Starting phenix.real_space_refine on Fri Mar 6 03:30:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7py8_13716/03_2026/7py8_13716.cif Found real_map, /net/cci-nas-00/data/ceres_data/7py8_13716/03_2026/7py8_13716.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 { model { file = "/net/cci-nas-00/data/ceres_data/7py8_13716/03_2026/7py8_13716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7py8_13716/03_2026/7py8_13716.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7py8_13716/03_2026/7py8_13716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7py8_13716/03_2026/7py8_13716.map" } 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= 0.003 sd= 0.037 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 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: {'RNA': 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 23.369 51.294 97.478 1.00138.11 S ATOM 16077 SG CYS D 88 25.681 49.287 100.881 1.00144.60 S ATOM 21765 SG CYS D 814 42.560 117.348 89.819 1.00124.56 S ATOM 22330 SG CYS D 888 43.897 113.805 90.543 1.00105.12 S ATOM 22381 SG CYS D 895 42.567 114.708 87.045 1.00108.43 S ATOM 22402 SG CYS D 898 45.720 116.144 88.118 1.00105.52 S Time building chain proxies: 5.60, per 1000 atoms: 0.20 Number of scatterers: 27442 At special positions: 0 Unit cell: (134.2, 161.7, 168.3, 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: 2.19 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " 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: 109 helices and 46 sheets defined 37.6% alpha, 13.7% beta 32 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.950A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 4.144A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) 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 154 through 159 removed outlier: 3.538A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 159' Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.781A 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 227 Processing helix chain 'C' and resid 6 through 10 removed outlier: 3.551A pdb=" N LYS C 9 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 36 removed outlier: 3.987A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.609A pdb=" N SER C 166 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 167' Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.929A 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 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.665A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.808A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP C 354 " --> pdb=" O THR C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.735A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.610A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.838A pdb=" N LYS C 527 " --> pdb=" O GLU C 523 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 4.056A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 614 removed outlier: 4.286A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 614' Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 688 removed outlier: 3.534A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 738 through 741 removed outlier: 3.601A pdb=" N MET C 741 " --> pdb=" O GLU C 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 738 through 741' Processing helix chain 'C' and resid 820 through 826 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.961A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 906 removed outlier: 3.630A pdb=" N ILE C 905 " --> pdb=" O LEU C 901 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 901 through 906' Processing helix chain 'C' and resid 942 through 981 removed outlier: 4.168A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 3.959A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.819A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 4.033A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.763A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1242 removed outlier: 3.702A pdb=" N ASP C1241 " --> pdb=" O LEU C1238 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS C1242 " --> pdb=" O VAL C1239 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1238 through 1242' Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1284 through 1293 Processing helix chain 'C' and resid 1298 through 1309 Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.853A 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 58 through 63 removed outlier: 3.716A pdb=" N PHE D 62 " --> pdb=" O CYS D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 removed outlier: 3.511A pdb=" N HIS D 80 " --> pdb=" O ARG D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.631A 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 Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.617A pdb=" N SER D 230 " --> pdb=" O ALA D 226 " (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: 3.715A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.886A 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 326 through 332 Processing helix chain 'D' and resid 370 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 416 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: 4.091A 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 504 through 514 removed outlier: 3.783A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.625A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 613 removed outlier: 3.545A pdb=" N GLY D 613 " --> pdb=" O TYR D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.627A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.517A pdb=" N SER D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.086A 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 Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.072A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.562A pdb=" N LEU D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 removed outlier: 4.024A pdb=" N GLU D 873 " --> pdb=" O CYS D 869 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU D 874 " --> pdb=" O ASP D 870 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.764A 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 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 1245 removed outlier: 4.078A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.412A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D1261 " --> pdb=" O VAL D1257 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1294 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1324 Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1347 through 1354 Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 3.697A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.879A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 74 removed outlier: 3.944A pdb=" N GLU E 74 " --> pdb=" O GLN E 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 34 Processing helix chain 'G' and resid 77 through 86 removed outlier: 3.582A 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 16 through 17 removed outlier: 3.556A pdb=" N VAL A 202 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 186 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.526A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 59 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.530A pdb=" N GLU A 122 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.968A 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 15 removed outlier: 3.907A pdb=" N ARG B 12 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 8.412A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.798A pdb=" N GLU B 122 " --> pdb=" O ARG B 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.661A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 