 441 GLU cc_start: 0.6866 (tp30) cc_final: 0.6600 (tp30) REVERT: C 478 ARG cc_start: 0.7817 (tpt90) cc_final: 0.7477 (tpt90) REVERT: C 481 LEU cc_start: 0.7435 (mt) cc_final: 0.6822 (tt) REVERT: C 504 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7347 (tm-30) REVERT: C 568 ASN cc_start: 0.8193 (p0) cc_final: 0.7598 (p0) REVERT: C 584 TYR cc_start: 0.8472 (m-10) cc_final: 0.8011 (m-10) REVERT: C 636 CYS cc_start: 0.7956 (m) cc_final: 0.7665 (m) REVERT: C 641 GLU cc_start: 0.6765 (pp20) cc_final: 0.6376 (pp20) REVERT: C 717 VAL cc_start: 0.8322 (p) cc_final: 0.7903 (t) REVERT: C 719 LYS cc_start: 0.8238 (mtmm) cc_final: 0.7414 (mtmm) REVERT: C 741 MET cc_start: 0.7109 (ttp) cc_final: 0.6815 (ttp) REVERT: C 793 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6695 (mt-10) REVERT: C 800 MET cc_start: 0.8209 (pmm) cc_final: 0.7898 (pmm) REVERT: C 848 GLU cc_start: 0.6602 (pt0) cc_final: 0.6201 (pt0) REVERT: C 930 ASP cc_start: 0.7577 (t70) cc_final: 0.7290 (t70) REVERT: C 950 GLU cc_start: 0.8088 (tp30) cc_final: 0.7420 (tp30) REVERT: C 951 MET cc_start: 0.7609 (mtp) cc_final: 0.7093 (mtp) REVERT: C 957 LYS cc_start: 0.8520 (tppt) cc_final: 0.8216 (tppt) REVERT: C 1032 LYS cc_start: 0.8438 (ptpp) cc_final: 0.8201 (pttt) REVERT: C 1033 ARG cc_start: 0.8369 (ttm110) cc_final: 0.7803 (ptm-80) REVERT: C 1064 ASP cc_start: 0.8118 (t0) cc_final: 0.7682 (t70) REVERT: C 1066 MET cc_start: 0.7157 (ttp) cc_final: 0.6903 (ttp) REVERT: C 1083 GLU cc_start: 0.7314 (pm20) cc_final: 0.7106 (pm20) REVERT: C 1131 MET cc_start: 0.7757 (ttm) cc_final: 0.7463 (ttp) REVERT: C 1160 ASP cc_start: 0.7546 (p0) cc_final: 0.7290 (p0) REVERT: C 1168 GLU cc_start: 0.7347 (pt0) cc_final: 0.6990 (pm20) REVERT: C 1188 ASP cc_start: 0.7262 (t0) cc_final: 0.7026 (t0) REVERT: C 1200 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8157 (ttpp) REVERT: C 1219 GLU cc_start: 0.7207 (pp20) cc_final: 0.6901 (pp20) REVERT: C 1220 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: C 1240 ASP cc_start: 0.7972 (p0) cc_final: 0.7632 (p0) REVERT: C 1241 ASP cc_start: 0.7508 (m-30) cc_final: 0.6816 (t0) REVERT: C 1304 MET cc_start: 0.7795 (ttp) cc_final: 0.7514 (ttt) REVERT: D 26 SER cc_start: 0.8434 (p) cc_final: 0.8216 (m) REVERT: D 33 TRP cc_start: 0.7051 (m-10) cc_final: 0.6548 (m-10) REVERT: D 53 ARG cc_start: 0.7080 (mmm-85) cc_final: 0.6857 (mtp-110) REVERT: D 74 LYS cc_start: 0.7918 (tmmt) cc_final: 0.7684 (tptp) REVERT: D 88 CYS cc_start: 0.6588 (t) cc_final: 0.5243 (t) REVERT: D 130 MET cc_start: 0.7014 (mtt) cc_final: 0.6663 (mtp) REVERT: D 146 VAL cc_start: 0.8389 (t) cc_final: 0.8045 (p) REVERT: D 148 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7097 (tm-30) REVERT: D 162 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7365 (mm-30) REVERT: D 176 PHE cc_start: 0.7199 (p90) cc_final: 0.6844 (p90) REVERT: D 192 MET cc_start: 0.8022 (ttp) cc_final: 0.7284 (tmm) REVERT: D 200 GLN cc_start: 0.7774 (pp30) cc_final: 0.7500 (pp30) REVERT: D 204 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7883 (mt-10) REVERT: D 216 LYS cc_start: 0.7571 (tttm) cc_final: 0.6980 (tttm) REVERT: D 222 LYS cc_start: 0.8070 (tmtt) cc_final: 0.7667 (tptp) REVERT: D 291 ILE cc_start: 0.7917 (mm) cc_final: 0.7687 (mm) REVERT: D 399 LYS cc_start: 0.8137 (tmmt) cc_final: 0.7585 (tmmt) REVERT: D 462 ASP cc_start: 0.7380 (p0) cc_final: 0.7178 (p0) REVERT: D 497 GLU cc_start: 0.7296 (pp20) cc_final: 0.7068 (pp20) REVERT: D 528 THR cc_start: 0.8111 (m) cc_final: 0.7908 (m) REVERT: D 591 ILE cc_start: 0.8188 (tp) cc_final: 0.7907 (pt) REVERT: D 667 GLN cc_start: 0.7869 (tt0) cc_final: 0.7594 (tm-30) REVERT: D 695 LYS cc_start: 0.8324 (tmmt) cc_final: 0.7879 (tmmt) REVERT: D 698 MET cc_start: 0.7882 (tpp) cc_final: 0.7633 (mmm) REVERT: D 715 LYS cc_start: 0.8300 (mtmm) cc_final: 0.7853 (mtmt) REVERT: D 723 TYR cc_start: 0.7694 (t80) cc_final: 0.7429 (t80) REVERT: D 795 TYR cc_start: 0.8030 (t80) cc_final: 0.7699 (t80) REVERT: D 802 ASP cc_start: 0.7142 (t0) cc_final: 0.6854 (t0) REVERT: D 805 GLN cc_start: 0.7591 (pp30) cc_final: 0.7385 (pp30) REVERT: D 867 GLN cc_start: 0.7733 (tm-30) cc_final: 0.6917 (tm-30) REVERT: D 915 ILE cc_start: 0.8767 (tt) cc_final: 0.8553 (tp) REVERT: D 951 GLN cc_start: 0.7848 (tp40) cc_final: 0.7509 (tp40) REVERT: D 992 LYS cc_start: 0.7404 (mptt) cc_final: 0.7203 (mmtt) REVERT: D 1040 MET cc_start: 0.2061 (ttt) cc_final: 0.1774 (ttp) REVERT: D 1155 ILE cc_start: 0.8506 (mp) cc_final: 0.8266 (mp) REVERT: D 1173 ARG cc_start: 0.4293 (mtm-85) cc_final: 0.3860 (mpp-170) REVERT: D 1175 LEU cc_start: 0.6595 (tt) cc_final: 0.6273 (tt) REVERT: D 1240 VAL cc_start: 0.7808 (t) cc_final: 0.7577 (p) REVERT: E 66 VAL cc_start: 0.9025 (t) cc_final: 0.8815 (p) REVERT: G 43 MET cc_start: 0.6826 (ppp) cc_final: 0.6223 (ppp) REVERT: G 82 LEU cc_start: 0.7302 (mt) cc_final: 0.7041 (mp) outliers start: 1 outliers final: 0 residues processed: 723 average time/residue: 0.2176 time to fit residues: 238.3018 Evaluate side-chains 639 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 638 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1220 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS C 613 ASN C1220 GLN D 489 ASN D 504 GLN D 716 GLN D 865 HIS D 929 GLN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.144008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.111864 restraints weight = 45468.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.115122 restraints weight = 24574.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.117310 restraints weight = 16159.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.118757 restraints weight = 12179.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119588 restraints weight = 10149.399| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 28014 Z= 0.223 Angle : 0.702 20.919 38147 Z= 0.361 Chirality : 0.055 1.661 4351 Planarity : 0.005 0.061 4731 Dihedral : 14.560 175.130 4437 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.69 % Favored : 94.25 % Rotamer: Outliers : 1.77 % Allowed : 11.95 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.14), residues: 3285 helix: 0.98 (0.16), residues: 1084 sheet: -0.26 (0.27), residues: 367 loop : -1.42 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 634 TYR 0.034 0.002 TYR D1232 PHE 0.031 0.002 PHE C 38 TRP 0.020 0.002 TRP C 997 HIS 0.008 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (28008) covalent geometry : angle 0.70040 / 0.36 (38141) hydrogen bonds : bond 0.05070 / 5.54 ( 1001) hydrogen bonds : angle 4.84828 / 5.58 ( 2771) metal coordination : bond 0.02152 / 1.82 ( 6) metal coordination : angle 4.01454 / 7.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 679 time to evaluate : 1.065 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: symmetry clash REVERT: A 143 ARG cc_start: 0.7347 (mpp80) cc_final: 0.6839 (mpp80) REVERT: A 204 GLU cc_start: 0.7412 (pp20) cc_final: 0.7068 (pp20) REVERT: A 215 GLU cc_start: 0.7340 (tm-30) cc_final: 0.7064 (mm-30) REVERT: B 58 GLU cc_start: 0.6996 (pt0) cc_final: 0.6790 (tt0) REVERT: B 76 GLU cc_start: 0.6285 (pm20) cc_final: 0.5908 (pm20) REVERT: B 174 ASP cc_start: 0.7532 (m-30) cc_final: 0.7240 (m-30) REVERT: B 185 TYR cc_start: 0.8518 (p90) cc_final: 0.8266 (p90) REVERT: B 200 LYS cc_start: 0.8547 (tttm) cc_final: 0.8031 (tttm) REVERT: C 14 ASP cc_start: 0.7376 (t0) cc_final: 0.6893 (t0) REVERT: C 101 ARG cc_start: 0.8060 (ttm-80) cc_final: 0.7827 (ttm-80) REVERT: C 124 MET cc_start: 0.6644 (ptm) cc_final: 0.6394 (ppp) REVERT: C 151 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7175 (mtm-85) REVERT: C 158 ASP cc_start: 0.7049 (m-30) cc_final: 0.6822 (m-30) REVERT: C 160 ASP cc_start: 0.6848 (t70) cc_final: 0.6438 (t0) REVERT: C 180 ARG cc_start: 0.7927 (ttp-170) cc_final: 0.7575 (ttp-170) REVERT: C 234 ASP cc_start: 0.7858 (p0) cc_final: 0.7544 (p0) REVERT: C 299 LYS cc_start: 0.7775 (tmtt) cc_final: 0.7532 (tmmt) REVERT: C 337 PHE cc_start: 0.6814 (t80) cc_final: 0.6440 (t80) REVERT: C 429 MET cc_start: 0.7254 (tpp) cc_final: 0.6946 (tpt) REVERT: C 481 LEU cc_start: 0.7707 (mt) cc_final: 0.7244 (tt) REVERT: C 549 ASP cc_start: 0.7088 (t0) cc_final: 0.6835 (t0) REVERT: C 568 ASN cc_start: 0.8272 (p0) cc_final: 0.7679 (p0) REVERT: C 636 CYS cc_start: 0.7841 (m) cc_final: 0.7492 (m) REVERT: C 641 GLU cc_start: 0.6831 (pp20) cc_final: 0.6484 (pp20) REVERT: C 704 MET cc_start: 0.7699 (ppp) cc_final: 0.7148 (ptm) REVERT: C 711 ASP cc_start: 0.7371 (t0) cc_final: 0.6711 (t0) REVERT: C 717 VAL cc_start: 0.8440 (p) cc_final: 0.8151 (t) REVERT: C 719 LYS cc_start: 0.8140 (mtmm) cc_final: 0.7568 (mtmm) REVERT: C 720 ARG cc_start: 0.8259 (mtp85) cc_final: 0.8044 (mtp85) REVERT: C 761 GLN cc_start: 0.8051 (mm110) cc_final: 0.7834 (mm-40) REVERT: C 800 MET cc_start: 0.8039 (pmm) cc_final: 0.7273 (ptp) REVERT: C 802 VAL cc_start: 0.8449 (t) cc_final: 0.8098 (p) REVERT: C 805 MET cc_start: 0.7449 (ttm) cc_final: 0.7213 (ttm) REVERT: C 848 GLU cc_start: 0.6501 (pt0) cc_final: 0.6229 (pt0) REVERT: C 877 VAL cc_start: 0.8877 (p) cc_final: 0.8543 (m) REVERT: C 914 LYS cc_start: 0.6712 (ptmm) cc_final: 0.6474 (ptmm) REVERT: C 930 ASP cc_start: 0.7541 (t70) cc_final: 0.7179 (t70) REVERT: C 950 GLU cc_start: 0.7681 (tp30) cc_final: 0.7072 (tp30) REVERT: C 951 MET cc_start: 0.7270 (mtp) cc_final: 0.6839 (mtp) REVERT: C 957 LYS cc_start: 0.8655 (tppt) cc_final: 0.8422 (tppt) REVERT: C 1033 ARG cc_start: 0.8297 (ttm110) cc_final: 0.7837 (ptm-80) REVERT: C 1064 ASP cc_start: 0.7873 (t0) cc_final: 0.7651 (t70) REVERT: C 1066 MET cc_start: 0.7504 (ttp) cc_final: 0.7304 (ttp) REVERT: C 1131 MET cc_start: 