188 through 190 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.664A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.570A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 68 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.844A pdb=" N ASN C 173 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP C 185 " --> pdb=" O ARG C 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 228 through 231 Processing sheet with id=AB8, first strand: chain 'C' and resid 239 through 240 removed outlier: 3.700A pdb=" N MET C 239 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 285 " --> pdb=" O MET C 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.797A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 301 through 302 removed outlier: 6.856A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.505A pdb=" N THR C 589 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 606 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC4, first strand: chain 'C' and resid 616 through 617 removed outlier: 3.682A pdb=" N ILE C 616 " --> pdb=" O ARG C 637 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 634 " --> pdb=" O PHE C 645 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 716 through 717 removed outlier: 7.491A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 783 " --> pdb=" O ALA C 716 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 750 through 752 removed outlier: 6.922A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1076 through 1080 removed outlier: 7.512A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.526A pdb=" N LEU C1054 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.546A pdb=" N GLY D 351 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N MET D 466 " --> pdb=" O SER D 353 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.657A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1337 removed outlier: 3.574A pdb=" N ILE D 20 " --> pdb=" O ASP D1342 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP D1342 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 103 through 112 removed outlier: 4.053A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.370A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AD7, first strand: chain 'D' and resid 253 through 254 removed outlier: 3.617A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.571A pdb=" N ARG D 551 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE1, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.541A pdb=" N VAL D 882 " --> pdb=" O ILE D 820 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET D 822 " --> pdb=" O VAL D 880 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 949 through 951 removed outlier: 4.032A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 991 through 996 removed outlier: 4.037A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 965 through 967 removed outlier: 3.916A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1024 through 1026 removed outlier: 3.704A pdb=" N ARG D1123 " --> pdb=" O ILE D1106 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE D1106 " --> pdb=" O ARG D1123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1035 through 1038 removed outlier: 4.092A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA D1077 " --> pdb=" O THR D1038 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU D1078 " --> pdb=" O TYR D1099 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1162 through 1165 removed outlier: 3.736A pdb=" N LEU D1175 " --> pdb=" O GLU D1188 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 3.691A pdb=" N THR D1265 " --> pdb=" O SER D1303 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AF1, first strand: chain 'G' and resid 47 through 48 984 hydrogen bonds defined for protein. 2760 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: 6.02 Time building geometry restraints manager: 2.95 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: 8860 1.34 - 1.46: 4024 1.46 - 1.58: 14779 1.58 - 1.70: 147 1.70 - 1.82: 198 Bond restraints: 28008 Sorted by residual: bond pdb=" C1' DC N 21 " pdb=" N1 DC N 21 " ideal model delta sigma weight residual 1.490 1.529 -0.039 3.00e-02 1.11e+03 1.70e+00 bond pdb=" C THR C1184 " pdb=" O THR C1184 " ideal model delta sigma weight residual 1.249 1.238 0.011 8.50e-03 1.38e+04 1.66e+00 bond pdb=" C3' DC N 35 " pdb=" O3' DC N 35 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" CG GLU E 68 " pdb=" CD GLU E 68 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.40e+00 bond pdb=" CA PRO D 246 " pdb=" C PRO D 246 " ideal model delta sigma weight residual 1.514 1.521 -0.006 5.50e-03 3.31e+04 1.37e+00 ... (remaining 28003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 37514 1.72 - 3.44: 540 3.44 - 5.16: 63 5.16 - 6.89: 18 6.89 - 8.61: 6 Bond angle restraints: 38141 Sorted by residual: angle pdb=" N GLU E 68 " pdb=" CA GLU E 68 " pdb=" CB GLU E 68 " ideal model delta sigma weight residual 110.28 116.90 -6.62 1.55e+00 4.16e-01 1.82e+01 angle pdb=" C PRO C 43 " pdb=" N GLU C 44 " pdb=" CA GLU C 44 " ideal model delta sigma weight residual 121.54 128.55 -7.01 1.91e+00 2.74e-01 1.35e+01 angle pdb=" N GLU C1279 " pdb=" CA GLU C1279 " pdb=" CB GLU C1279 " ideal model delta sigma weight residual 110.41 116.30 -5.89 1.68e+00 3.54e-01 1.23e+01 angle pdb=" N ILE D 915 " pdb=" CA ILE D 915 " pdb=" C ILE D 915 " ideal model delta sigma weight residual 113.53 110.19 3.34 9.80e-01 1.04e+00 1.16e+01 angle pdb=" C LEU C1278 " pdb=" N GLU C1279 " pdb=" CA GLU C1279 " ideal model delta sigma weight residual 121.58 114.99 6.59 1.95e+00 2.63e-01 1.14e+01 ... (remaining 38136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 16544 35.51 - 71.01: 502 71.01 - 106.52: 27 106.52 - 142.02: 1 142.02 - 177.53: 1 Dihedral angle restraints: 17075 sinusoidal: 7590 harmonic: 9485 Sorted by residual: dihedral pdb=" CA GLU D1146 " pdb=" C GLU D1146 " pdb=" N ALA D1147 " pdb=" CA ALA D1147 " ideal model delta harmonic sigma weight residual 180.00 150.42 29.58 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" C4' DC N 35 " pdb=" C3' DC N 35 " pdb=" O3' DC N 35 " pdb=" P DA N 36 " ideal model delta sinusoidal sigma weight residual -140.00 37.53 -177.53 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC T 15 " pdb=" C3' DC T 15 " pdb=" O3' DC T 15 " pdb=" P DG T 16 " ideal model delta sinusoidal sigma weight residual 220.00 86.02 133.98 1 3.50e+01 8.16e-04 1.33e+01 ... (remaining 17072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3207 0.040 - 0.080: 808 0.080 - 0.120: 304 0.120 - 0.160: 28 0.160 - 0.200: 4 Chirality restraints: 4351 Sorted by residual: chirality pdb=" CB THR D1024 " pdb=" CA THR D1024 " pdb=" OG1 THR D1024 " pdb=" CG2 THR D1024 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.98e-01 chirality pdb=" CB ILE C 854 " pdb=" CA ILE C 854 " pdb=" CG1 ILE C 854 " pdb=" CG2 ILE C 854 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CB ILE C 572 " pdb=" CA ILE C 572 " pdb=" CG1 ILE C 572 " pdb=" CG2 ILE C 572 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 4348 not shown) Planarity restraints: 4731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 29 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO A 30 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 29 " 0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO B 30 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 850 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO D 851 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 851 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 851 " 0.023 5.00e-02 4.00e+02 ... (remaining 4728 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 