0.7630 (ttm) cc_final: 0.7423 (ttp) REVERT: C 1141 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7280 (tt) REVERT: C 1200 LYS cc_start: 0.8359 (ttmt) cc_final: 0.8087 (ttpp) REVERT: C 1240 ASP cc_start: 0.8039 (p0) cc_final: 0.7812 (p0) REVERT: C 1241 ASP cc_start: 0.7658 (m-30) cc_final: 0.7026 (t0) REVERT: C 1274 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6496 (mm-30) REVERT: C 1297 ASP cc_start: 0.7411 (t0) cc_final: 0.7059 (t0) REVERT: D 26 SER cc_start: 0.8609 (p) cc_final: 0.8265 (m) REVERT: D 33 TRP cc_start: 0.7424 (m-10) cc_final: 0.6812 (m-10) REVERT: D 60 ARG cc_start: 0.7088 (ttm-80) cc_final: 0.6673 (ttm-80) REVERT: D 71 LEU cc_start: 0.8778 (tp) cc_final: 0.8560 (tt) REVERT: D 117 LEU cc_start: 0.8474 (tp) cc_final: 0.8240 (tt) REVERT: D 130 MET cc_start: 0.7094 (mtt) cc_final: 0.6756 (mtp) REVERT: D 146 VAL cc_start: 0.8253 (t) cc_final: 0.7940 (p) REVERT: D 158 GLN cc_start: 0.7792 (tt0) cc_final: 0.7313 (tt0) REVERT: D 162 GLU cc_start: 0.7290 (mm-30) cc_final: 0.7012 (mm-30) REVERT: D 176 PHE cc_start: 0.7541 (p90) cc_final: 0.6960 (p90) REVERT: D 192 MET cc_start: 0.7832 (ttp) cc_final: 0.7092 (tmm) REVERT: D 200 GLN cc_start: 0.7693 (pp30) cc_final: 0.7428 (pp30) REVERT: D 216 LYS cc_start: 0.7640 (tttm) cc_final: 0.7350 (tttm) REVERT: D 222 LYS cc_start: 0.8148 (tmtt) cc_final: 0.7862 (tttm) REVERT: D 322 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6990 (pmt170) REVERT: D 399 LYS cc_start: 0.8186 (tmmt) cc_final: 0.7544 (tmmt) REVERT: D 402 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6901 (tm-30) REVERT: D 534 GLU cc_start: 0.6740 (tm-30) cc_final: 0.6315 (tp30) REVERT: D 538 ARG cc_start: 0.8231 (tpp80) cc_final: 0.7684 (tpp80) REVERT: D 555 TYR cc_start: 0.8399 (m-80) cc_final: 0.8147 (m-80) REVERT: D 556 GLU cc_start: 0.6990 (pm20) cc_final: 0.6732 (pm20) REVERT: D 591 ILE cc_start: 0.8150 (tp) cc_final: 0.7726 (tp) REVERT: D 648 GLU cc_start: 0.7371 (pm20) cc_final: 0.7131 (tp30) REVERT: D 695 LYS cc_start: 0.8450 (tmmt) cc_final: 0.7900 (tmmt) REVERT: D 697 MET cc_start: 0.7979 (tmm) cc_final: 0.7673 (tmm) REVERT: D 698 MET cc_start: 0.7999 (tpp) cc_final: 0.7684 (mmm) REVERT: D 715 LYS cc_start: 0.8274 (mtmm) cc_final: 0.7863 (mtmt) REVERT: D 802 ASP cc_start: 0.7350 (t0) cc_final: 0.6993 (t0) REVERT: D 805 GLN cc_start: 0.7820 (pp30) cc_final: 0.7524 (pp30) REVERT: D 871 LEU cc_start: 0.8328 (tp) cc_final: 0.8119 (tt) REVERT: D 992 LYS cc_start: 0.7863 (mptt) cc_final: 0.7640 (mmtt) REVERT: D 1231 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.6536 (ttm170) REVERT: D 1343 GLU cc_start: 0.7000 (pm20) cc_final: 0.6748 (pm20) REVERT: E 53 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7550 (mm-30) REVERT: G 43 MET cc_start: 0.6780 (ppp) cc_final: 0.6279 (ppp) REVERT: G 76 ASN cc_start: 0.8115 (m-40) cc_final: 0.7763 (m-40) REVERT: G 82 LEU cc_start: 0.7359 (mt) cc_final: 0.7038 (mt) outliers start: 50 outliers final: 34 residues processed: 697 average time/residue: 0.2238 time to fit residues: 233.7743 Evaluate side-chains 687 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 649 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 557 LYS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1231 ARG Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1326 GLN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 74 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 2 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 179 optimal weight: 0.3980 chunk 204 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 221 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 ASN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 613 ASN C 673 HIS D 875 ASN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.144700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.112543 restraints weight = 45367.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.115892 restraints weight = 24407.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.118127 restraints weight = 15927.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119575 restraints weight = 11916.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.120308 restraints weight = 9915.162| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28014 Z= 0.158 Angle : 0.620 12.427 38147 Z= 0.324 Chirality : 0.047 0.805 4351 Planarity : 0.004 0.066 4731 Dihedral : 14.572 177.747 4434 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.48 % Favored : 94.46 % Rotamer: Outliers : 2.20 % Allowed : 15.93 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.14), residues: 3285 helix: 1.04 (0.16), residues: 1085 sheet: -0.06 (0.27), residues: 372 loop : -1.45 (0.13), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 478 TYR 0.028 0.002 TYR D1232 PHE 0.031 0.001 PHE C 38 TRP 0.013 0.001 TRP C 997 HIS 0.006 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (28008) covalent geometry : angle 0.61841 / 0.32 (38141) hydrogen bonds : bond 0.04633 / 5.11 ( 1001) hydrogen bonds : angle 4.63043 / 5.39 ( 2771) metal coordination : bond 0.00711 / 0.78 ( 6) metal coordination : angle 3.80860 / 6.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 673 time to evaluate : 1.091 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: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8036 (t0) cc_final: 0.7768 (t0) REVERT: A 204 GLU cc_start: 0.7463 (pp20) cc_final: 0.7064 (pp20) REVERT: A 215 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6963 (mm-30) REVERT: B 58 GLU cc_start: 0.6997 (pt0) cc_final: 0.6734 (pt0) REVERT: B 76 GLU cc_start: 0.6178 (pm20) cc_final: 0.5898 (pm20) REVERT: B 174 ASP cc_start: 0.7526 (m-30) cc_final: 0.7242 (m-30) REVERT: B 206 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6741 (tt0) REVERT: C 14 ASP cc_start: 0.7355 (t0) cc_final: 0.6877 (t0) REVERT: C 36 GLN cc_start: 0.7841 (tp40) cc_final: 0.6930 (tm-30) REVERT: C 101 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7716 (ttm-80) REVERT: C 122 VAL cc_start: 0.7928 (p) cc_final: 0.7625 (p) REVERT: C 124 MET cc_start: 0.6588 (ptm) cc_final: 0.6287 (ppp) REVERT: C 151 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7218 (mtm-85) REVERT: C 158 ASP cc_start: 0.7050 (m-30) cc_final: 0.6797 (m-30) REVERT: C 160 ASP cc_start: 0.6839 (t70) cc_final: 0.6427 (t0) REVERT: C 180 ARG cc_start: 0.7925 (ttp-170) cc_final: 0.7708 (tmm-80) REVERT: C 234 ASP cc_start: 0.7890 (p0) cc_final: 0.7538 (p0) REVERT: C 337 PHE cc_start: 0.6730 (t80) cc_final: 0.6331 (t80) REVERT: C 429 MET cc_start: 0.7254 (tpp) cc_final: 0.6926 (tpt) REVERT: C 441 GLU cc_start: 0.6984 (tp30) cc_final: 0.6783 (tp30) REVERT: C 568 ASN cc_start: 0.8282 (p0) cc_final: 0.7685 (p0) REVERT: C 611 GLU cc_start: 0.7459 (tt0) cc_final: 0.7230 (tm-30) REVERT: C 636 CYS cc_start: 0.7878 (m) cc_final: 0.7512 (m) REVERT: C 641 GLU cc_start: 0.6845 (pp20) cc_final: 0.6483 (pp20) REVERT: C 704 MET cc_start: 0.7574 (ppp) cc_final: 0.7016 (ptm) REVERT: C 711 ASP cc_start: 0.7405 (t0) cc_final: 0.6710 (t0) REVERT: C 717 VAL cc_start: 0.8432 (p) cc_final: 0.8142 (t) REVERT: C 719 LYS cc_start: 0.8157 (mtmm) cc_final: 0.7568 (mtmm) REVERT: C 720 ARG cc_start: 0.8231 (mtp85) cc_final: 0.7956 (mtp85) REVERT: C 793 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6595 (mt-10) REVERT: C 800 MET cc_start: 0.7939 (pmm) cc_final: 0.7131 (ptp) REVERT: C 848 GLU cc_start: 0.6482 (pt0) cc_final: 0.6203 (pt0) REVERT: C 877 VAL cc_start: 0.8916 (p) cc_final: 0.8610 (m) REVERT: C 914 LYS cc_start: 0.6723 (ptmm) cc_final: 0.6478 (ptmm) REVERT: C 930 ASP cc_start: 0.7511 (t70) cc_final: 0.7161 (t70) REVERT: C 936 ARG cc_start: 0.7198 (ptt90) cc_final: 0.6941 (ppt90) REVERT: C 950 GLU cc_start: 0.7732 (tp30) cc_final: 0.7131 (tp30) REVERT: C 951 MET cc_start: 0.7271 (mtp) cc_final: 0.6849 (mtp) REVERT: C 957 LYS cc_start: 0.8646 (tppt) cc_final: 0.8398 (tppt) REVERT: C 1033 ARG cc_start: 0.8239 (ttm110) cc_final: 0.7841 (ptm-80) REVERT: C 1064 ASP cc_start: 0.7837 (t0) cc_final: 0.7622 (t70) REVERT: C 1066 MET cc_start: 0.7508 (ttp) cc_final: 0.7247 (mtm) REVERT: C 1131 MET cc_start: 0.7639 (ttm) cc_final: 0.7423 (ttp) REVERT: C 1141 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7210 (tt) REVERT: C 1200 LYS cc_start: 0.8342 (ttmt) cc_final: 0.8054 (ttpp) REVERT: C 1231 TYR cc_start: 0.8468 (t80) cc_final: 0.8193 (t80) REVERT: C 1232 MET cc_start: 0.7582 (mtp) cc_final: 0.7340 (mtt) REVERT: C 1240 ASP cc_start: 0.8112 (p0) cc_final: 0.7760 (p0) REVERT: C 1241 ASP cc_start: 0.7680 (m-30) cc_final: 0.6985 (t0) REVERT: C 1270 PHE cc_start: 0.7730 (t80) cc_final: 0.7500 (t80) REVERT: C 1297 ASP cc_start: 0.7442 (t0) cc_final: 0.7069 (t0) REVERT: D 26 SER cc_start: 0.8584 (p) cc_final: 0.8268 (m) REVERT: D 33 TRP cc_start: 0.7240 (m-10) cc_final: 0.6839 (m-10) REVERT: D 60 ARG cc_start: 0.7075 (ttm-80) cc_final: 0.6592 (ttm-80) REVERT: D 71 LEU cc_start: 0.8780 (tp) cc_final: 0.8548 (tt) REVERT: D 117 LEU cc_start: 0.8478 (tp) cc_final: 0.8244 (tt) REVERT: D 130 MET cc_start: 0.7073 (mtt) cc_final: 0.6765 (mtp) REVERT: D 162 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6992 (mm-30) REVERT: D 176 PHE cc_start: 0.7498 (p90) cc_final: 0.6888 (p90) REVERT: D 192 MET cc_start: 0.7839 (ttp) cc_final: 0.7121 (tmm) REVERT: D 222 LYS cc_start: 0.8135 (tmtt) cc_final: 0.7818 (tttm) REVERT: D 235 GLU cc_start: 0.7699 (pt0) cc_final: 0.7376 (pt0) REVERT: D 322 ARG cc_start: 0.7330 (pmt170) cc_final: 0.6971 (pmt170) REVERT: D 399 LYS cc_start: 0.8165 (tmmt) cc_final: 0.7443 (tmmt) REVERT: D 402 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6712 (tm-30) REVERT: D 416 ILE cc_start: 0.8017 (tt) cc_final: 0.7668 (tt) REVERT: D 534 GLU cc_start: 0.6734 (tm-30) cc_final: 0.6475 (tm-30) REVERT: D 538 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7909 (tpp80) REVERT: D 556 GLU cc_start: 0.7119 (pm20) cc_final: 0.6764 (pm20) REVERT: D 591 ILE cc_start: 0.8028 (tp) cc_final: 0.7756 (tp) REVERT: D 634 ARG cc_start: 0.7862 (mmm-85) cc_final: 0.7507 (mmm-85) REVERT: D 663 GLU cc_start: 0.7572 (pp20) cc_final: 0.6715 (pp20) REVERT: D 667 GLN cc_start: 0.6858 (pt0) cc_final: 0.6630 (pm20) REVERT: D 695 LYS cc_start: 0.8457 (tmmt) cc_final: 0.7898 (tmmt) REVERT: D 697 MET cc_start: 0.7944 (tmm) cc_final: 0.7536 (tmm) REVERT: D 698 MET cc_start: 0.8008 (tpp) cc_final: 0.7347 (tmm) REVERT: D 715 LYS cc_start: 0.8278 (mtmm) cc_final: 0.7880 (mtmt) REVERT: D 802 ASP cc_start: 0.7400 (t0) cc_final: 0.7036 (t0) REVERT: D 805 GLN cc_start: 0.7821 (pp30) cc_final: 0.7560 (pp30) REVERT: D 822 MET cc_start: 0.6628 (OUTLIER) cc_final: 0.6357 (tpp) REVERT: D 873 GLU cc_start: 0.7563 (tt0) cc_final: 0.7204 (tm-30) REVERT: D 951 GLN cc_start: 0.7401 (tp40) cc_final: 0.7106 (tp40) REVERT: D 1261 LEU cc_start: 0.8246 (pp) cc_final: 0.7871 (pp) REVERT: D 1343 GLU cc_start: 0.6913 (pm20) cc_final: 0.6627 (pm20) REVERT: E 53 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7539 (mm-30) REVERT: G 43 MET cc_start: 0.6783 (ppp) cc_final: 0.6203 (ppp) REVERT: G 68 TYR cc_start: 0.7354 (m-10) cc_final: 0.7085 (m-80) REVERT: G 76 ASN cc_start: 0.7980 (m-40) cc_final: 0.6982 (p0) REVERT: G 82 LEU cc_start: 0.7365 (mt) cc_final: 0.7009 (mt) outliers start: 62 outliers final: 45 residues processed: 694 average time/residue: 0.2180 time to fit residues: 227.3554 Evaluate side-chains 708 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 659 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 118 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 271 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 225 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C 659 GLN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS D1279 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.142804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.110371 restraints weight = 45050.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113679 restraints weight = 24352.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.115902 restraints weight = 15972.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.117250 restraints weight = 12054.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.118195 restraints weight = 10082.762| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 28014 Z= 0.219 Angle : 0.654 9.045 38147 Z= 0.344 Chirality : 0.046 0.330 4351 Planarity : 0.005 0.069 4731 Dihedral : 14.714 179.710 4434 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.12 % Favored : 93.82 % Rotamer: Outliers : 3.44 % Allowed : 17.63 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.14), residues: 3285 helix: 0.90 (0.16), residues: 1084 sheet: -0.17 (0.26), residues: 377 loop : -1.51 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1345 TYR 0.029 0.002 TYR D1232 PHE 0.033 0.002 PHE C 38 TRP 0.017 0.002 TRP D1193 HIS 0.011 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.22 (28008) covalent geometry : angle 0.65246 / 0.34 (38141) hydrogen bonds : bond 0.05076 / 5.58 ( 1001) hydrogen bonds : angle 4.55146 / 5.34 ( 2771) metal coordination : bond 0.01051 / 1.11 ( 6) metal coordination : angle 4.15006 / 7.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 682 time to evaluate : 0.953 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8102 (t0) cc_final: 0.7810 (t0) REVERT: A 204 GLU cc_start: 0.7432 (pp20) cc_final: 0.6949 (pp20) REVERT: A 215 GLU cc_start: 0.7269 (tm-30) cc_final: 0.6984 (mm-30) REVERT: B 58 GLU cc_start: 0.7149 (pt0) cc_final: 0.6848 (pt0) REVERT: B 76 GLU cc_start: 0.6099 (pm20) cc_final: 0.5896 (pm20) REVERT: B 150 ARG cc_start: 0.7287 (ttp-110) cc_final: 0.6874 (ttm-80) REVERT: B 174 ASP cc_start: 0.7562 (m-30) cc_final: 0.7289 (m-30) REVERT: C 8 LYS cc_start: 0.8400 (tttt) cc_final: 0.8091 (mtpt) REVERT: C 14 ASP cc_start: 0.7438 (t0) cc_final: 0.6959 (t0) REVERT: C 36 GLN cc_start: 0.7938 (tp40) cc_final: 0.6973 (tm-30) REVERT: C 122 VAL cc_start: 0.8050 (p) cc_final: 0.7745 (p) REVERT: C 126 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6702 (mm-30) REVERT: C 158 ASP cc_start: 0.7118 (m-30) cc_final: 0.6864 (m-30) REVERT: C 160 ASP cc_start: 0.6971 (t70) cc_final: 0.6572 (t0) REVERT: C 180 ARG cc_start: 0.7924 (ttp-170) cc_final: 0.7697 (tmm-80) REVERT: C 199 ASP cc_start: 0.6804 (t0) cc_final: 0.6603 (t0) REVERT: C 234 ASP cc_start: 0.7931 (p0) cc_final: 0.7603 (p0) REVERT: C 370 MET cc_start: 0.7487 (tpp) cc_final: 0.7225 (tpp) REVERT: C 386 GLU cc_start: 0.7406 (tp30) cc_final: 0.6936 (tp30) REVERT: C 411 ARG cc_start: 0.8207 (tpp80) cc_final: 0.7972 (tpp80) REVERT: C 429 MET cc_start: 0.7355 (tpp) cc_final: 0.7077 (tpt) REVERT: C 441 GLU cc_start: 0.7071 (tp30) cc_final: 0.6857 (tp30) REVERT: C 461 GLU cc_start: 0.7244 (tt0) cc_final: 0.6624 (tp30) REVERT: C 503 LYS cc_start: 0.7925 (tppt) cc_final: 0.7613 (mtpp) REVERT: C 568 ASN cc_start: 0.8346 (p0) cc_final: 0.7959 (p0) REVERT: C 636 CYS cc_start: 0.7861 (m) cc_final: 0.7544 (m) REVERT: C 641 GLU cc_start: 0.6840 (pp20) cc_final: 0.6490 (pp20) REVERT: C 704 MET cc_start: 0.7656 (ppp) cc_final: 0.7298 (ptm) REVERT: C 711 ASP cc_start: 0.7446 (t0) cc_final: 0.6803 (t0) REVERT: C 717 VAL cc_start: 0.8485 (p) cc_final: 0.8208 (t) REVERT: C 719 LYS cc_start: 0.8064 (mtmm) cc_final: 0.7538 (mtmm) REVERT: C 720 ARG cc_start: 0.8310 (mtp85) cc_final: 0.7775 (mtp85) REVERT: C 740 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6581 (tp30) REVERT: C 793 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6625 (mt-10) REVERT: C 800 MET cc_start: 0.7817 (pmm) cc_final: 0.7153 (ptp) REVERT: C 853 ASP cc_start: 0.7609 (m-30) cc_final: 0.7244 (m-30) REVERT: C 877 VAL cc_start: 0.8890 (p) cc_final: 0.8567 (m) REVERT: C 930 ASP cc_start: 0.7486 (t70) cc_final: 0.7109 (t70) REVERT: C 936 ARG cc_start: 0.7230 (ptt90) cc_final: 0.6945 (ppt90) REVERT: C 950 GLU cc_start: 0.7708 (tp30) cc_final: 0.7100 (tp30) REVERT: C 951 MET cc_start: 0.7301 (mtp) cc_final: 0.6833 (mtp) REVERT: C 957 LYS cc_start: 0.8649 (tppt) cc_final: 0.8438 (tppt) REVERT: C 1033 ARG cc_start: 0.8252 (ttm110) cc_final: 0.8029 (ttm-80) REVERT: C 1064 ASP cc_start: 0.7831 (t0) cc_final: 0.7496 (t70) REVERT: C 1066 MET cc_start: 0.7668 (ttp) cc_final: 0.7444 (mtp) REVERT: C 1131 MET cc_start: 0.7650 (ttm) cc_final: 0.7430 (ttp) REVERT: C 1141 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7357 (tt) REVERT: C 1229 TYR cc_start: 0.7627 (m-80) cc_final: 0.6969 (m-80) REVERT: C 1231 TYR cc_start: 0.8487 (t80) cc_final: 0.8281 (t80) REVERT: C 1240 ASP cc_start: 0.8042 (p0) cc_final: 0.7713 (p0) REVERT: C 1241 ASP cc_start: 0.7652 (m-30) cc_final: 0.6996 (t0) REVERT: C 1297 ASP cc_start: 0.7441 (t0) cc_final: 0.7111 (t0) REVERT: D 33 TRP cc_start: 0.7487 (m-10) cc_final: 0.6980 (m-10) REVERT: D 96 LYS cc_start: 0.8145 (tppt) cc_final: 0.7647 (tppt) REVERT: D 114 ILE cc_start: 0.8226 (mm) cc_final: 0.7780 (tp) REVERT: D 117 LEU cc_start: 0.8565 (tp) cc_final: 0.8297 (tt) REVERT: D 130 MET cc_start: 0.7188 (mtt) cc_final: 0.6901 (mtp) REVERT: D 146 VAL cc_start: 0.8168 (t) cc_final: 0.7792 (p) REVERT: D 162 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7072 (mm-30) REVERT: D 192 MET cc_start: 0.7860 (ttp) cc_final: 0.6970 (tmm) REVERT: D 222 LYS cc_start: 0.8127 (tmtt) cc_final: 0.7852 (tttm) REVERT: D 252 LEU cc_start: 0.7683 (tp) cc_final: 0.7454 (tp) REVERT: D 295 GLU cc_start: 0.6953 (tt0) cc_final: 0.6624 (tt0) REVERT: D 357 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8262 (t) REVERT: D 402 GLU cc_start: 0.7107 (tm-30) cc_final: 0.6731 (tm-30) REVERT: D 416 ILE cc_start: 0.8082 (tt) cc_final: 0.7798 (tt) REVERT: D 556 GLU cc_start: 0.7199 (pm20) cc_final: 0.6769 (pm20) REVERT: D 591 ILE cc_start: 0.8109 (tp) cc_final: 0.7833 (tp) REVERT: D 625 MET cc_start: 0.7262 (tmm) cc_final: 0.6816 (tmm) REVERT: D 695 LYS cc_start: 0.8497 (tmmt) cc_final: 0.8007 (tmmt) REVERT: D 697 MET cc_start: 0.7987 (tmm) cc_final: 0.7556 (tmm) REVERT: D 698 MET cc_start: 0.7971 (tpp) cc_final: 0.7324 (tmm) REVERT: D 715 LYS cc_start: 0.8243 (mtmm) cc_final: 0.7838 (mtmt) REVERT: D 802 ASP cc_start: 0.7534 (t0) cc_final: 0.7127 (t0) REVERT: D 822 MET cc_start: 0.6735 (ttm) cc_final: 0.6413 (tpp) REVERT: D 867 GLN cc_start: 0.7407 (tm-30) cc_final: 0.7072 (tm-30) REVERT: D 873 GLU cc_start: 0.7571 (tt0) cc_final: 0.7224 (tm-30) REVERT: D 905 ARG cc_start: 0.7836 (mmm160) cc_final: 0.7603 (mmm-85) REVERT: D 915 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8013 (pt) REVERT: D 992 LYS cc_start: 0.8006 (mmtt) cc_final: 0.7762 (mmtt) REVERT: D 1146 GLU cc_start: 0.7398 (tm-30) cc_final: 0.6890 (tm-30) REVERT: D 1261 LEU cc_start: 0.8296 (pp) cc_final: 0.7892 (pp) REVERT: D 1343 GLU cc_start: 0.7023 (pm20) cc_final: 0.6736 (pm20) REVERT: E 53 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7597 (mm-30) REVERT: G 43 MET cc_start: 0.6833 (ppp) cc_final: 0.6230 (ppp) REVERT: G 76 ASN cc_start: 0.8105 (m-40) cc_final: 0.7062 (p0) REVERT: G 80 TRP cc_start: 0.7495 (t60) cc_final: 0.7262 (t60) REVERT: G 82 LEU cc_start: 0.7406 (mt) cc_final: 0.7049 (mt) REVERT: G 84 ARG cc_start: 0.7815 (ttm170) cc_final: 0.7461 (ttm170) outliers start: 97 outliers final: 66 residues processed: 728 average time/residue: 0.2119 time to fit residues: 232.2312 Evaluate side-chains 728 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 659 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 224 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 293 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 153 optimal weight: 0.0370 chunk 297 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS B 41 ASN C 258 ASN ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 ASN C 613 ASN C 761 GLN C1099 ASN D 875 ASN ** D 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS D1279 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.144509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.112065 restraints weight = 44495.