962 2.71 - 3.26: 27072 3.26 - 3.81: 42997 3.81 - 4.35: 50199 4.35 - 4.90: 83377 Nonbonded interactions: 204607 Sorted by model distance: nonbonded pdb=" OG SER D 977 " pdb=" OG1 THR D 980 " model vdw 2.163 3.040 nonbonded pdb=" O3' G R 14 " pdb="MG MG D1501 " model vdw 2.190 2.170 nonbonded pdb=" O VAL G 49 " pdb=" OG SER G 60 " model vdw 2.192 3.040 nonbonded pdb=" OH TYR D 679 " pdb=" O ILE D 754 " model vdw 2.211 3.040 nonbonded pdb=" OE2 GLU D1146 " pdb=" NE ARG D1148 " model vdw 2.223 3.120 ... (remaining 204602 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 29.760 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 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 : 0.002 0.043 28014 Z= 0.105 Angle : 0.524 8.608 38147 Z= 0.277 Chirality : 0.041 0.200 4351 Planarity : 0.003 0.056 4731 Dihedral : 15.674 177.526 10973 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.04 % Allowed : 0.25 % Favored : 99.72 % 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 (0.15), residues: 3285 helix: 1.22 (0.16), residues: 1098 sheet: -0.65 (0.26), residues: 393 loop : -1.41 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D1123 TYR 0.010 0.001 TYR D 631 PHE 0.014 0.001 PHE A 231 TRP 0.006 0.001 TRP G 80 HIS 0.007 0.001 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00222 (28008) covalent geometry : angle 0.52265 (38141) hydrogen bonds : bond 0.18404 ( 1063) hydrogen bonds : angle 6.27361 ( 2930) metal coordination : bond 0.00490 ( 6) metal coordination : angle 3.13759 ( 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 956 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 955 time to evaluate : 0.950 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: 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 16 ILE cc_start: 0.8607 (mt) cc_final: 0.8344 (tt) REVERT: A 33 ARG cc_start: 0.7792 (ptm160) cc_final: 0.7291 (ptm160) REVERT: A 46 ILE cc_start: 0.7685 (mm) cc_final: 0.7450 (tp) REVERT: A 67 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7168 (mt-10) REVERT: A 74 VAL cc_start: 0.8170 (m) cc_final: 0.7774 (p) REVERT: A 76 GLU cc_start: 0.7133 (pm20) cc_final: 0.6429 (pm20) REVERT: A 80 GLU cc_start: 0.7709 (tp30) cc_final: 0.7476 (tp30) REVERT: A 101 THR cc_start: 0.7914 (m) cc_final: 0.6885 (p) REVERT: A 104 LYS cc_start: 0.8243 (tptp) cc_final: 0.7861 (tptp) REVERT: A 122 GLU cc_start: 0.7306 (pp20) cc_final: 0.7084 (pp20) REVERT: A 148 ARG cc_start: 0.7454 (mtp180) cc_final: 0.7137 (mtp85) REVERT: A 188 GLU cc_start: 0.7487 (pm20) cc_final: 0.7284 (pm20) REVERT: A 204 GLU cc_start: 0.7932 (pt0) cc_final: 0.7233 (pt0) REVERT: A 205 MET cc_start: 0.7413 (ttp) cc_final: 0.6839 (ptp) REVERT: A 206 GLU cc_start: 0.7520 (tm-30) cc_final: 0.6958 (tm-30) REVERT: A 226 GLU cc_start: 0.6862 (tm-30) cc_final: 0.6620 (tm-30) REVERT: B 7 GLU cc_start: 0.6362 (pm20) cc_final: 0.5920 (pm20) REVERT: B 58 GLU cc_start: 0.7445 (pt0) cc_final: 0.7100 (pt0) REVERT: B 64 VAL cc_start: 0.7329 (t) cc_final: 0.7124 (p) REVERT: B 66 HIS cc_start: 0.7483 (t-90) cc_final: 0.6836 (t70) REVERT: B 80 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6442 (tm-30) REVERT: B 81 ILE cc_start: 0.7892 (pt) cc_final: 0.7347 (pt) REVERT: B 97 GLU cc_start: 0.7239 (pm20) cc_final: 0.6649 (pm20) REVERT: B 98 VAL cc_start: 0.7943 (p) cc_final: 0.7644 (m) REVERT: B 100 LEU cc_start: 0.8539 (mm) cc_final: 0.7853 (tp) REVERT: B 128 HIS cc_start: 0.8045 (t-90) cc_final: 0.7613 (t-90) REVERT: B 148 ARG cc_start: 0.6658 (ttm-80) cc_final: 0.6264 (mtm-85) REVERT: B 188 GLU cc_start: 0.7145 (pt0) cc_final: 0.6843 (pt0) REVERT: B 205 MET cc_start: 0.7621 (ppp) cc_final: 0.6581 (ppp) REVERT: C 8 LYS cc_start: 0.8166 (mttt) cc_final: 0.7788 (mtpp) REVERT: C 17 LYS cc_start: 0.8026 (mptt) cc_final: 0.7541 (mmtt) REVERT: C 69 GLN cc_start: 0.7120 (mt0) cc_final: 0.6908 (mt0) REVERT: C 87 ILE cc_start: 0.8185 (mt) cc_final: 0.7940 (pt) REVERT: C 92 TYR cc_start: 0.8494 (t80) cc_final: 0.8055 (t80) REVERT: C 99 LYS cc_start: 0.8060 (ttmm) cc_final: 0.7457 (mtmm) REVERT: C 121 GLU cc_start: 0.6533 (mm-30) cc_final: 0.6186 (mm-30) REVERT: C 135 THR cc_start: 0.7529 (p) cc_final: 0.7077 (p) REVERT: C 142 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7195 (mt-10) REVERT: C 151 ARG cc_start: 0.7907 (ttm110) cc_final: 0.7628 (ttm110) REVERT: C 180 ARG cc_start: 0.7051 (ttp80) cc_final: 0.6820 (ttp80) REVERT: C 185 ASP cc_start: 0.6597 (p0) cc_final: 0.5816 (p0) REVERT: C 187 GLU cc_start: 0.7342 (mp0) cc_final: 0.6230 (mp0) REVERT: C 214 ASN cc_start: 0.8687 (t0) cc_final: 0.8289 (t0) REVERT: C 339 ASN cc_start: 0.7493 (t0) cc_final: 0.7214 (t0) REVERT: C 349 GLU cc_start: 0.8125 (pm20) cc_final: 0.7761 (pm20) REVERT: C 368 ARG cc_start: 0.8067 (ttp-110) cc_final: 0.7680 (mtm-85) REVERT: C 369 MET cc_start: 0.8216 (tpp) cc_final: 0.7989 (tpp) REVERT: C 374 GLU cc_start: 0.6515 (pt0) cc_final: 0.4701 (pt0) REVERT: C 387 ASN cc_start: 0.7749 (m-40) cc_final: 0.7240 (t0) REVERT: C 389 PHE cc_start: 0.8295 (m-80) cc_final: 0.8012 (m-10) REVERT: C 392 GLU cc_start: 0.7475 (mp0) cc_final: 0.7209 (mp0) REVERT: C 402 ARG cc_start: 0.8235 (tpt170) cc_final: 0.7999 (tpp-160) REVERT: C 404 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7698 (tttp) REVERT: C 427 ASP cc_start: 0.7289 (m-30) cc_final: 0.6953 (m-30) REVERT: C 430 LYS cc_start: 0.8077 (mtpp) cc_final: 0.7864 (mttm) REVERT: C 459 MET cc_start: 0.6779 (mtm) cc_final: 0.6540 (mtp) REVERT: C 531 SER cc_start: 0.8688 (t) cc_final: 0.8264 (p) REVERT: C 549 ASP cc_start: 0.7130 (t0) cc_final: 0.6637 (t0) REVERT: C 572 ILE cc_start: 0.8430 (mm) cc_final: 0.8034 (mm) REVERT: C 592 ARG cc_start: 0.7667 (mtp180) cc_final: 0.6167 (ttm170) REVERT: C 593 LYS cc_start: 0.7973 (tptt) cc_final: 0.7658 (tptp) REVERT: C 611 GLU cc_start: 0.7505 (tt0) cc_final: 0.7250 (tt0) REVERT: C 616 ILE cc_start: 0.8555 (mp) cc_final: 0.8262 (mm) REVERT: C 633 LEU cc_start: 0.7807 (tp) cc_final: 0.6903 (tp) REVERT: C 653 MET cc_start: 0.7376 (ttm) cc_final: 0.7016 (ttp) REVERT: C 654 ASP cc_start: 0.7501 (m-30) cc_final: 0.6904 (m-30) REVERT: C 656 SER cc_start: 0.8501 (t) cc_final: 0.8051 (m) REVERT: C 685 MET cc_start: 0.7365 (mtm) cc_final: 0.7098 (mtm) REVERT: C 696 ASP cc_start: 0.7043 (t0) cc_final: 0.6741 (t0) REVERT: C 723 VAL cc_start: 0.8195 (t) cc_final: 0.7875 (m) REVERT: C 730 SER cc_start: 0.8701 (m) cc_final: 0.8199 (t) REVERT: C 778 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7323 (mp0) REVERT: C 788 SER cc_start: 0.8326 (m) cc_final: 0.7841 (p) REVERT: C 790 ASP cc_start: 0.7574 (t70) cc_final: 0.6699 (p0) REVERT: C 808 ASN cc_start: 0.8172 (t0) cc_final: 0.7946 (m-40) REVERT: C 930 ASP cc_start: 0.7825 (t0) cc_final: 0.7290 (m-30) REVERT: C 947 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7549 (tm-30) REVERT: C 950 GLU cc_start: 0.8435 (pt0) cc_final: 0.8234 (pt0) REVERT: C 960 LEU cc_start: 0.8176 (mp) cc_final: 0.7755 (pp) REVERT: C 1028 LYS cc_start: 0.8535 (ptpp) cc_final: 0.8125 (pttm) REVERT: C 1030 GLU cc_start: 0.8568 (tp30) cc_final: 0.7955 (tp30) REVERT: C 1032 LYS cc_start: 0.9235 (tptt) cc_final: 0.8780 (mttt) REVERT: C 1035 LYS cc_start: 0.8586 (tppt) cc_final: 0.7915 (tppt) REVERT: C 1090 ASN cc_start: 0.7772 (t0) cc_final: 0.7284 (t0) REVERT: C 1095 ASP cc_start: 0.7293 (m-30) cc_final: 0.6937 (m-30) REVERT: C 1114 GLU cc_start: 0.7443 (tt0) cc_final: 0.7213 (tt0) REVERT: C 1122 LYS cc_start: 0.8129 (tptm) cc_final: 0.7537 (tptp) REVERT: C 1126 ASP cc_start: 0.7313 (m-30) cc_final: 0.6732 (m-30) REVERT: C 1127 LYS cc_start: 0.8542 (ttmt) cc_final: 0.8331 (tptp) REVERT: C 1131 MET cc_start: 0.8371 (ttt) cc_final: 0.7789 (ptp) REVERT: C 1143 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7329 (tm-30) REVERT: C 1177 ARG cc_start: 0.7723 (ptm160) cc_final: 0.7233 (ptp90) REVERT: C 1178 LYS cc_start: 0.8313 (tptm) cc_final: 0.8021 (mmmm) REVERT: C 1200 LYS cc_start: 0.8255 (tttt) cc_final: 0.7745 (mtpt) REVERT: C 1210 ILE cc_start: 0.8123 (tt) cc_final: 0.7852 (pt) REVERT: C 1216 ARG cc_start: 0.6907 (mtm180) cc_final: 0.5997 (mtm180) REVERT: C 1244 HIS cc_start: 0.7419 (t-90) cc_final: 0.7173 (t70) REVERT: C 1262 LYS cc_start: 0.7965 (tttt) cc_final: 0.7715 (ttpp) REVERT: C 1264 GLN cc_start: 0.8247 (mp10) cc_final: 0.7886 (mp10) REVERT: C 1279 GLU cc_start: 0.7215 (pm20) cc_final: 0.6835 (pm20) REVERT: C 1289 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6993 (mm-30) REVERT: C 1292 THR cc_start: 0.8121 (m) cc_final: 0.7920 (p) REVERT: C 1293 VAL cc_start: 0.7838 (t) cc_final: 0.6939 (m) REVERT: C 1321 GLU cc_start: 0.6564 (tt0) cc_final: 0.6261 (pp20) REVERT: C 1329 GLU cc_start: 0.6763 (tt0) cc_final: 0.6228 (tp30) REVERT: C 1331 ARG cc_start: 0.7117 (ttm170) cc_final: 0.6905 (ttm170) REVERT: D 21 LYS cc_start: 0.8223 (ptpt) cc_final: 0.7583 (ptmm) REVERT: D 33 TRP cc_start: 0.8072 (m-10) cc_final: 0.7748 (m-10) REVERT: D 39 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7916 (mtmm) REVERT: D 48 THR cc_start: 0.8194 (p) cc_final: 0.7805 (p) REVERT: D 50 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7824 (mtpt) REVERT: D 53 ARG cc_start: 0.7042 (ttt90) cc_final: 0.6839 (ttt90) REVERT: D 66 LYS cc_start: 0.7786 (mtpp) cc_final: 0.7519 (mtpp) REVERT: D 115 TRP cc_start: 0.8448 (m-10) cc_final: 0.8136 (m-10) REVERT: D 118 LYS cc_start: 0.8203 (mmmt) cc_final: 0.7853 (mmmt) REVERT: D 128 LEU cc_start: 0.7932 (mt) cc_final: 0.7542 (mt) REVERT: D 137 ARG cc_start: 0.7632 (mtm110) cc_final: 0.7269 (ttp-110) REVERT: D 141 PHE cc_start: 0.7978 (m-80) cc_final: 0.7581 (m-10) REVERT: D 148 GLU cc_start: 0.6925 (tm-30) cc_final: 0.6343 (tm-30) REVERT: D 151 MET cc_start: 0.7789 (pmm) cc_final: 0.7298 (pmm) REVERT: D 159 ILE cc_start: 0.8141 (tt) cc_final: 0.7880 (mt) REVERT: D 167 ASP cc_start: 0.8341 (t0) cc_final: 0.8102 (t0) REVERT: D 198 CYS cc_start: 0.8362 (t) cc_final: 0.6566 (t) REVERT: D 199 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8134 (mm-30) REVERT: D 202 ARG cc_start: 0.8407 (mtp85) cc_final: 0.8019 (ptp-110) REVERT: D 215 LYS cc_start: 0.8921 (mtmm) cc_final: 0.8607 (ptpt) REVERT: D 235 GLU cc_start: 0.7124 (pm20) cc_final: 0.6746 (pm20) REVERT: D 236 TRP cc_start: 0.8420 (m-10) cc_final: 0.7968 (m-10) REVERT: D 241 VAL cc_start: 0.8842 (t) cc_final: 0.8566 (m) REVERT: D 275 ARG cc_start: 0.7840 (tpp-160) cc_final: 0.7473 (tpp-160) REVERT: D 288 PRO cc_start: 0.6193 (Cg_endo) cc_final: 0.5518 (Cg_exo) REVERT: D 297 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7393 (tmm-80) REVERT: D 298 MET cc_start: 0.7754 (ttp) cc_final: 0.6369 (ttp) REVERT: D 325 LYS cc_start: 0.7926 (mmpt) cc_final: 0.7631 (tptt) REVERT: D 332 LYS cc_start: 0.7254 (mtmm) cc_final: 0.6765 (mtpp) REVERT: D 363 LEU cc_start: 0.6279 (pt) cc_final: 0.5934 (pp) REVERT: D 370 LYS cc_start: 0.7781 (ttmm) cc_final: 0.7452 (ttpt) REVERT: D 375 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7180 (tm-30) REVERT: D 386 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6990 (mm-30) REVERT: D 400 MET cc_start: 0.7309 (tmm) cc_final: 0.6862 (tmm) REVERT: D 414 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7321 (tm-30) REVERT: D 475 GLU cc_start: 0.7456 (mp0) cc_final: 0.7116 (mp0) REVERT: D 495 ASN cc_start: 0.7180 (m-40) cc_final: 0.6804 (m-40) REVERT: D 497 GLU cc_start: 0.8077 (mp0) cc_final: 0.7846 (mp0) REVERT: D 500 ILE cc_start: 0.8249 (mm) cc_final: 0.7826 (tt) REVERT: D 504 GLN cc_start: 0.7700 (mt0) cc_final: 0.7491 (mt0) REVERT: D 511 TYR cc_start: 0.8391 (t80) cc_final: 0.7648 (t80) REVERT: D 521 LYS cc_start: 0.7963 (tttm) cc_final: 0.7754 (mtpp) REVERT: D 556 GLU cc_start: 0.7788 (tt0) cc_final: 0.7333 (tm-30) REVERT: D 589 TYR cc_start: 0.8502 (t80) cc_final: 0.8085 (t80) REVERT: D 610 ARG cc_start: 0.7935 (tpp-160) cc_final: 0.7637 (mmt-90) REVERT: D 644 MET cc_start: 0.7007 (mpp) cc_final: 0.6646 (mtt) REVERT: D 649 LYS cc_start: 0.8501 (mmmt) cc_final: 0.8063 (mmmt) REVERT: D 684 ASP cc_start: 0.7402 (m-30) cc_final: 0.7072 (m-30) REVERT: D 691 ASP cc_start: 0.8006 (m-30) cc_final: 0.7691 (m-30) REVERT: D 695 LYS cc_start: 0.8483 (tmtt) cc_final: 0.7784 (ttpp) REVERT: D 703 THR cc_start: 0.8075 (m) cc_final: 0.7659 (t) REVERT: D 716 GLN cc_start: 0.7865 (pt0) cc_final: 0.7584 (pt0) REVERT: D 725 MET cc_start: 0.7406 (mtm) cc_final: 0.7119 (mtp) REVERT: D 770 LEU cc_start: 0.7687 (mm) cc_final: 0.7449 (mp) REVERT: D 789 LYS cc_start: 0.7960 (ttpt) cc_final: 0.7516 (ptmm) REVERT: D 793 SER cc_start: 0.7658 (p) cc_final: 0.7446 (p) REVERT: D 806 ASP cc_start: 0.7216 (m-30) cc_final: 0.5790 (m-30) REVERT: D 838 ARG cc_start: 0.8361 (ttt180) cc_final: 0.7758 (tpp80) REVERT: D 842 ARG cc_start: 0.6574 (mtt180) cc_final: 0.5826 (mtt180) REVERT: D 865 HIS cc_start: 0.6518 (p90) cc_final: 0.6140 (p90) REVERT: D 869 CYS cc_start: 0.8369 (t) cc_final: 0.7769 (p) REVERT: D 870 ASP cc_start: 0.8110 (m-30) cc_final: 0.7122 (m-30) REVERT: D 910 ASN cc_start: 0.7481 (m110) cc_final: 0.7272 (m-40) REVERT: D 1025 MET cc_start: 0.8666 (mpp) cc_final: 0.8358 (mpp) REVERT: D 1143 ASP cc_start: 0.7698 (t70) cc_final: 0.7372 (t0) REVERT: D 1189 MET cc_start: 0.7013 (tpt) cc_final: 0.6638 (tpt) REVERT: D 1206 ARG cc_start: 0.7814 (ptm160) cc_final: 0.7606 (ttp80) REVERT: D 1218 HIS cc_start: 0.8217 (m90) cc_final: 0.7503 (m90) REVERT: D 1224 ARG cc_start: 0.7713 (mtt180) cc_final: 0.7499 (mtm180) REVERT: D 1242 ARG cc_start: 0.7311 (ttm110) cc_final: 0.6931 (ptp-110) REVERT: D 1254 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6848 (mt-10) REVERT: D 1262 ARG cc_start: 0.7386 (ttp-110) cc_final: 0.6857 (ttp80) REVERT: D 1281 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7051 (tm-30) REVERT: D 1305 ASP cc_start: 0.7752 (p0) cc_final: 0.7112 (t70) REVERT: D 1306 LEU cc_start: 0.8115 (tp) cc_final: 0.7734 (tp) REVERT: D 1343 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6358 (mp0) REVERT: D 1365 TYR cc_start: 0.8056 (t80) cc_final: 0.7553 (t80) REVERT: E 52 ARG cc_start: 0.7668 (ttp80) cc_final: 0.7357 (ttp80) REVERT: E 53 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7961 (mm-30) REVERT: G 22 VAL cc_start: 0.9061 (t) cc_final: 0.8837 (p) REVERT: G 27 ARG cc_start: 0.8225 (mtm180) cc_final: 0.7798 (mtm-85) REVERT: G 43 MET cc_start: 0.7366 (tmm) cc_final: 0.6926 (tmm) REVERT: G 72 GLN cc_start: 0.7825 (mm110) cc_final: 0.7439 (mm110) REVERT: G 74 VAL cc_start: 0.7119 (p) cc_final: 0.6464 (m) REVERT: G 76 ASN cc_start: 0.4095 (p0) cc_final: 0.3873 (p0) REVERT: G 80 TRP cc_start: 0.7615 (t60) cc_final: 0.6651 (t60) REVERT: G 84 ARG cc_start: 0.8126 (tpp80) cc_final: 0.7762 (tpt90) outliers start: 1 outliers final: 0 residues processed: 956 average time/residue: 0.2153 time to fit residues: 303.1097 Evaluate side-chains 808 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 808 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 0.0070 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.0170 chunk 298 optimal weight: 6.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 93 GLN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 811 ASN C1013 GLN C1237 HIS C1268 GLN D 157 GLN D1023 HIS D1114 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.140913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.112301 restraints weight = 49835.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.115847 restraints weight = 25049.