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.115413 restraints weight = 23996.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117708 restraints weight = 15727.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.119164 restraints weight = 11789.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.119928 restraints weight = 9837.509| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 28014 Z= 0.166 Angle : 0.628 9.202 38147 Z= 0.330 Chirality : 0.045 0.332 4351 Planarity : 0.004 0.069 4731 Dihedral : 14.721 178.422 4434 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.78 % Favored : 94.16 % Rotamer: Outliers : 3.23 % Allowed : 19.76 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.14), residues: 3285 helix: 1.00 (0.16), residues: 1084 sheet: -0.24 (0.26), residues: 390 loop : -1.51 (0.13), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1222 TYR 0.032 0.002 TYR D1186 PHE 0.028 0.001 PHE C 38 TRP 0.017 0.001 TRP D1193 HIS 0.007 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (28008) covalent geometry : angle 0.62672 / 0.33 (38141) hydrogen bonds : bond 0.04487 / 4.95 ( 1001) hydrogen bonds : angle 4.42017 / 5.24 ( 2771) metal coordination : bond 0.00719 / 0.75 ( 6) metal coordination : angle 3.36089 / 6.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 659 time to evaluate : 0.864 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: symmetry clash REVERT: A 204 GLU cc_start: 0.7433 (pp20) cc_final: 0.6951 (pp20) REVERT: A 215 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6943 (mm-30) REVERT: B 58 GLU cc_start: 0.7106 (pt0) cc_final: 0.6854 (pt0) REVERT: B 61 ILE cc_start: 0.7731 (tp) cc_final: 0.7085 (pt) REVERT: B 62 ASP cc_start: 0.7743 (p0) cc_final: 0.7482 (p0) REVERT: B 150 ARG cc_start: 0.7241 (ttp-110) cc_final: 0.6904 (ttm-80) REVERT: B 174 ASP cc_start: 0.7518 (m-30) cc_final: 0.7283 (m-30) REVERT: C 8 LYS cc_start: 0.8379 (tttt) cc_final: 0.8090 (mtpt) REVERT: C 14 ASP cc_start: 0.7378 (t0) cc_final: 0.6936 (t0) REVERT: C 36 GLN cc_start: 0.7949 (tp40) cc_final: 0.6959 (tm-30) REVERT: C 124 MET cc_start: 0.6645 (ptm) cc_final: 0.6366 (ppp) REVERT: C 126 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6652 (mm-30) REVERT: C 158 ASP cc_start: 0.7047 (m-30) cc_final: 0.6805 (m-30) REVERT: C 160 ASP cc_start: 0.6967 (t70) cc_final: 0.6568 (t0) REVERT: C 180 ARG cc_start: 0.7934 (ttp-170) cc_final: 0.7702 (tmm-80) REVERT: C 370 MET cc_start: 0.7468 (tpp) cc_final: 0.7193 (mmm) REVERT: C 429 MET cc_start: 0.7402 (tpp) cc_final: 0.7062 (tpt) REVERT: C 441 GLU cc_start: 0.7070 (tp30) cc_final: 0.6831 (tp30) REVERT: C 503 LYS cc_start: 0.7914 (tppt) cc_final: 0.7616 (mtpp) REVERT: C 568 ASN cc_start: 0.8341 (OUTLIER) cc_final: 0.7946 (p0) REVERT: C 633 LEU cc_start: 0.6762 (mp) cc_final: 0.6260 (tp) REVERT: C 636 CYS cc_start: 0.7833 (m) cc_final: 0.7565 (m) REVERT: C 641 GLU cc_start: 0.6832 (pp20) cc_final: 0.6471 (pp20) REVERT: C 704 MET cc_start: 0.7631 (ppp) cc_final: 0.7319 (ptm) REVERT: C 711 ASP cc_start: 0.7418 (t0) cc_final: 0.6819 (t0) REVERT: C 717 VAL cc_start: 0.8473 (p) cc_final: 0.8169 (t) REVERT: C 719 LYS cc_start: 0.8150 (mtmm) cc_final: 0.7626 (mtmm) REVERT: C 720 ARG cc_start: 0.8301 (mtp85) cc_final: 0.7772 (mtp85) REVERT: C 740 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6585 (tp30) REVERT: C 793 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6589 (mt-10) REVERT: C 800 MET cc_start: 0.7751 (pmm) cc_final: 0.7130 (ptp) REVERT: C 853 ASP cc_start: 0.7647 (m-30) cc_final: 0.7282 (m-30) REVERT: C 877 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8588 (m) REVERT: C 930 ASP cc_start: 0.7454 (t70) cc_final: 0.7107 (t70) REVERT: C 936 ARG cc_start: 0.7195 (ptt90) cc_final: 0.6923 (ppt90) REVERT: C 950 GLU cc_start: 0.7723 (tp30) cc_final: 0.7106 (tp30) REVERT: C 951 MET cc_start: 0.7280 (mtp) cc_final: 0.6833 (mtp) REVERT: C 957 LYS cc_start: 0.8637 (tppt) cc_final: 0.8404 (tppt) REVERT: C 1131 MET cc_start: 0.7671 (ttm) cc_final: 0.7442 (ttp) REVERT: C 1141 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7279 (tt) REVERT: C 1194 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6854 (mt-10) REVERT: C 1229 TYR cc_start: 0.7574 (m-80) cc_final: 0.6835 (m-80) REVERT: C 1231 TYR cc_start: 0.8510 (t80) cc_final: 0.8291 (t80) REVERT: C 1240 ASP cc_start: 0.8042 (p0) cc_final: 0.7696 (p0) REVERT: C 1241 ASP cc_start: 0.7664 (m-30) cc_final: 0.6964 (t0) REVERT: C 1297 ASP cc_start: 0.7436 (t0) cc_final: 0.6522 (p0) REVERT: D 33 TRP cc_start: 0.7407 (m-10) cc_final: 0.6977 (m-10) REVERT: D 60 ARG cc_start: 0.7075 (ttm-80) cc_final: 0.6562 (ttm-80) REVERT: D 96 LYS cc_start: 0.8092 (tppt) cc_final: 0.7703 (tppt) REVERT: D 100 GLU cc_start: 0.7049 (mp0) cc_final: 0.6784 (mp0) REVERT: D 114 ILE cc_start: 0.8229 (mm) cc_final: 0.7770 (tp) REVERT: D 117 LEU cc_start: 0.8552 (tp) cc_final: 0.8306 (tt) REVERT: D 130 MET cc_start: 0.7118 (mtt) cc_final: 0.6845 (mtp) REVERT: D 162 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7039 (mm-30) REVERT: D 176 PHE cc_start: 0.7453 (p90) cc_final: 0.7245 (p90) REVERT: D 190 LYS cc_start: 0.8277 (tptm) cc_final: 0.7887 (tptp) REVERT: D 192 MET cc_start: 0.7818 (ttp) cc_final: 0.6972 (tmm) REVERT: D 193 ASP cc_start: 0.6917 (t0) cc_final: 0.6682 (t0) REVERT: D 222 LYS cc_start: 0.8139 (tmtt) cc_final: 0.7850 (tttm) REVERT: D 252 LEU cc_start: 0.7597 (tp) cc_final: 0.7374 (tp) REVERT: D 280 LYS cc_start: 0.8368 (tptp) cc_final: 0.8138 (tppp) REVERT: D 295 GLU cc_start: 0.7022 (tt0) cc_final: 0.6662 (tt0) REVERT: D 416 ILE cc_start: 0.8073 (tt) cc_final: 0.7766 (tt) REVERT: D 497 GLU cc_start: 0.7131 (pp20) cc_final: 0.6805 (pp20) REVERT: D 538 ARG cc_start: 0.8176 (tpp80) cc_final: 0.7896 (tpp80) REVERT: D 556 GLU cc_start: 0.7192 (pm20) cc_final: 0.6769 (pm20) REVERT: D 591 ILE cc_start: 0.8118 (tp) cc_final: 0.7913 (tp) REVERT: D 625 MET cc_start: 0.7263 (tmm) cc_final: 0.6840 (tmm) REVERT: D 695 LYS cc_start: 0.8472 (tmmt) cc_final: 0.8003 (tmmt) REVERT: D 697 MET cc_start: 0.7982 (tmm) cc_final: 0.7519 (tmm) REVERT: D 698 MET cc_start: 0.7944 (tpp) cc_final: 0.7279 (tmm) REVERT: D 715 LYS cc_start: 0.8228 (mtmm) cc_final: 0.7829 (mtmt) REVERT: D 802 ASP cc_start: 0.7585 (t0) cc_final: 0.6877 (t0) REVERT: D 822 MET cc_start: 0.6560 (ttm) cc_final: 0.6247 (tpp) REVERT: D 867 GLN cc_start: 0.7545 (tm-30) cc_final: 0.7208 (tm-30) REVERT: D 883 ARG cc_start: 0.8031 (ttm170) cc_final: 0.7449 (mtp180) REVERT: D 915 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.7926 (pt) REVERT: D 992 LYS cc_start: 0.8169 (mmtt) cc_final: 0.7797 (mmtt) REVERT: D 1146 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7014 (tp30) REVERT: D 1261 LEU cc_start: 0.8184 (pp) cc_final: 0.7750 (pp) REVERT: D 1325 PHE cc_start: 0.8475 (t80) cc_final: 0.8225 (t80) REVERT: D 1343 GLU cc_start: 0.7050 (pm20) cc_final: 0.6742 (pm20) REVERT: E 53 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7582 (mm-30) REVERT: G 43 MET cc_start: 0.6770 (ppp) cc_final: 0.6169 (ppp) REVERT: G 76 ASN cc_start: 0.8046 (m-40) cc_final: 0.7066 (p0) REVERT: G 80 TRP cc_start: 0.7480 (t60) cc_final: 0.7246 (t60) REVERT: G 82 LEU cc_start: 0.7402 (mt) cc_final: 0.7075 (mt) REVERT: G 84 ARG cc_start: 0.7811 (ttm170) cc_final: 0.7581 (ttm170) outliers start: 91 outliers final: 62 residues processed: 705 average time/residue: 0.2092 time to fit residues: 221.9310 Evaluate side-chains 715 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 649 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 568 ASN Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 808 ASN Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1326 GLN Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 162 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 215 optimal weight: 0.0170 chunk 166 optimal weight: 0.1980 chunk 139 optimal weight: 0.0570 chunk 297 optimal weight: 0.6980 chunk 174 optimal weight: 0.0970 chunk 311 optimal weight: 0.1980 chunk 74 optimal weight: 0.0670 chunk 132 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 overall best weight: 0.0872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C 618 GLN C 761 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.146749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114198 restraints weight = 44632.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.117638 restraints weight = 24002.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119981 restraints weight = 15616.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.121504 restraints weight = 11703.