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.118189 restraints weight = 15402.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.119657 restraints weight = 10933.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120691 restraints weight = 8746.338| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 28014 Z= 0.140 Angle : 0.620 12.204 38147 Z= 0.321 Chirality : 0.044 0.261 4351 Planarity : 0.005 0.072 4731 Dihedral : 14.583 175.543 4488 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.81 % Allowed : 12.24 % Favored : 85.95 % 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: -0.53 (0.15), residues: 3285 helix: 1.18 (0.16), residues: 1111 sheet: -0.41 (0.26), residues: 416 loop : -1.39 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 731 TYR 0.022 0.001 TYR D 995 PHE 0.022 0.001 PHE D 892 TRP 0.007 0.001 TRP D 409 HIS 0.008 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00314 (28008) covalent geometry : angle 0.61864 (38141) hydrogen bonds : bond 0.04332 ( 1063) hydrogen bonds : angle 4.91362 ( 2930) metal coordination : bond 0.00463 ( 6) metal coordination : angle 3.07933 ( 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 918 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 867 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.8663 (mt) cc_final: 0.8403 (tt) REVERT: A 33 ARG cc_start: 0.7746 (ptm160) cc_final: 0.7255 (ptm160) REVERT: A 74 VAL cc_start: 0.8522 (m) cc_final: 0.8130 (p) REVERT: A 76 GLU cc_start: 0.6766 (pm20) cc_final: 0.6371 (pm20) REVERT: A 104 LYS cc_start: 0.8207 (tptp) cc_final: 0.7658 (tptp) REVERT: A 122 GLU cc_start: 0.7039 (pp20) cc_final: 0.6665 (pp20) REVERT: A 142 MET cc_start: 0.7699 (mtm) cc_final: 0.7437 (mtm) REVERT: A 153 VAL cc_start: 0.8869 (t) cc_final: 0.8561 (m) REVERT: A 170 ARG cc_start: 0.8085 (ttp-110) cc_final: 0.7377 (ttm-80) REVERT: A 204 GLU cc_start: 0.7810 (pt0) cc_final: 0.7474 (pt0) REVERT: A 206 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7115 (tm-30) REVERT: A 226 GLU cc_start: 0.6801 (tm-30) cc_final: 0.6537 (tm-30) REVERT: B 23 HIS cc_start: 0.7147 (t70) cc_final: 0.6709 (t-170) REVERT: B 32 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6959 (tm-30) REVERT: B 58 GLU cc_start: 0.7166 (pt0) cc_final: 0.6916 (pt0) REVERT: B 82 LEU cc_start: 0.8361 (mt) cc_final: 0.8033 (pp) REVERT: B 97 GLU cc_start: 0.7129 (pm20) cc_final: 0.6551 (pm20) REVERT: B 188 GLU cc_start: 0.7087 (pt0) cc_final: 0.6816 (pt0) REVERT: B 205 MET cc_start: 0.7652 (ppp) cc_final: 0.6599 (ppp) REVERT: B 206 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6473 (mm-30) REVERT: C 8 LYS cc_start: 0.8433 (mttt) cc_final: 0.8098 (mtpt) REVERT: C 17 LYS cc_start: 0.7970 (mptt) cc_final: 0.7635 (mmtt) REVERT: C 92 TYR cc_start: 0.8692 (t80) cc_final: 0.8124 (t80) REVERT: C 99 LYS cc_start: 0.8144 (ttmm) cc_final: 0.7465 (mtmm) REVERT: C 101 ARG cc_start: 0.7728 (mtp85) cc_final: 0.7503 (mmm-85) REVERT: C 121 GLU cc_start: 0.6587 (mm-30) cc_final: 0.6063 (mm-30) REVERT: C 151 ARG cc_start: 0.7891 (ttm110) cc_final: 0.7150 (mtm110) REVERT: C 180 ARG cc_start: 0.7300 (ttp80) cc_final: 0.7024 (ttp80) REVERT: C 183 TRP cc_start: 0.8084 (m-10) cc_final: 0.7690 (m-10) REVERT: C 186 PHE cc_start: 0.8084 (m-80) cc_final: 0.7240 (m-10) REVERT: C 187 GLU cc_start: 0.7209 (mp0) cc_final: 0.6707 (mp0) REVERT: C 202 ARG cc_start: 0.7381 (mtm110) cc_final: 0.6831 (ttp80) REVERT: C 203 LYS cc_start: 0.8089 (ttmt) cc_final: 0.7324 (ttmm) REVERT: C 214 ASN cc_start: 0.8531 (t0) cc_final: 0.8109 (t0) REVERT: C 245 ARG cc_start: 0.7669 (mtt180) cc_final: 0.7427 (mmm-85) REVERT: C 346 TYR cc_start: 0.6728 (m-80) cc_final: 0.6243 (m-80) REVERT: C 349 GLU cc_start: 0.7953 (pm20) cc_final: 0.7544 (pm20) REVERT: C 365 GLU cc_start: 0.7835 (tp30) cc_final: 0.7570 (tp30) REVERT: C 369 MET cc_start: 0.7664 (tpp) cc_final: 0.6310 (tpp) REVERT: C 371 ARG cc_start: 0.6805 (mtp180) cc_final: 0.6520 (mtp-110) REVERT: C 389 PHE cc_start: 0.8151 (m-80) cc_final: 0.7945 (m-10) REVERT: C 392 GLU cc_start: 0.7177 (mp0) cc_final: 0.6883 (mp0) REVERT: C 404 LYS cc_start: 0.8331 (mmmt) cc_final: 0.8078 (tptp) REVERT: C 407 ARG cc_start: 0.7761 (mmm-85) cc_final: 0.7458 (mmm-85) REVERT: C 410 LEU cc_start: 0.8891 (mm) cc_final: 0.8596 (tp) REVERT: C 427 ASP cc_start: 0.7171 (m-30) cc_final: 0.6935 (m-30) REVERT: C 430 LYS cc_start: 0.8250 (mtpp) cc_final: 0.7430 (mttm) REVERT: C 434 ASP cc_start: 0.7764 (m-30) cc_final: 0.7324 (m-30) REVERT: C 499 SER cc_start: 0.7824 (p) cc_final: 0.7515 (p) REVERT: C 523 GLU cc_start: 0.7403 (tp30) cc_final: 0.7200 (tp30) REVERT: C 549 ASP cc_start: 0.7005 (t0) cc_final: 0.6559 (t0) REVERT: C 593 LYS cc_start: 0.8253 (tptt) cc_final: 0.7834 (tppt) REVERT: C 611 GLU cc_start: 0.7344 (tt0) cc_final: 0.6747 (tt0) REVERT: C 616 ILE cc_start: 0.8547 (mp) cc_final: 0.8295 (mm) REVERT: C 644 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7691 (tt) REVERT: C 656 SER cc_start: 0.8508 (t) cc_final: 0.7976 (m) REVERT: C 723 VAL cc_start: 0.8439 (t) cc_final: 0.8006 (m) REVERT: C 730 SER cc_start: 0.8757 (m) cc_final: 0.8347 (t) REVERT: C 731 ARG cc_start: 0.7846 (ptp-110) cc_final: 0.7489 (ptm160) REVERT: C 777 VAL cc_start: 0.8348 (m) cc_final: 0.8125 (m) REVERT: C 778 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7242 (mp0) REVERT: C 785 ASP cc_start: 0.6772 (p0) cc_final: 0.6483 (p0) REVERT: C 788 SER cc_start: 0.8377 (m) cc_final: 0.7829 (p) REVERT: C 790 ASP cc_start: 0.7569 (t70) cc_final: 0.6714 (p0) REVERT: C 800 MET cc_start: 0.7385 (mmp) cc_final: 0.7017 (mmt) REVERT: C 808 ASN cc_start: 0.8146 (t0) cc_final: 0.7869 (m-40) REVERT: C 811 ASN cc_start: 0.7968 (p0) cc_final: 0.7717 (p0) REVERT: C 914 LYS cc_start: 0.7961 (tppt) cc_final: 0.7666 (tppt) REVERT: C 930 ASP cc_start: 0.7868 (t0) cc_final: 0.7231 (m-30) REVERT: C 943 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7958 (pttp) REVERT: C 947 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7191 (tm-30) REVERT: C 1028 LYS cc_start: 0.8535 (ptpp) cc_final: 0.8071 (pttm) REVERT: C 1030 GLU cc_start: 0.7793 (tp30) cc_final: 0.7265 (tp30) REVERT: C 1035 LYS cc_start: 0.8413 (tppt) cc_final: 0.7863 (tppt) REVERT: C 1088 ASP cc_start: 0.7335 (p0) cc_final: 0.7083 (p0) REVERT: C 1090 ASN cc_start: 0.7586 (t0) cc_final: 0.7279 (t0) REVERT: C 1122 LYS cc_start: 0.8283 (tptm) cc_final: 0.7345 (tppp) REVERT: C 1126 ASP cc_start: 0.7219 (m-30) cc_final: 0.6531 (m-30) REVERT: C 1140 LYS cc_start: 0.7604 (ptpt) cc_final: 0.7376 (ptpp) REVERT: C 1142 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7409 (mtp180) REVERT: C 1146 GLN cc_start: 0.7779 (tp40) cc_final: 0.7088 (tp-100) REVERT: C 1147 ARG cc_start: 0.8178 (mmm-85) cc_final: 0.7620 (tmm-80) REVERT: C 1176 LEU cc_start: 0.7657 (mp) cc_final: 0.7397 (tt) REVERT: C 1177 ARG cc_start: 0.7895 (ptm160) cc_final: 0.7485 (ptp90) REVERT: C 1178 LYS cc_start: 0.8324 (tptm) cc_final: 0.8096 (mmmm) REVERT: C 1200 LYS cc_start: 0.8386 (tttt) cc_final: 0.7905 (mtpt) REVERT: C 1210 ILE cc_start: 0.8103 (tt) cc_final: 0.7730 (pt) REVERT: C 1216 ARG cc_start: 0.7141 (mtm180) cc_final: 0.6155 (mtm180) REVERT: C 1229 TYR cc_start: 0.8297 (m-80) cc_final: 0.7889 (m-10) REVERT: C 1244 HIS cc_start: 0.7275 (t-90) cc_final: 0.6999 (t70) REVERT: C 1264 GLN cc_start: 0.8322 (mp10) cc_final: 0.8004 (mp10) REVERT: C 1278 LEU cc_start: 0.8381 (tp) cc_final: 0.8168 (tp) REVERT: C 1279 GLU cc_start: 0.7351 (pm20) cc_final: 0.6703 (pm20) REVERT: C 1288 GLN cc_start: 0.7364 (tm-30) cc_final: 0.6981 (tt0) REVERT: C 1290 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6917 (mpp) REVERT: C 1296 ASP cc_start: 0.6794 (t0) cc_final: 0.6572 (t0) REVERT: C 1303 LYS cc_start: 0.7928 (mtmm) cc_final: 0.7651 (mtmm) REVERT: C 1340 GLU cc_start: 0.6327 (tp30) cc_final: 0.5995 (tp30) REVERT: D 17 PHE cc_start: 0.7802 (p90) cc_final: 0.7554 (p90) REVERT: D 21 LYS cc_start: 0.8111 (ptpt) cc_final: 0.7504 (ptmm) REVERT: D 33 TRP cc_start: 0.8069 (m-10) cc_final: 0.7837 (m-10) REVERT: D 39 LYS cc_start: 0.8210 (mtpp) cc_final: 0.7986 (mtpt) REVERT: D 53 ARG cc_start: 0.6924 (ttt90) cc_final: 0.6333 (ttt90) REVERT: D 54 ASP cc_start: 0.7459 (t0) cc_final: 0.7186 (t0) REVERT: D 60 ARG cc_start: 0.7304 (ttm-80) cc_final: 0.6701 (mtp180) REVERT: D 115 TRP cc_start: 0.8494 (m-10) cc_final: 0.8240 (m-10) REVERT: D 118 LYS cc_start: 0.8095 (mmmt) cc_final: 0.7833 (mmmt) REVERT: D 132 LEU cc_start: 0.7963 (mt) cc_final: 0.7737 (mm) REVERT: D 141 PHE cc_start: 0.7849 (m-80) cc_final: 0.7414 (m-10) REVERT: D 148 GLU cc_start: 0.6884 (tm-30) cc_final: 0.6477 (tm-30) REVERT: D 151 MET cc_start: 0.7460 (pmm) cc_final: 0.6869 (pmm) REVERT: D 157 GLN cc_start: 0.7577 (mt0) cc_final: 0.7322 (mt0) REVERT: D 180 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.6676 (ppp) REVERT: D 198 CYS cc_start: 0.7718 (t) cc_final: 0.5322 (t) REVERT: D 215 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8513 (ptpt) REVERT: D 219 LYS cc_start: 0.8784 (ttmt) cc_final: 0.8389 (ttpp) REVERT: D 235 GLU cc_start: 0.7135 (pm20) cc_final: 0.6831 (pm20) REVERT: D 236 TRP cc_start: 0.8267 (m-10) cc_final: 0.8015 (m-10) REVERT: D 275 ARG cc_start: 0.7840 (tpp-160) cc_final: 0.7383 (tpp-160) REVERT: D 282 LEU cc_start: 0.8428 (mt) cc_final: 0.8153 (tt) REVERT: D 297 ARG cc_start: 0.7819 (ttp80) cc_final: 0.7392 (tmm-80) REVERT: D 298 MET cc_start: 0.7527 (ttp) cc_final: 0.5967 (ttp) REVERT: D 325 LYS cc_start: 0.8001 (mmpt) cc_final: 0.7677 (mmtp) REVERT: D 332 LYS cc_start: 0.7089 (mtmm) cc_final: 0.6613 (mtpp) REVERT: D 400 MET cc_start: 0.6842 (tmm) cc_final: 0.6615 (tmm) REVERT: D 404 GLU cc_start: 0.8188 (tp30) cc_final: 0.7917 (tp30) REVERT: D 466 MET cc_start: 0.7349 (pmm) cc_final: 0.6144 (ptp) REVERT: D 475 GLU cc_start: 0.7497 (mp0) cc_final: 0.7170 (mp0) REVERT: D 495 ASN cc_start: 0.7347 (m-40) cc_final: 0.6827 (m110) REVERT: D 500 ILE cc_start: 0.8340 (mm) cc_final: 0.7944 (tt) REVERT: D 511 TYR cc_start: 0.8113 (t80) cc_final: 0.7529 (t80) REVERT: D 549 LYS cc_start: 0.7753 (tptt) cc_final: 0.7511 (mmtt) REVERT: D 573 THR cc_start: 0.8361 (p) cc_final: 0.8103 (m) REVERT: D 610 ARG cc_start: 0.7765 (tpp-160) cc_final: 0.7483 (mmt-90) REVERT: D 641 ILE cc_start: 0.8231 (tp) cc_final: 0.8002 (tp) REVERT: D 649 LYS cc_start: 0.8446 (mmmt) cc_final: 0.7927 (mmmt) REVERT: D 652 GLU cc_start: 0.8363 (mp0) cc_final: 0.7366 (mp0) REVERT: D 665 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7407 (mp10) REVERT: D 684 ASP cc_start: 0.7161 (m-30) cc_final: 0.6854 (m-30) REVERT: D 691 ASP cc_start: 0.7832 (m-30) cc_final: 0.7540 (m-30) REVERT: D 695 LYS cc_start: 0.8565 (tmtt) cc_final: 0.7771 (ttpp) REVERT: D 724 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7243 (mpp) REVERT: D 733 SER cc_start: 0.7475 (t) cc_final: 0.7274 (p) REVERT: D 772 TYR cc_start: 0.8588 (t80) cc_final: 0.8338 (t80) REVERT: D 781 LYS cc_start: 0.8490 (ttmt) cc_final: 0.8214 (tptp) REVERT: D 789 LYS cc_start: 0.8056 (ttpt) cc_final: 0.7484 (ptmt) REVERT: D 793 SER cc_start: 0.7945 (p) cc_final: 0.7678 (p) REVERT: D 808 VAL cc_start: 0.8546 (t) cc_final: 0.8250 (m) REVERT: D 822 MET cc_start: 0.6344 (tmm) cc_final: 0.6007 (tmm) REVERT: D 838 ARG cc_start: 0.8080 (ttt180) cc_final: 0.7876 (tpp80) REVERT: D 842 ARG cc_start: 0.6962 (mtt180) cc_final: 0.6346 (mtt180) REVERT: D 865 HIS cc_start: 0.6616 (p90) cc_final: 0.6190 (p90) REVERT: D 981 GLU cc_start: 0.6489 (tm-30) cc_final: 0.6238 (tm-30) REVERT: D 1146 GLU cc_start: 0.6643 (pp20) cc_final: 0.6214 (pp20) REVERT: D 1155 ILE cc_start: 0.8978 (mp) cc_final: 0.8745 (mp) REVERT: D 1173 ARG cc_start: 0.8167 (ptm160) cc_final: 0.7946 (ptm160) REVERT: D 1188 GLU cc_start: 0.6091 (pm20) cc_final: 0.5409 (pp20) REVERT: D 1218 HIS cc_start: 0.7483 (m-70) cc_final: 0.7262 (m-70) REVERT: D 1242 ARG cc_start: 0.7471 (ttm110) cc_final: 0.7269 (ptp-110) REVERT: D 1248 ILE cc_start: 0.7866 (mm) cc_final: 0.7511 (tp) REVERT: D 1250 ASP cc_start: 0.7594 (p0) cc_final: 0.7348 (p0) REVERT: D 1262 ARG cc_start: 0.7216 (ttp-110) cc_final: 0.6900 (ttp80) REVERT: D 1355 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7366 (ptp-170) REVERT: D 1365 TYR cc_start: 0.8008 (t80) cc_final: 0.7621 (t80) REVERT: E 52 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7728 (ttp80) REVERT: E 53 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7496 (mm-30) REVERT: G 27 ARG cc_start: 0.8049 (mtm180) cc_final: 0.7663 (mtm-85) REVERT: G 33 HIS cc_start: 0.8418 (OUTLIER) cc_final: 0.8120 (t-90) REVERT: G 43 MET cc_start: 0.7528 (tmm) cc_final: 0.7277 (tmm) REVERT: G 74 VAL cc_start: 0.7595 (p) cc_final: 0.7237 (m) REVERT: G 80 TRP cc_start: 0.7637 (t60) cc_final: 0.7061 (t60) REVERT: G 84 ARG cc_start: 0.8073 (tpp80) cc_final: 0.7374 (tpp-160) outliers start: 51 outliers final: 30 residues processed: 885 average time/residue: 0.2144 time to fit residues: 279.3964 Evaluate side-chains 835 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 797 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 665 GLN Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1355 ARG Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 33 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 2 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 204 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 221 optimal weight: 0.9990 chunk 140 optimal weight: 20.0000 chunk 248 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 93 optimal weight: 0.0040 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN C 314 ASN C 343 HIS ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS C 613 ASN C1237 HIS C1268 GLN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 910 ASN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.139903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.111207 restraints weight = 49407.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.114821 restraints weight = 24803.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.117244 restraints weight = 15224.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.118732 restraints weight = 10776.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.119634 restraints weight = 8644.088| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 28014 Z= 0.144 Angle : 0.617 10.426 38147 Z= 0.319 Chirality : 0.044 0.256 4351 Planarity : 0.005 0.125 4731 Dihedral : 14.597 178.045 4488 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.02 % Allowed : 15.89 % Favored : 81.09 % 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: -0.61 (0.14), residues: 3285 helix: 1.13 (0.16), residues: 1105 sheet: -0.45 (0.27), residues: 384 loop : -1.44 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 12 TYR 0.022 0.002 TYR D 589 PHE 0.017 0.001 PHE D 892 TRP 0.021 0.001 TRP D1193 HIS 0.013 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00319 (28008) covalent geometry : angle 0.61548 (38141) hydrogen bonds : bond 0.04055 ( 1063) hydrogen bonds : angle 4.55557 ( 2930) metal coordination : bond 0.03022 ( 6) metal coordination : angle 3.44250 ( 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 917 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 832 time to evaluate : 0.956 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: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.8620 (mt) cc_final: 0.8335 (tt) REVERT: A 33 ARG cc_start: 0.7693 (ptm160) cc_final: 0.7246 (ptm160) REVERT: A 58 GLU cc_start: 0.7392 (pp20) cc_final: 0.6813 (pp20) REVERT: A 59 VAL cc_start: 0.8252 (OUTLIER) cc_final: 0.7717 (p) REVERT: A 74 VAL cc_start: 0.8561 (m) cc_final: 0.8080 (p) REVERT: A 80 GLU cc_start: 0.7572 (tp30) cc_final: 0.7026 (mp0) REVERT: A 104 LYS cc_start: 0.8256 (tptp) cc_final: 0.7649 (tptp) REVERT: A 122 GLU cc_start: 0.6964 (pp20) cc_final: 0.6556 (pp20) REVERT: A 153 VAL cc_start: 0.8864 (t) cc_final: 0.8570 (m) REVERT: A 170 ARG cc_start: 0.8138 (ttp-110) cc_final: 0.7269 (ttm-80) REVERT: A 171 LEU cc_start: 0.8666 (pp) cc_final: 0.8211 (pp) REVERT: A 188 GLU cc_start: 0.7825 (pm20) cc_final: 0.7257 (pm20) REVERT: A 198 LEU cc_start: 0.7480 (mm) cc_final: 0.7007 (mm) REVERT: A 204 GLU cc_start: 0.7786 (pt0) cc_final: 0.7459 (pt0) REVERT: A 206 GLU cc_start: 0.7349 (tm-30) cc_final: 0.7133 (tm-30) REVERT: A 218 ARG cc_start: 0.7867 (mmt90) cc_final: 0.7451 (mmt90) REVERT: B 32 GLU cc_start: 0.7289 (tm-30) cc_final: 0.6981 (tm-30) REVERT: B 51 MET cc_start: 0.7490 (mmm) cc_final: 0.7228 (mmm) REVERT: B 58 GLU cc_start: 0.7255 (pt0) cc_final: 0.7021 (pt0) REVERT: B 97 GLU cc_start: 0.7100 (pm20) cc_final: 0.6532 (pm20) REVERT: B 136 GLU cc_start: 0.8707 (pm20) cc_final: 0.8280 (pp20) REVERT: B 188 GLU cc_start: 0.6959 (pt0) cc_final: 0.6647 (pt0) REVERT: B 205 MET cc_start: 0.7682 (ppp) cc_final: 0.6836 (ppp) REVERT: B 214 GLU cc_start: 0.6181 (tm-30) cc_final: 0.5742 (tm-30) REVERT: C 5 TYR cc_start: 0.6105 (t80) cc_final: 0.5676 (t80) REVERT: C 8 LYS cc_start: 0.8419 (mttt) cc_final: 0.8138 (mtpt) REVERT: C 17 LYS cc_start: 0.7971 (mptt) cc_final: 0.7608 (mmtp) REVERT: C 99 LYS cc_start: 0.8151 (ttmm) cc_final: 0.7436 (mtmm) REVERT: C 118 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7267 (mtpt) REVERT: C 121 GLU cc_start: 0.6585 (mm-30) cc_final: 0.6044 (mm-30) REVERT: C 151 ARG cc_start: 0.7891 (ttm110) cc_final: 0.7138 (mtm110) REVERT: C 180 ARG cc_start: 0.7333 (ttp80) cc_final: 0.7017 (ttp80) REVERT: C 183 TRP cc_start: 0.8105 (m-10) cc_final: 0.7728 (m-10) REVERT: C 185 ASP cc_start: 0.6239 (p0) cc_final: 0.5895 (p0) REVERT: C 186 PHE cc_start: 0.8088 (m-80) cc_final: 0.7628 (m-10) REVERT: C 187 GLU cc_start: 0.7041 (mp0) cc_final: 0.6608 (mp0) REVERT: C 195 PHE cc_start: 0.8004 (m-80) cc_final: 0.7639 (m-80) REVERT: C 203 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7520 (ttmm) REVERT: C 214 ASN cc_start: 0.8484 (t0) cc_final: 0.8080 (t0) REVERT: C 346 TYR cc_start: 0.6875 (m-80) cc_final: 0.6514 (m-80) REVERT: C 349 GLU cc_start: 0.7874 (pm20) cc_final: 0.7510 (pm20) REVERT: C 365 GLU cc_start: 0.7784 (tp30) cc_final: 0.7570 (tp30) REVERT: C 368 ARG cc_start: 0.8004 (mtm-85) cc_final: 0.7380 (mtm110) REVERT: C 390 PHE cc_start: 0.6862 (m-80) cc_final: 0.6500 (m-80) REVERT: C 392 GLU cc_start: 0.7173 (mp0) cc_final: 0.6945 (mp0) REVERT: C 404 LYS cc_start: 0.8359 (mmmt) cc_final: 0.8107 (tppt) REVERT: C 427 ASP cc_start: 0.7153 (m-30) cc_final: 0.6898 (m-30) REVERT: C 430 LYS cc_start: 0.8229 (mtpp) cc_final: 0.7491 (mttm) REVERT: C 434 ASP cc_start: 0.7795 (m-30) cc_final: 0.7341 (m-30) REVERT: C 499 SER cc_start: 0.7790 (p) cc_final: 0.7490 (p) REVERT: C 523 GLU cc_start: 0.7474 (tp30) cc_final: 0.7248 (tp30) REVERT: C 549 ASP cc_start: 0.7114 (t0) cc_final: 0.6639 (t0) REVERT: C 593 LYS cc_start: 0.8322 (tptt) cc_final: 0.7841 (tppt) REVERT: C 611 GLU cc_start: 0.7361 (tt0) cc_final: 0.6707 (tt0) REVERT: C 616 ILE cc_start: 0.8523 (mp) cc_final: 0.8235 (mm) REVERT: C 656 SER cc_start: 0.8518 (t) cc_final: 0.7925 (m) REVERT: C 686 GLN cc_start: 0.7834 (tp-100) cc_final: 0.7583 (tp40) REVERT: C 696 ASP cc_start: 0.6657 (t0) cc_final: 0.6435 (t0) REVERT: C 723 VAL cc_start: 0.8382 (t) cc_final: 0.7911 (m) REVERT: C 730 SER cc_start: 0.8782 (m) cc_final: 0.8362 (t) REVERT: C 731 ARG cc_start: 0.7925 (ptp-110) cc_final: 0.7686 (ptm160) REVERT: C 734 ILE cc_start: 0.8023 (mp) cc_final: 0.7785 (pt) REVERT: C 740 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6373 (mt-10) REVERT: C 749 ASP cc_start: 0.6787 (m-30) cc_final: 0.5991 (m-30) REVERT: C 785 ASP cc_start: 0.6676 (p0) cc_final: 0.6466 (p0) REVERT: C 788 SER cc_start: 0.8439 (m) cc_final: 0.7819 (p) REVERT: C 790 ASP cc_start: 0.7501 (t70) cc_final: 0.6718 (p0) REVERT: C 800 MET cc_start: 0.7366 (mmp) cc_final: 0.7041 (mmt) REVERT: C 808 ASN cc_start: 0.8154 (t0) cc_final: 0.7833 (m-40) REVERT: C 811 ASN cc_start: 0.7953 (p0) cc_final: 0.7694 (p0) REVERT: C 914 LYS cc_start: 0.7834 (tppt) cc_final: 0.7565 (tppt) REVERT: C 930 ASP cc_start: 0.7854 (t0) cc_final: 0.7225 (m-30) REVERT: C 947 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7235 (tm-30) REVERT: C 948 ILE cc_start: 0.8862 (mm) cc_final: 0.8310 (mm) REVERT: C 1035 LYS cc_start: 0.8398 (tppt) cc_final: 0.7865 (tppt) REVERT: C 1095 ASP cc_start: 0.7418 (m-30) cc_final: 0.7031 (m-30) REVERT: C 1122 LYS cc_start: 0.8315 (tptm) cc_final: 0.7349 (tppp) REVERT: C 1126 ASP cc_start: 0.7242 (m-30) cc_final: 0.6540 (m-30) REVERT: C 1140 LYS cc_start: 0.7650 (ptpt) cc_final: 0.7247 (ptpt) REVERT: C 1146 GLN cc_start: 0.7740 (tp40) cc_final: 0.7180 (tp-100) REVERT: C 1167 GLU cc_start: 0.7565 (pm20) cc_final: 0.7301 (pm20) REVERT: C 1176 LEU cc_start: 0.7682 (mp) cc_final: 0.7431 (tt) REVERT: C 1178 LYS cc_start: 0.8337 (tptm) cc_final: 0.8044 (mmmm) REVERT: C 1200 LYS cc_start: 0.8289 (tttt) cc_final: 0.7979 (tttt) REVERT: C 1210 ILE cc_start: 0.8156 (tt) cc_final: 0.7772 (pt) REVERT: C 1216 ARG cc_start: 0.7314 (mtm180) cc_final: 0.6388 (mtm180) REVERT: C 1229 TYR cc_start: 0.8263 (m-80) cc_final: 0.7795 (m-10) REVERT: C 1244 HIS cc_start: 0.7213 (t-90) cc_final: 0.6999 (t70) REVERT: C 1264 GLN cc_start: 0.8323 (mp10) cc_final: 0.8013 (mp10) REVERT: C 1303 LYS cc_start: 0.7976 (mtmm) cc_final: 0.7687 (mtmm) REVERT: C 1340 GLU cc_start: 0.6466 (tp30) cc_final: 0.6156 (tp30) REVERT: D 21 LYS cc_start: 0.8153 (ptpt) cc_final: 0.7538 (ptmm) REVERT: D 29 MET cc_start: 0.7503 (ttt) cc_final: 0.7277 (ttt) REVERT: D 33 TRP cc_start: 0.7944 (m-10) cc_final: 0.7514 (m-10) REVERT: D 52 GLU cc_start: 0.6538 (tm-30) cc_final: 0.6311 (tm-30) REVERT: D 53 ARG cc_start: 0.6961 (ttt90) cc_final: 0.6418 (ttt90) REVERT: D 60 ARG cc_start: 0.7320 (ttm-80) cc_final: 0.6589 (mtp180) REVERT: D 115 TRP cc_start: 0.8516 (m-10) cc_final: 0.8295 (m-10) REVERT: D 118 LYS cc_start: 0.8085 (mmmt) cc_final: 0.7816 (mmmt) REVERT: D 132 LEU cc_start: 0.8144 (mt) cc_final: 0.7864 (mm) REVERT: D 148 GLU cc_start: 0.7071 (tm-30) cc_final: 0.6632 (tm-30) REVERT: D 151 MET cc_start: 0.7403 (pmm) cc_final: 0.6755 (pmm) REVERT: D 180 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6739 (ppp) REVERT: D 198 CYS cc_start: 0.7281 (t) cc_final: 0.6478 (t) REVERT: D 200 GLN cc_start: 0.8015 (pp30) cc_final: 0.7626 (pp30) REVERT: D 201 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8458 (mm) REVERT: D 215 LYS cc_start: 0.8809 (mtmm) cc_final: 0.8525 (ptpt) REVERT: D 219 LYS cc_start: 0.8760 (ttmt) cc_final: 0.8351 (ttpp) REVERT: D 235 GLU cc_start: 0.7186 (pm20) cc_final: 0.6794 (pm20) REVERT: D 236 TRP cc_start: 0.8321 (m-10) cc_final: 0.7976 (m-10) REVERT: D 282 LEU cc_start: 0.8429 (mt) cc_final: 0.8224 (tt) REVERT: D 297 ARG cc_start: 0.7940 (ttp80) cc_final: 0.7573 (tmm-80) REVERT: D 325 LYS cc_start: 0.8072 (mmpt) cc_final: 0.7858 (mmmt) REVERT: D 332 LYS cc_start: 0.7224 (mtmm) cc_final: 0.6729 (mtpp) REVERT: D 375 GLU cc_start: 0.6968 (tm-30) cc_final: 0.6748 (tm-30) REVERT: D 404 GLU cc_start: 0.8215 (tp30) cc_final: 0.7990 (tp30) REVERT: D 405 GLU cc_start: 0.6981 (mp0) cc_final: 0.6716 (mp0) REVERT: D 442 ILE cc_start: 0.8402 (tt) cc_final: 0.8009 (pt) REVERT: D 466 MET cc_start: 0.7347 (pmm) cc_final: 0.6444 (ptp) REVERT: D 475 GLU