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.122391 restraints weight = 9683.721| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28014 Z= 0.116 Angle : 0.607 9.641 38147 Z= 0.316 Chirality : 0.044 0.330 4351 Planarity : 0.004 0.068 4731 Dihedral : 14.682 178.232 4434 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.11 % Favored : 94.82 % Rotamer: Outliers : 2.80 % Allowed : 21.28 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.14), residues: 3285 helix: 1.19 (0.16), residues: 1082 sheet: -0.03 (0.27), residues: 369 loop : -1.41 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1222 TYR 0.033 0.001 TYR D1186 PHE 0.018 0.001 PHE D 892 TRP 0.021 0.001 TRP D1193 HIS 0.004 0.001 HIS D1218 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (28008) covalent geometry : angle 0.60589 / 0.32 (38141) hydrogen bonds : bond 0.03649 / 4.06 ( 1001) hydrogen bonds : angle 4.27584 / 5.08 ( 2771) metal coordination : bond 0.00367 / 0.36 ( 6) metal coordination : angle 2.81930 / 5.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 664 time to evaluate : 0.995 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.7441 (pp20) cc_final: 0.7015 (pp20) REVERT: A 215 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6893 (mm-30) REVERT: B 58 GLU cc_start: 0.6942 (pt0) cc_final: 0.6733 (pt0) REVERT: B 61 ILE cc_start: 0.7651 (tp) cc_final: 0.7001 (pt) REVERT: B 150 ARG cc_start: 0.7116 (ttp-110) cc_final: 0.6764 (ttp80) REVERT: B 181 GLU cc_start: 0.7217 (pm20) cc_final: 0.6817 (pm20) REVERT: C 8 LYS cc_start: 0.8382 (tttt) cc_final: 0.7968 (mtpt) REVERT: C 36 GLN cc_start: 0.7847 (tp40) cc_final: 0.6725 (tm-30) REVERT: C 151 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.7160 (mtm-85) REVERT: C 158 ASP cc_start: 0.6927 (m-30) cc_final: 0.6695 (m-30) REVERT: C 160 ASP cc_start: 0.6899 (t70) cc_final: 0.6537 (t0) REVERT: C 370 MET cc_start: 0.7354 (tpp) cc_final: 0.7149 (tpp) REVERT: C 429 MET cc_start: 0.7281 (tpp) cc_final: 0.6975 (tpt) REVERT: C 568 ASN cc_start: 0.8066 (p0) cc_final: 0.7742 (p0) REVERT: C 592 ARG cc_start: 0.8367 (mtp180) cc_final: 0.8125 (mtp180) REVERT: C 633 LEU cc_start: 0.6634 (mp) cc_final: 0.6195 (tp) REVERT: C 636 CYS cc_start: 0.7685 (m) cc_final: 0.7314 (m) REVERT: C 641 GLU cc_start: 0.6686 (pp20) cc_final: 0.6306 (pp20) REVERT: C 711 ASP cc_start: 0.7285 (t0) cc_final: 0.6763 (t0) REVERT: C 717 VAL cc_start: 0.8436 (p) cc_final: 0.8149 (t) REVERT: C 719 LYS cc_start: 0.8183 (mtmm) cc_final: 0.7634 (mtmm) REVERT: C 720 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7734 (mtp85) REVERT: C 740 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6457 (tp30) REVERT: C 793 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6617 (mt-10) REVERT: C 800 MET cc_start: 0.7722 (pmm) cc_final: 0.7162 (ptp) REVERT: C 853 ASP cc_start: 0.7575 (m-30) cc_final: 0.7199 (m-30) REVERT: C 877 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8606 (m) REVERT: C 930 ASP cc_start: 0.7496 (t70) cc_final: 0.7194 (t70) REVERT: C 950 GLU cc_start: 0.7577 (tp30) cc_final: 0.6953 (tp30) REVERT: C 951 MET cc_start: 0.7176 (mtp) cc_final: 0.6735 (mtp) REVERT: C 957 LYS cc_start: 0.8636 (tppt) cc_final: 0.8414 (tppt) REVERT: C 1107 MET cc_start: 0.6723 (mmm) cc_final: 0.6448 (mtm) REVERT: C 1122 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7995 (ttmt) REVERT: C 1131 MET cc_start: 0.7588 (ttm) cc_final: 0.7341 (ttp) REVERT: C 1229 TYR cc_start: 0.7430 (m-80) cc_final: 0.6846 (m-80) REVERT: C 1240 ASP cc_start: 0.8061 (p0) cc_final: 0.7707 (p0) REVERT: C 1241 ASP cc_start: 0.7646 (m-30) cc_final: 0.6960 (t0) REVERT: C 1274 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6584 (mm-30) REVERT: C 1297 ASP cc_start: 0.7335 (t0) cc_final: 0.6995 (t0) REVERT: C 1329 GLU cc_start: 0.7229 (tp30) cc_final: 0.6961 (tp30) REVERT: D 33 TRP cc_start: 0.7239 (m-10) cc_final: 0.6973 (m-10) REVERT: D 114 ILE cc_start: 0.8290 (mm) cc_final: 0.7868 (tp) REVERT: D 117 LEU cc_start: 0.8439 (tp) cc_final: 0.8172 (tt) REVERT: D 130 MET cc_start: 0.6995 (mtt) cc_final: 0.6706 (mtp) REVERT: D 162 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6924 (mm-30) REVERT: D 190 LYS cc_start: 0.8233 (tptm) cc_final: 0.7895 (tptp) REVERT: D 192 MET cc_start: 0.7717 (ttp) cc_final: 0.6905 (tmm) REVERT: D 193 ASP cc_start: 0.6862 (t0) cc_final: 0.6660 (t0) REVERT: D 222 LYS cc_start: 0.8188 (tmtt) cc_final: 0.7897 (tttm) REVERT: D 280 LYS cc_start: 0.8365 (tptp) cc_final: 0.8073 (tppp) REVERT: D 295 GLU cc_start: 0.6934 (tt0) cc_final: 0.6599 (tt0) REVERT: D 357 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8264 (t) REVERT: D 416 ILE cc_start: 0.8156 (tt) cc_final: 0.7869 (tt) REVERT: D 497 GLU cc_start: 0.7086 (pp20) cc_final: 0.6747 (pp20) REVERT: D 534 GLU cc_start: 0.6699 (tm-30) cc_final: 0.6498 (tp30) REVERT: D 556 GLU cc_start: 0.7198 (pm20) cc_final: 0.6781 (pm20) REVERT: D 625 MET cc_start: 0.7194 (tmm) cc_final: 0.6880 (tmm) REVERT: D 695 LYS cc_start: 0.8505 (tmmt) cc_final: 0.8041 (tmmt) REVERT: D 697 MET cc_start: 0.7979 (tmm) cc_final: 0.7492 (tmm) REVERT: D 698 MET cc_start: 0.7919 (tpp) cc_final: 0.7201 (tmm) REVERT: D 802 ASP cc_start: 0.7425 (t0) cc_final: 0.6759 (t0) REVERT: D 822 MET cc_start: 0.6459 (OUTLIER) cc_final: 0.6101 (tpp) REVERT: D 867 GLN cc_start: 0.7579 (tm-30) cc_final: 0.7353 (tm-30) REVERT: D 888 CYS cc_start: 0.7095 (t) cc_final: 0.6686 (t) REVERT: D 898 CYS cc_start: 0.6015 (m) cc_final: 0.5550 (m) REVERT: D 915 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7951 (pt) REVERT: D 954 ASN cc_start: 0.8487 (m110) cc_final: 0.7957 (t0) REVERT: D 992 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7724 (mmtt) REVERT: D 1146 GLU cc_start: 0.7442 (tm-30) cc_final: 0.6971 (tp30) REVERT: D 1158 GLU cc_start: 0.7214 (pm20) cc_final: 0.6885 (pp20) REVERT: D 1261 LEU cc_start: 0.8199 (pp) cc_final: 0.7792 (pp) REVERT: D 1286 LYS cc_start: 0.8042 (ttmm) cc_final: 0.7605 (ttmt) REVERT: D 1325 PHE cc_start: 0.8440 (t80) cc_final: 0.8235 (t80) REVERT: E 53 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7562 (mm-30) REVERT: G 43 MET cc_start: 0.6723 (ppp) cc_final: 0.6183 (ppp) REVERT: G 76 ASN cc_start: 0.7932 (m-40) cc_final: 0.6981 (p0) outliers start: 79 outliers final: 50 residues processed: 704 average time/residue: 0.2111 time to fit residues: 223.8910 Evaluate side-chains 705 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 650 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1095 MET Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 65 optimal weight: 1.9990 chunk 54 optimal weight: 0.0020 chunk 334 optimal weight: 0.8980 chunk 287 optimal weight: 40.0000 chunk 332 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 chunk 150 optimal weight: 4.9990 chunk 17 optimal weight: 0.0670 chunk 217 optimal weight: 2.9990 overall best weight: 0.4928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 HIS ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 GLN ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C 761 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.146095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.113489 restraints weight = 44472.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.116869 restraints weight = 23990.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.119138 restraints weight = 15689.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.120649 restraints weight = 11827.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.121518 restraints weight = 9814.278| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28014 Z= 0.121 Angle : 0.613 10.305 38147 Z= 0.317 Chirality : 0.044 0.326 4351 Planarity : 0.004 0.067 4731 Dihedral : 14.683 178.450 4434 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.70 % Rotamer: Outliers : 2.87 % Allowed : 22.49 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3285 helix: 1.21 (0.16), residues: 1075 sheet: -0.12 (0.27), residues: 374 loop : -1.39 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1222 TYR 0.024 0.001 TYR D1232 PHE 0.020 0.001 PHE C1270 TRP 0.031 0.002 TRP G 80 HIS 0.005 0.001 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (28008) covalent geometry : angle 0.61150 / 0.32 (38141) hydrogen bonds : bond 0.03690 / 4.10 ( 1001) hydrogen bonds : angle 4.24096 / 5.07 ( 2771) metal coordination : bond 0.00824 / 0.59 ( 6) metal coordination : angle 2.97600 / 5.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 655 time to evaluate : 1.002 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.7453 (pp20) cc_final: 0.7047 (pp20) REVERT: A 215 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6909 (mm-30) REVERT: B 58 GLU cc_start: 0.6967 (pt0) cc_final: 0.6734 (pt0) REVERT: B 61 ILE cc_start: 0.7647 (tp) cc_final: 0.6955 (pt) REVERT: B 181 GLU cc_start: 0.7262 (pm20) cc_final: 0.6688 (pm20) REVERT: C 8 LYS cc_start: 0.8380 (tttt) cc_final: 0.7951 (mtpt) REVERT: C 36 GLN cc_start: 0.7840 (tp40) cc_final: 0.6688 (tm-30) REVERT: C 101 ARG cc_start: 0.7775 (ttm-80) cc_final: 0.7247 (ttm-80) REVERT: C 151 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.7168 (mtm-85) REVERT: C 158 ASP cc_start: 0.6854 (m-30) cc_final: 0.6632 (m-30) REVERT: C 160 ASP cc_start: 0.6890 (t70) cc_final: 0.6531 (t0) REVERT: C 370 MET cc_start: 0.7373 (tpp) cc_final: 0.7171 (tpp) REVERT: C 429 MET cc_start: 0.7267 (tpp) cc_final: 0.6963 (tpt) REVERT: C 592 ARG cc_start: 0.8395 (mtp180) cc_final: 0.8138 (mtp180) REVERT: C 636 CYS cc_start: 0.7796 (m) cc_final: 0.7494 (m) REVERT: C 641 GLU cc_start: 0.6727 (pp20) cc_final: 0.6326 (pp20) REVERT: C 711 ASP cc_start: 0.7307 (t0) cc_final: 0.6754 (t0) REVERT: C 717 VAL cc_start: 0.8436 (p) cc_final: 0.8151 (t) REVERT: C 719 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7761 (mtmm) REVERT: C 720 ARG cc_start: 0.8270 (mtp85) cc_final: 0.7731 (mtp85) REVERT: C 740 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6465 (tp30) REVERT: C 793 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6625 (mt-10) REVERT: C 800 MET cc_start: 0.7710 (pmm) cc_final: 0.7191 (ptp) REVERT: C 853 ASP cc_start: 0.7589 (m-30) cc_final: 0.7218 (m-30) REVERT: C 877 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8614 (m) REVERT: C 930 ASP cc_start: 0.7502 (t70) cc_final: 0.7171 (t70) REVERT: C 950 GLU cc_start: 0.7590 (tp30) cc_final: 0.6975 (tp30) REVERT: C 951 MET cc_start: 0.7199 (mtp) cc_final: 0.6742 (mtp) REVERT: C 957 LYS cc_start: 0.8637 (tppt) cc_final: 0.8427 (tppt) REVERT: C 1107 MET cc_start: 0.6710 (mmm) cc_final: 0.6475 (mtm) REVERT: C 1119 MET cc_start: 0.7418 (tpt) cc_final: 0.7204 (tpt) REVERT: C 1122 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7722 (ttmt) REVERT: C 1126 ASP cc_start: 0.6718 (m-30) cc_final: 0.6345 (m-30) REVERT: C 1131 MET cc_start: 0.7591 (ttm) cc_final: 0.7343 (ttp) REVERT: C 1229 TYR cc_start: 0.7460 (m-80) cc_final: 0.6846 (m-80) REVERT: C 1240 ASP cc_start: 0.8061 (p0) cc_final: 0.7714 (p0) REVERT: C 1241 ASP cc_start: 0.7627 (m-30) cc_final: 0.6946 (t0) REVERT: C 1274 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6613 (mm-30) REVERT: C 1297 ASP cc_start: 0.7333 (t0) cc_final: 0.6976 (t0) REVERT: D 33 TRP cc_start: 0.7298 (m-10) cc_final: 0.7026 (m-10) REVERT: D 114 ILE cc_start: 0.8284 (mm) cc_final: 0.7892 (tp) REVERT: D 117 LEU cc_start: 0.8446 (tp) cc_final: 0.8214 (tt) REVERT: D 130 MET cc_start: 0.6997 (mtt) cc_final: 0.6710 (mtp) REVERT: D 162 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6951 (mm-30) REVERT: D 190 LYS cc_start: 0.8285 (tptm) cc_final: 0.7974 (tptp) REVERT: D 192 MET cc_start: 0.7712 (ttp) cc_final: 0.6945 (tmm) REVERT: D 193 ASP cc_start: 0.6841 (t0) cc_final: 0.6640 (t0) REVERT: D 222 LYS cc_start: 0.8217 (tmtt) cc_final: 0.7918 (tttm) REVERT: D 280 LYS cc_start: 0.8356 (tptp) cc_final: 0.8080 (tppp) REVERT: D 295 GLU cc_start: 0.6967 (tt0) cc_final: 0.6593 (tt0) REVERT: D 357 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8351 (t) REVERT: D 416 ILE cc_start: 0.8157 (tt) cc_final: 0.7851 (tt) REVERT: D 497 GLU cc_start: 0.7091 (pp20) cc_final: 0.6753 (pp20) REVERT: D 532 GLU cc_start: 0.7337 (pp20) cc_final: 0.7119 (pp20) REVERT: D 556 GLU cc_start: 0.7200 (pm20) cc_final: 0.6768 (pm20) REVERT: D 625 MET cc_start: 0.7266 (tmm) cc_final: 0.6914 (tmm) REVERT: D 643 ASP cc_start: 0.6937 (OUTLIER) cc_final: 0.6313 (t0) REVERT: D 695 LYS cc_start: 0.8501 (tmmt) cc_final: 0.8047 (tmmt) REVERT: D 697 MET cc_start: 0.7993 (tmm) cc_final: 0.7505 (tmm) REVERT: D 698 MET cc_start: 0.7912 (tpp) cc_final: 0.7223 (tmm) REVERT: D 715 LYS cc_start: 0.8177 (mtmm) cc_final: 0.7803 (mtmt) REVERT: D 802 ASP cc_start: 0.7412 (t0) cc_final: 0.6805 (t0) REVERT: D 822 MET cc_start: 0.6502 (ttm) cc_final: 0.6130 (tpp) REVERT: D 867 GLN cc_start: 0.7647 (tm-30) cc_final: 0.7396 (tm-30) REVERT: D 915 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7995 (pt) REVERT: D 954 ASN cc_start: 0.8480 (m110) cc_final: 0.7936 (t0) REVERT: D 992 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7787 (mmtt) REVERT: D 1146 GLU cc_start: 0.7444 (tm-30) cc_final: 0.6928 (tp30) REVERT: D 1158 GLU cc_start: 0.7225 (pm20) cc_final: 0.6763 (pp20) REVERT: D 1261 LEU cc_start: 0.8191 (pp) cc_final: 0.7771 (pp) REVERT: D 1286 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7782 (ttmm) REVERT: D 1325 PHE cc_start: 0.8474 (t80) cc_final: 0.8252 (t80) REVERT: E 53 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7542 (mm-30) REVERT: G 43 MET cc_start: 0.6734 (ppp) cc_final: 0.6255 (ppp) REVERT: G 76 ASN cc_start: 0.7953 (m-40) cc_final: 0.7013 (p0) outliers start: 81 outliers final: 59 residues processed: 697 average time/residue: 0.2118 time to fit residues: 222.3105 Evaluate side-chains 711 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 647 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1244 HIS Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1095 MET Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 233 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 268 optimal weight: 0.4980 chunk 217 optimal weight: 0.9980 chunk 53 optimal weight: 0.0970 chunk 139 optimal weight: 0.9980 chunk 282 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS C 613 ASN C 761 GLN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.146333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113571 restraints weight = 44537.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.116947 restraints weight = 24097.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.119282 restraints weight = 15791.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.120773 restraints weight = 11803.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.121673 restraints weight = 9813.469| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28014 Z= 0.127 Angle : 0.624 10.848 38147 Z= 0.321 Chirality : 0.044 0.325 4351 Planarity : 0.004 0.064 4731 Dihedral : 14.696 178.560 4434 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.70 % Rotamer: Outliers : 2.87 % Allowed : 22.74 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.14), residues: 3285 helix: 1.15 (0.16), residues: 1083 sheet: -0.08 (0.26), residues: 378 loop : -1.43 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D1222 TYR 0.025 0.001 TYR D1232 PHE 0.018 0.001 PHE D 892 TRP 0.023 0.002 TRP D1193 HIS 0.004 0.001 HIS D 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (28008) covalent geometry : angle 0.62309 / 0.32 (38141) hydrogen bonds : bond 0.03739 / 4.15 ( 1001) hydrogen bonds : angle 4.17564 / 5.00 ( 2771) metal coordination : bond 0.00490 / 0.52 ( 6) metal coordination : angle 2.70853 / 4.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 652 time to evaluate : 1.014 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.7467 (pp20) cc_final: 0.7018 (pp20) REVERT: A 215 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6901 (mm-30) REVERT: B 58 GLU cc_start: 0.7069 (pt0) cc_final: 0.6811 (pt0) REVERT: B 61 ILE cc_start: 0.7620 (tp) cc_final: 0.6935 (pt) REVERT: B 181 GLU cc_start: 0.7249 (pm20) cc_final: 0.6614 (pm20) REVERT: C 8 LYS cc_start: 0.8372 (tttt) cc_final: 0.7872 (mtpt) REVERT: C 14 ASP cc_start: 0.7304 (t0) cc_final: 0.7043 (m-30) REVERT: C 36 GLN cc_start: 0.7847 (tp40) cc_final: 0.6694 (tm-30) REVERT: C 101 ARG cc_start: 0.7825 (ttm-80) cc_final: 0.7276 (ttm-80) REVERT: C 151 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.7191 (mtm-85) REVERT: C 160 ASP cc_start: 0.6948 (t70) cc_final: 0.6527 (t0) REVERT: C 429 MET cc_start: 0.7368 (tpp) cc_final: 0.7019 (tpt) REVERT: C 592 ARG cc_start: 0.8367 (mtp180) cc_final: 0.8084 (mtp180) REVERT: C 636 CYS cc_start: 0.7698 (m) cc_final: 0.7271 (m) REVERT: C 641 GLU cc_start: 0.6779 (pp20) cc_final: 0.6379 (pp20) REVERT: C 711 ASP cc_start: 0.7324 (t0) cc_final: 0.6791 (t0) REVERT: C 717 VAL cc_start: 0.8421 (p) cc_final: 0.8147 (t) REVERT: C 719 LYS cc_start: 0.8282 (mtmm) cc_final: 0.7771 (mtmm) REVERT: C 720 ARG cc_start: 0.8309 (mtp85) cc_final: 0.7758 (mtp85) REVERT: C 740 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6511 (tp30) REVERT: C 793 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6585 (mt-10) REVERT: C 800 MET cc_start: 0.7661 (pmm) cc_final: 0.7194 (ptp) REVERT: C 877 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8595 (m) REVERT: C 930 ASP cc_start: 0.7541 (t70) cc_final: 0.7168 (t70) REVERT: C 950 GLU cc_start: 0.7708 (tp30) cc_final: 0.7079 (tp30) REVERT: C 951 MET cc_start: 0.7305 (mtp) cc_final: 0.6819 (mtp) REVERT: C 957 LYS cc_start: 0.8619 (tppt) cc_final: 0.8396 (tppt) REVERT: C 1119 MET cc_start: 0.7405 (tpt) cc_final: 0.7203 (tpt) REVERT: C 1122 LYS cc_start: 0.8085 (ttmt) cc_final: 0.7640 (ttmt) REVERT: C 1124 ILE cc_start: 0.8113 (mm) cc_final: 0.7895 (mt) REVERT: C 1126 ASP cc_start: 0.6746 (m-30) cc_final: 0.6372 (m-30) REVERT: C 1131 MET cc_start: 0.7645 (ttm) cc_final: 0.7399 (ttp) REVERT: C 1220 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7892 (tm-30) REVERT: C 1229 TYR cc_start: 0.7489 (m-80) cc_final: 0.6817 (m-80) REVERT: C 1240 ASP cc_start: 0.8056 (p0) cc_final: 0.7729 (p0) REVERT: C 1241 ASP cc_start: 0.7666 (m-30) cc_final: 0.6989 (t0) REVERT: C 1274 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6620 (mm-30) REVERT: C 1297 ASP cc_start: 0.7415 (t0) cc_final: 0.7015 (t0) REVERT: D 33 TRP cc_start: 0.7251 (m-10) cc_final: 0.6918 (m-10) REVERT: D 114 ILE cc_start: 0.8267 (mm) cc_final: 0.7847 (tp) REVERT: D 117 LEU cc_start: 0.8454 (tp) cc_final: 0.8236 (tt) REVERT: D 130 MET cc_start: 0.7081 (mtt) cc_final: 0.6809 (mtp) REVERT: D 162 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7076 (mm-30) REVERT: D 190 LYS cc_start: 0.8277 (tptm) cc_final: 0.7999 (tptm) REVERT: D 192 MET cc_start: 0.7805 (ttp) cc_final: 0.6963 (tmm) REVERT: D 193 ASP cc_start: 0.6908 (t0) cc_final: 0.6591 (t0) REVERT: D 213 LYS cc_start: 0.8300 (mmmm) cc_final: 0.8049 (mtpp) REVERT: D 222 LYS cc_start: 0.8198 (tmtt) cc_final: 0.7896 (tttp) REVERT: D 280 LYS cc_start: 0.8352 (tptp) cc_final: 0.8061 (tppp) REVERT: D 295 GLU cc_start: 0.7035 (tt0) cc_final: 0.6662 (tt0) REVERT: D 357 VAL cc_start: 0.8654 (OUTLIER) cc_final: 0.8369 (t) REVERT: D 416 ILE cc_start: 0.8117 (tt) cc_final: 0.7842 (tt) REVERT: D 497 GLU cc_start: 0.7120 (pp20) cc_final: 0.6770 (pp20) REVERT: D 532 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7123 (pp20) REVERT: D 538 ARG cc_start: 0.8023 (tpp80) cc_final: 0.7662 (tpp80) REVERT: D 556 GLU cc_start: 0.7169 (pm20) cc_final: 0.6730 (pm20) REVERT: D 625 MET cc_start: 0.7260 (tmm) cc_final: 0.6895 (tmm) REVERT: D 643 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6329 (t0) REVERT: D 695 LYS cc_start: 0.8451 (tmmt) cc_final: 0.7983 (tmmt) REVERT: D 697 MET cc_start: 0.8008 (tmm) cc_final: 0.7502 (tmm) REVERT: D 698 MET cc_start: 0.7942 (tpp) cc_final: 0.7234 (tmm) REVERT: D 715 LYS cc_start: 0.8246 (mtmm) cc_final: 0.7840 (mtmt) REVERT: D 802 ASP cc_start: 0.7513 (t0) cc_final: 0.7031 (t0) REVERT: D 822 MET cc_start: 0.6551 (ttm) cc_final: 0.6185 (tpp) REVERT: D 867 GLN cc_start: 0.7673 (tm-30) cc_final: 0.7452 (tm-30) REVERT: D 915 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7971 (pt) REVERT: D 954 ASN cc_start: 0.8469 (m110) cc_final: 0.7856 (t0) REVERT: D 992 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7752 (mmtt) REVERT: D 1146 GLU cc_start: 0.7439 (tm-30) cc_final: 0.6905 (tp30) REVERT: D 1158 GLU cc_start: 0.7253 (pm20) cc_final: 0.6801 (pp20) REVERT: D 1261 LEU cc_start: 0.8072 (pp) cc_final: 0.7694 (pp) REVERT: D 1263 LYS cc_start: 0.7426 (mmmm) cc_final: 0.7156 (mmmt) REVERT: E 53 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7560 (mm-30) REVERT: G 43 MET cc_start: 0.6789 (ppp) cc_final: 0.6280 (ppp) REVERT: G 76 ASN cc_start: 0.7970 (m-40) cc_final: 0.7021 (p0) REVERT: G 84 ARG cc_start: 0.7688 (ttm170) cc_final: 0.7318 (ttm170) outliers start: 81 outliers final: 65 residues processed: 690 average time/residue: 0.2115 time to fit residues: 219.2851 Evaluate side-chains 727 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 656 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1244 HIS Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1095 MET Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1281 GLU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 217 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 234 optimal weight: 0.6980 chunk 127 optimal weight: 0.0970 chunk 202 optimal weight: 8.9990 chunk 29 optimal weight: 0.5980 chunk 136 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 240 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 GLN ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C 761 GLN C1108 ASN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.146703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.113898 restraints weight = 44708.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.117281 restraints weight = 24148.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.119587 restraints weight = 15835.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.120997 restraints weight = 11910.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.122005 restraints weight = 9949.022| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 28014 Z= 0.123 Angle : 0.632 11.209 38147 Z= 0.323 Chirality : 0.044 0.328 4351 Planarity : 0.004 0.061 4731 Dihedral : 14.704 178.473 4434 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.18 % Favored : 94.76 % Rotamer: Outliers : 2.87 % Allowed : 22.63 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 3285 helix: 1.16 (0.16), residues: 1085 sheet: -0.09 (0.26), residues: 383 loop : -1.42 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D1222 TYR 0.024 0.001 TYR D1232 PHE 0.017 0.001 PHE D 892 TRP 0.023 0.001 TRP D1193 HIS 0.004 0.001 HIS D1218 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (28008) covalent geometry : angle 0.62830 / 0.32 (38141) hydrogen bonds : bond 0.03629 / 4.02 ( 1001) hydrogen bonds : angle 4.12291 / 4.96 ( 2771) metal coordination : bond 0.00979 / 1.14 ( 6) metal coordination : angle 5.79442 / 11.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 653 time to evaluate : 1.206 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LYS cc_start: 0.8327 (ttpp) cc_final: 0.8058 (ttpp) REVERT: A 204 GLU cc_start: 0.7449 (pp20) cc_final: 0.7058 (pp20) REVERT: A 215 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6902 (mm-30) REVERT: B 58 GLU cc_start: 0.6947 (pt0) cc_final: 0.6737 (pt0) REVERT: B 61 ILE cc_start: 0.7621 (tp) cc_final: 0.6942 (pt) REVERT: B 150 ARG cc_start: 0.7219 (ttm110) cc_final: 0.6768 (ttm-80) REVERT: B 181 GLU cc_start: 0.7224 (pm20) cc_final: 0.6594 (pm20) REVERT: B 185 TYR cc_start: 0.8496 (p90) cc_final: 0.8183 (p90) REVERT: C 8 LYS cc_start: 0.8358 (tttt) cc_final: 0.7962 (mtpt) REVERT: C 14 ASP cc_start: 0.7201 (t0) cc_final: 0.6938 (m-30) REVERT: C 36 GLN cc_start: 0.7827 (tp40) cc_final: 0.6722 (tm-30) REVERT: C 70 TYR cc_start: 0.8202 (t80) cc_final: 0.7980 (t80) REVERT: C 151 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.7158 (mtm-85) REVERT: C 160 ASP cc_start: 0.6872 (t70) cc_final: 0.6505 (t0) REVERT: C 370 MET cc_start: 0.7387 (tpp) cc_final: 0.7166 (tpp) REVERT: C 429 MET cc_start: 0.7276 (tpp) cc_final: 0.6984 (tpt) REVERT: C 503 LYS cc_start: 0.7801 (tppt) cc_final: 0.7563 (mmmm) REVERT: C 592 ARG cc_start: 0.8425 (mtp180) cc_final: 0.8152 (mtp180) REVERT: C 636 CYS cc_start: 0.7692 (m) cc_final: 0.7276 (m) REVERT: C 641 GLU cc_start: 0.6788 (pp20) cc_final: 0.6326 (pp20) REVERT: C 711 ASP cc_start: 0.7262 (t0) cc_final: 0.6742 (t0) REVERT: C 717 VAL cc_start: 0.8420 (p) cc_final: 0.8149 (t) REVERT: C 719 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7712 (mtmm) REVERT: C 720 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7781 (mtp85) REVERT: C 728 ASP cc_start: 0.6996 (t0) cc_final: 0.6618 (t0) REVERT: C 740 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6616 (tp30) REVERT: C 793 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6618 (mt-10) REVERT: C 800 MET cc_start: 0.7619 (pmm) cc_final: 0.7185 (ptp) REVERT: C 877 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8613 (m) REVERT: C 930 ASP cc_start: 0.7497 (t70) cc_final: 0.7163 (t70) REVERT: C 950 GLU cc_start: 0.7575 (tp30) cc_final: 0.6961 (tp30) REVERT: C 951 MET cc_start: 0.7179 (mtp) cc_final: 0.6724 (mtp) REVERT: C 957 LYS cc_start: 0.8625 (tppt) cc_final: 0.8421 (tppt) REVERT: C 1108 ASN cc_start: 0.7154 (OUTLIER) cc_final: 0.6914 (p0) REVERT: C 1122 LYS cc_start: 0.8141 (ttmt) cc_final: 0.7710 (ttmt) REVERT: C 1124 ILE cc_start: 0.8145 (mm) cc_final: 0.7925 (mt) REVERT: C 1126 ASP cc_start: 0.6713 (m-30) cc_final: 0.6358 (m-30) REVERT: C 1131 MET cc_start: 0.7574 (ttm) cc_final: 0.7358 (ttp) REVERT: C 1220 GLN cc_start: 0.8180 (tm-30) cc_final: 0.7846 (tm-30) REVERT: C 1229 TYR cc_start: 0.7466 (m-80) cc_final: 0.6860 (m-80) REVERT: C 1240 ASP cc_start: 0.8065 (p0) cc_final: 0.7706 (p0) REVERT: C 1241 ASP cc_start: 0.7642 (m-30) cc_final: 0.6975 (t0) REVERT: C 1253 LEU cc_start: 0.7669 (mt) cc_final: 0.7288 (mt) REVERT: C 1274 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6610 (mm-30) REVERT: C 1297 ASP cc_start: 0.7353 (t0) cc_final: 0.6971 (t0) REVERT: D 33 TRP cc_start: 0.7314 (m-10) cc_final: 0.7046 (m-10) REVERT: D 114 ILE cc_start: 0.8328 (mm) cc_final: 0.7907 (tp) REVERT: D 117 LEU cc_start: 0.8496 (tp) cc_final: 0.8286 (tt) REVERT: D 130 MET cc_start: 0.6897 (mtt) cc_final: 0.6615 (mtp) REVERT: D 162 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6971 (mm-30) REVERT: D 190 LYS cc_start: 0.8284 (tptm) cc_final: 0.8007 (tptm) REVERT: D 192 MET cc_start: 0.7717 (ttp) cc_final: 0.6921 (tmm) REVERT: D 193 ASP cc_start: 0.6850 (t0) cc_final: 0.6640 (t0) REVERT: D 213 LYS cc_start: 0.8227 (mmmm) cc_final: 0.7981 (mtpp) REVERT: D 222 LYS cc_start: 0.8254 (tmtt) cc_final: 0.7907 (tttm) REVERT: D 280 LYS cc_start: 0.8357 (tptp) cc_final: 0.8077 (tppp) REVERT: D 295 GLU cc_start: 0.6926 (tt0) cc_final: 0.6578 (tt0) REVERT: D 357 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8360 (t) REVERT: D 399 LYS cc_start: 0.8309 (tmmt) cc_final: 0.7841 (tmmt) REVERT: D 416 ILE cc_start: 0.8160 (tt) cc_final: 0.7865 (tt) REVERT: D 478 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7421 (tp) REVERT: D 497 GLU cc_start: 0.7063 (pp20) cc_final: 0.6743 (pp20) REVERT: D 532 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.7085 (pp20) REVERT: D 538 ARG cc_start: 0.8009 (tpp80) cc_final: 0.7505 (tpp-160) REVERT: D 556 GLU cc_start: 0.7179 (pm20) cc_final: 0.6766 (pm20) REVERT: D 625 MET cc_start: 0.7212 (tmm) cc_final: 0.6876 (tmm) REVERT: D 643 ASP cc_start: 0.6912 (m-30) cc_final: 0.6293 (t0) REVERT: D 695 LYS cc_start: 0.8488 (tmmt) cc_final: 0.8037 (tmmt) REVERT: D 697 MET cc_start: 0.7998 (tmm) cc_final: 0.7482 (tmm) REVERT: D 698 MET cc_start: 0.7893 (tpp) cc_final: 0.7199 (tmm) REVERT: D 715 LYS cc_start: 0.8268 (mtmm) cc_final: 0.7890 (mtmt) REVERT: D 802 ASP cc_start: 0.7411 (t0) cc_final: 0.6745 (t0) REVERT: D 822 MET cc_start: 0.6525 (ttm) cc_final: 0.6133 (tpp) REVERT: D 915 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8007 (pt) REVERT: D 954 ASN cc_start: 0.8462 (m110) cc_final: 0.7879 (t0) REVERT: D 992 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7794 (mmtt) REVERT: D 1146 GLU cc_start: 0.7421 (tm-30) cc_final: 0.6874 (tp30) REVERT: D 1158 GLU cc_start: 0.7232 (pm20) cc_final: 0.6803 (pp20) REVERT: D 1261 LEU cc_start: 0.8171 (pp) cc_final: 0.7779 (pp) REVERT: D 1279 GLN cc_start: 0.7498 (tp40) cc_final: 0.7253 (tm-30) REVERT: D 1325 PHE cc_start: 0.8443 (t80) cc_final: 0.8169 (t80) REVERT: E 53 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7539 (mm-30) REVERT: G 43 MET cc_start: 0.6741 (ppp) cc_final: 0.6298 (ppp) REVERT: G 76 ASN cc_start: 0.7933 (m-40) cc_final: 0.7038 (p0) REVERT: G 84 ARG cc_start: 0.7686 (ttm170) cc_final: 0.7291 (ttm170) outliers start: 81 outliers final: 65 residues processed: 692 average time/residue: 0.2115 time to fit residues: 220.8729 Evaluate side-chains 713 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 641 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1244 HIS Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1095 MET Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 0.0170 chunk 23 optimal weight: 0.0770 chunk 212 optimal weight: 1.9990 chunk 314 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 267 optimal weight: 0.0020 chunk 282 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 308 optimal weight: 0.6980 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C 761 GLN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.146446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.113823 restraints weight = 44434.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.117203 restraints weight = 24012.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.119473 restraints weight = 15738.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.121020 restraints weight = 11834.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.121936 restraints weight = 9801.245| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 28014 Z= 0.142 Angle : 0.742 59.200 38147 Z= 0.404 Chirality : 0.044 0.388 4351 Planarity : 0.004 0.061 4731 Dihedral : 14.710 178.473 4434 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.70 % Rotamer: Outliers : 2.73 % Allowed : 23.24 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 3285 helix: 1.16 (0.16), residues: 1084 sheet: -0.09 (0.26), residues: 383 loop : -1.42 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D1222 TYR 0.025 0.001 TYR D1232 PHE 0.017 0.001 PHE D 892 TRP 0.028 0.002 TRP D1193 HIS 0.004 0.001 HIS D1218 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (28008) covalent geometry : angle 0.73838 / 0.40 (38141) hydrogen bonds : bond 0.03612 / 4.00 ( 1001) hydrogen bonds : angle 4.12513 / 4.97 ( 2771) metal coordination : bond 0.00883 / 0.92 ( 6) metal coordination : angle 5.67412 / 10.82 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 639 time to evaluate : 1.090 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LYS cc_start: 0.8309 (ttpp) cc_final: 0.8035 (ttpp) REVERT: A 204 GLU cc_start: 0.7471 (pp20) cc_final: 0.7031 (pp20) REVERT: A 215 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6910 (mm-30) REVERT: B 58 GLU cc_start: 0.7053 (pt0) cc_final: 0.6809 (pt0) REVERT: B 61 ILE cc_start: 0.7595 (tp) cc_final: 0.6916 (pt) REVERT: B 150 ARG cc_start: 0.7270 (ttm110) cc_final: 0.6779 (ttm-80) REVERT: B 181 GLU cc_start: 0.7214 (pm20) cc_final: 0.6561 (pm20) REVERT: B 185 TYR cc_start: 0.8511 (p90) cc_final: 0.8173 (p90) REVERT: C 8 LYS cc_start: 0.8321 (tttt) cc_final: 0.7925 (mtpt) REVERT: C 14 ASP cc_start: 0.7252 (t0) cc_final: 0.6992 (m-30) REVERT: C 36 GLN cc_start: 0.7836 (tp40) cc_final: 0.6707 (tm-30) REVERT: C 70 TYR cc_start: 0.8219 (t80) cc_final: 0.8015 (t80) REVERT: C 151 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.7188 (mtm-85) REVERT: C 160 ASP cc_start: 0.6938 (t70) cc_final: 0.6518 (t0) REVERT: C 370 MET cc_start: 0.7438 (tpp) cc_final: 0.7189 (tpp) REVERT: C 429 MET cc_start: 0.7355 (tpp) cc_final: 0.7007 (tpt) REVERT: C 503 LYS cc_start: 0.7852 (tppt) cc_final: 0.7595 (mmmm) REVERT: C 592 ARG cc_start: 0.8396 (mtp180) cc_final: 0.8103 (mtp180) REVERT: C 636 CYS cc_start: 0.7686 (m) cc_final: 0.7262 (m) REVERT: C 641 GLU cc_start: 0.6852 (pp20) cc_final: 0.6388 (pp20) REVERT: C 711 ASP cc_start: 0.7300 (t0) cc_final: 0.6791 (t0) REVERT: C 717 VAL cc_start: 0.8406 (p) cc_final: 0.8137 (t) REVERT: C 719 LYS cc_start: 0.8218 (mtmm) cc_final: 0.7708 (mtmm) REVERT: C 720 ARG cc_start: 0.8307 (mtp85) cc_final: 0.7778 (mtp85) REVERT: C 740 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6645 (tp30) REVERT: C 793 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6589 (mt-10) REVERT: C 800 MET cc_start: 0.7641 (pmm) cc_final: 0.7213 (ptp) REVERT: C 877 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8588 (m) REVERT: C 930 ASP cc_start: 0.7541 (t70) cc_final: 0.7169 (t70) REVERT: C 950 GLU cc_start: 0.7662 (tp30) cc_final: 0.7039 (tp30) REVERT: C 951 MET cc_start: 0.7265 (mtp) cc_final: 0.6785 (mtp) REVERT: C 957 LYS cc_start: 0.8621 (tppt) cc_final: 0.8402 (tppt) REVERT: C 1122 LYS cc_start: 0.8087 (ttmt) cc_final: 0.7634 (ttmt) REVERT: C 1124 ILE cc_start: 0.8068 (mm) cc_final: 0.7852 (mt) REVERT: C 1126 ASP cc_start: 0.6754 (m-30) cc_final: 0.6371 (m-30) REVERT: C 1131 MET cc_start: 0.7634 (ttm) cc_final: 0.7395 (ttp) REVERT: C 1220 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7857 (tm-30) REVERT: C 1229 TYR cc_start: 0.7464 (m-80) cc_final: 0.6818 (m-80) REVERT: C 1240 ASP cc_start: 0.8055 (p0) cc_final: 0.7717 (p0) REVERT: C 1241 ASP cc_start: 0.7673 (m-30) cc_final: 0.7003 (t0) REVERT: C 1253 LEU cc_start: 0.7652 (mt) cc_final: 0.7283 (mt) REVERT: C 1274 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6615 (mm-30) REVERT: C 1297 ASP cc_start: 0.7403 (t0) cc_final: 0.7006 (t0) REVERT: D 33 TRP cc_start: 0.7230 (m-10) cc_final: 0.6944 (m-10) REVERT: D 114 ILE cc_start: 0.8265 (mm) cc_final: 0.7851 (tp) REVERT: D 117 LEU cc_start: 0.8489 (tp) cc_final: 0.8289 (tt) REVERT: D 130 MET cc_start: 0.6972 (mtt) cc_final: 0.6684 (mtp) REVERT: D 162 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7081 (mm-30) REVERT: D 190 LYS cc_start: 0.8269 (tptm) cc_final: 0.7986 (tptm) REVERT: D 192 MET cc_start: 0.7802 (ttp) cc_final: 0.6948 (tmm) REVERT: D 193 ASP cc_start: 0.6901 (t0) cc_final: 0.6689 (t0) REVERT: D 213 LYS cc_start: 0.8284 (mmmm) cc_final: 0.8034 (mtpp) REVERT: D 222 LYS cc_start: 0.8226 (tmtt) cc_final: 0.7879 (tttm) REVERT: D 280 LYS cc_start: 0.8342 (tptp) cc_final: 0.8063 (tppp) REVERT: D 295 GLU cc_start: 0.6983 (tt0) cc_final: 0.6615 (tt0) REVERT: D 357 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8364 (t) REVERT: D 399 LYS cc_start: 0.8302 (tmmt) cc_final: 0.7825 (tmmt) REVERT: D 416 ILE cc_start: 0.8117 (tt) cc_final: 0.7826 (tt) REVERT: D 478 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7428 (mm) REVERT: D 497 GLU cc_start: 0.7102 (pp20) cc_final: 0.6759 (pp20) REVERT: D 532 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7107 (pp20) REVERT: D 538 ARG cc_start: 0.8011 (tpp80) cc_final: 0.7502 (tpp-160) REVERT: D 556 GLU cc_start: 0.7170 (pm20) cc_final: 0.6729 (pm20) REVERT: D 625 MET cc_start: 0.7239 (tmm) cc_final: 0.6900 (tmm) REVERT: D 643 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6315 (t0) REVERT: D 695 LYS cc_start: 0.8425 (tmmt) cc_final: 0.7971 (tmmt) REVERT: D 697 MET cc_start: 0.8007 (tmm) cc_final: 0.7493 (tmm) REVERT: D 698 MET cc_start: 0.7925 (tpp) cc_final: 0.7224 (tmm) REVERT: D 715 LYS cc_start: 0.8299 (mtmm) cc_final: 0.7893 (mtmt) REVERT: D 802 ASP cc_start: 0.7489 (t0) cc_final: 0.6845 (t0) REVERT: D 822 MET cc_start: 0.6536 (ttm) cc_final: 0.6150 (tpp) REVERT: D 915 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7992 (pt) REVERT: D 954 ASN cc_start: 0.8469 (m110) cc_final: 0.7848 (t0) REVERT: D 992 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7754 (mmtt) REVERT: D 1146 GLU cc_start: 0.7438 (tm-30) cc_final: 0.6873 (tp30) REVERT: D 1158 GLU cc_start: 0.7231 (pm20) cc_final: 0.7015 (pm20) REVERT: D 1259 GLN cc_start: 0.7819 (mm110) cc_final: 0.7617 (mm110) REVERT: D 1261 LEU cc_start: 0.8048 (pp) cc_final: 0.7696 (pp) REVERT: D 1279 GLN cc_start: 0.7532 (tp40) cc_final: 0.7262 (tm-30) REVERT: D 1325 PHE cc_start: 0.8449 (t80) cc_final: 0.8191 (t80) REVERT: E 53 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7570 (mm-30) REVERT: G 43 MET cc_start: 0.6775 (ppp) cc_final: 0.6282 (ppp) REVERT: G 76 ASN cc_start: 0.7960 (m-40) cc_final: 0.7036 (p0) outliers start: 77 outliers final: 67 residues processed: 678 average time/residue: 0.2115 time to fit residues: 215.8732 Evaluate side-chains 713 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 639 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1244 HIS Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1095 MET Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1281 GLU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 311 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 300 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 195 optimal weight: 3.9990 chunk 206 optimal weight: 0.4980 chunk 185 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C 761 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.146436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.113851 restraints weight = 44156.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117227 restraints weight = 23901.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.119591 restraints weight = 15691.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.120844 restraints weight = 11684.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.121966 restraints weight = 9855.306| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 28014 Z= 0.142 Angle : 0.742 59.200 38147 Z= 0.404 Chirality : 0.044 0.388 4351 Planarity : 0.004 0.061 4731 Dihedral : 14.710 178.473 4434 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.70 % Rotamer: Outliers : 2.66 % Allowed : 23.41 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 3285 helix: 1.16 (0.16), residues: 1084 sheet: -0.09 (0.26), residues: 383 loop : -1.42 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D1222 TYR 0.025 0.001 TYR D1232 PHE 0.017 0.001 PHE D 892 TRP 0.028 0.002 TRP D1193 HIS 0.004 0.001 HIS D1218 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (28008) covalent geometry : angle 0.73838 / 0.40 (38141) hydrogen bonds : bond 0.03612 / 4.00 ( 1001) hydrogen bonds : angle 4.12513 / 4.97 ( 2771) metal coordination : bond 0.00883 / 0.92 ( 6) metal coordination : angle 5.67412 / 10.82 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5683.38 seconds wall clock time: 98 minutes 27.58 seconds (5907.58 seconds total)