cc_start: 0.7559 (mp0) cc_final: 0.7137 (mp0) REVERT: D 495 ASN cc_start: 0.7395 (m-40) cc_final: 0.6858 (m110) REVERT: D 500 ILE cc_start: 0.8336 (mm) cc_final: 0.7983 (tt) REVERT: D 513 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6762 (mmt) REVERT: D 549 LYS cc_start: 0.7791 (tptt) cc_final: 0.7541 (tptt) REVERT: D 554 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6983 (tm-30) REVERT: D 555 TYR cc_start: 0.7709 (m-10) cc_final: 0.7312 (m-80) REVERT: D 556 GLU cc_start: 0.6318 (tm-30) cc_final: 0.6043 (tm-30) REVERT: D 573 THR cc_start: 0.8355 (p) cc_final: 0.8066 (m) REVERT: D 579 LEU cc_start: 0.8425 (tp) cc_final: 0.8170 (tp) REVERT: D 610 ARG cc_start: 0.7695 (tpp-160) cc_final: 0.7320 (mmt90) REVERT: D 649 LYS cc_start: 0.8388 (mmmt) cc_final: 0.7999 (mmmt) REVERT: D 652 GLU cc_start: 0.8346 (mp0) cc_final: 0.7494 (mp0) REVERT: D 665 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7432 (mp10) REVERT: D 684 ASP cc_start: 0.7173 (m-30) cc_final: 0.6948 (m-30) REVERT: D 691 ASP cc_start: 0.7820 (m-30) cc_final: 0.7558 (m-30) REVERT: D 692 ARG cc_start: 0.7462 (tmm-80) cc_final: 0.7242 (tmm-80) REVERT: D 695 LYS cc_start: 0.8575 (tmtt) cc_final: 0.8227 (tmtt) REVERT: D 724 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7296 (mpp) REVERT: D 770 LEU cc_start: 0.7873 (mm) cc_final: 0.7482 (mt) REVERT: D 772 TYR cc_start: 0.8598 (t80) cc_final: 0.8281 (t80) REVERT: D 781 LYS cc_start: 0.8483 (ttmt) cc_final: 0.8203 (tptp) REVERT: D 789 LYS cc_start: 0.7964 (ttpt) cc_final: 0.7400 (ptmt) REVERT: D 793 SER cc_start: 0.8038 (p) cc_final: 0.7715 (p) REVERT: D 808 VAL cc_start: 0.8556 (t) cc_final: 0.8334 (m) REVERT: D 822 MET cc_start: 0.6408 (tmm) cc_final: 0.6132 (tmm) REVERT: D 842 ARG cc_start: 0.6870 (mtt180) cc_final: 0.6348 (mtt180) REVERT: D 870 ASP cc_start: 0.7446 (m-30) cc_final: 0.7062 (m-30) REVERT: D 915 ILE cc_start: 0.8301 (tt) cc_final: 0.7874 (pt) REVERT: D 981 GLU cc_start: 0.6498 (tm-30) cc_final: 0.6162 (tm-30) REVERT: D 992 LYS cc_start: 0.7821 (mmmm) cc_final: 0.7411 (mmmt) REVERT: D 1099 TYR cc_start: 0.7523 (m-80) cc_final: 0.6717 (m-80) REVERT: D 1146 GLU cc_start: 0.6696 (pp20) cc_final: 0.6298 (pp20) REVERT: D 1155 ILE cc_start: 0.8981 (mp) cc_final: 0.8731 (mp) REVERT: D 1173 ARG cc_start: 0.8185 (ptm160) cc_final: 0.7911 (ptm160) REVERT: D 1188 GLU cc_start: 0.6283 (pm20) cc_final: 0.5054 (pp20) REVERT: D 1218 HIS cc_start: 0.7454 (m-70) cc_final: 0.7187 (m-70) REVERT: D 1248 ILE cc_start: 0.8121 (mm) cc_final: 0.7792 (tp) REVERT: D 1250 ASP cc_start: 0.7512 (p0) cc_final: 0.7091 (p0) REVERT: D 1254 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6651 (mt-10) REVERT: D 1262 ARG cc_start: 0.7202 (ttp-110) cc_final: 0.6978 (ttp80) REVERT: D 1365 TYR cc_start: 0.8061 (t80) cc_final: 0.7680 (t80) REVERT: E 31 GLN cc_start: 0.7919 (tp40) cc_final: 0.7671 (tp40) REVERT: E 52 ARG cc_start: 0.8058 (ttp80) cc_final: 0.7755 (ttp80) REVERT: E 53 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7327 (mm-30) REVERT: G 27 ARG cc_start: 0.8026 (mtm180) cc_final: 0.7592 (mtm-85) REVERT: G 33 HIS cc_start: 0.8489 (OUTLIER) cc_final: 0.8147 (t-90) REVERT: G 72 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7842 (mm110) REVERT: G 74 VAL cc_start: 0.7639 (p) cc_final: 0.7387 (m) REVERT: G 83 VAL cc_start: 0.8958 (t) cc_final: 0.8750 (p) REVERT: G 84 ARG cc_start: 0.8065 (tpp80) cc_final: 0.7850 (tpt90) outliers start: 85 outliers final: 52 residues processed: 872 average time/residue: 0.2120 time to fit residues: 272.1790 Evaluate side-chains 849 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 789 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 665 GLN Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1283 SER Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 86 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 118 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 271 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS B 128 HIS ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN ** C1237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN D 910 ASN G 29 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.136972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.107892 restraints weight = 49491.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111500 restraints weight = 24781.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.113901 restraints weight = 15267.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.115456 restraints weight = 10828.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.116465 restraints weight = 8637.992| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 28014 Z= 0.215 Angle : 0.657 11.364 38147 Z= 0.345 Chirality : 0.045 0.246 4351 Planarity : 0.005 0.076 4731 Dihedral : 14.681 178.375 4488 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.26 % Allowed : 17.63 % Favored : 78.11 % 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: -0.75 (0.14), residues: 3285 helix: 0.91 (0.16), residues: 1107 sheet: -0.41 (0.26), residues: 400 loop : -1.48 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 275 TYR 0.024 0.002 TYR D 995 PHE 0.017 0.002 PHE D 35 TRP 0.013 0.002 TRP D1193 HIS 0.007 0.001 HIS C1244 Details of bonding type rmsd covalent geometry : bond 0.00470 (28008) covalent geometry : angle 0.65520 (38141) hydrogen bonds : bond 0.04715 ( 1063) hydrogen bonds : angle 4.56189 ( 2930) metal coordination : bond 0.01181 ( 6) metal coordination : angle 3.94400 ( 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 940 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 820 time to evaluate : 0.927 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: symmetry clash REVERT: A 16 ILE cc_start: 0.8568 (mt) cc_final: 0.8260 (tt) REVERT: A 33 ARG cc_start: 0.7691 (ptm160) cc_final: 0.7215 (ptm160) REVERT: A 58 GLU cc_start: 0.7529 (pp20) cc_final: 0.7042 (pp20) REVERT: A 59 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.7884 (p) REVERT: A 74 VAL cc_start: 0.8578 (m) cc_final: 0.8146 (p) REVERT: A 80 GLU cc_start: 0.7705 (tp30) cc_final: 0.7071 (mp0) REVERT: A 101 THR cc_start: 0.8304 (m) cc_final: 0.7945 (t) REVERT: A 104 LYS cc_start: 0.8159 (tptp) cc_final: 0.7459 (tptp) REVERT: A 122 GLU cc_start: 0.6807 (pp20) cc_final: 0.6503 (pp20) REVERT: A 153 VAL cc_start: 0.8845 (t) cc_final: 0.8566 (m) REVERT: A 170 ARG cc_start: 0.8286 (ttp-110) cc_final: 0.7356 (ttm-80) REVERT: A 171 LEU cc_start: 0.8721 (pp) cc_final: 0.8296 (pp) REVERT: A 188 GLU cc_start: 0.7756 (pm20) cc_final: 0.7195 (pm20) REVERT: A 198 LEU cc_start: 0.7716 (mm) cc_final: 0.7248 (mm) REVERT: A 204 GLU cc_start: 0.7726 (pt0) cc_final: 0.7422 (pt0) REVERT: A 212 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6918 (m-30) REVERT: B 16 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7771 (mt) REVERT: B 32 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6973 (tm-30) REVERT: B 51 MET cc_start: 0.7513 (mmm) cc_final: 0.7275 (mmm) REVERT: B 97 GLU cc_start: 0.6946 (pm20) cc_final: 0.6484 (pm20) REVERT: B 136 GLU cc_start: 0.8724 (pm20) cc_final: 0.8122 (pp20) REVERT: B 188 GLU cc_start: 0.6897 (pt0) cc_final: 0.6651 (pt0) REVERT: B 198 LEU cc_start: 0.7204 (mt) cc_final: 0.6970 (mp) REVERT: B 205 MET cc_start: 0.7746 (ppp) cc_final: 0.6893 (ppp) REVERT: B 214 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.5952 (tm-30) REVERT: B 231 PHE cc_start: 0.8368 (m-10) cc_final: 0.8149 (m-10) REVERT: C 8 LYS cc_start: 0.8455 (mttt) cc_final: 0.8170 (mtpt) REVERT: C 17 LYS cc_start: 0.8055 (mptt) cc_final: 0.7620 (mmtp) REVERT: C 87 ILE cc_start: 0.8421 (tp) cc_final: 0.8009 (pt) REVERT: C 99 LYS cc_start: 0.8144 (ttmm) cc_final: 0.7532 (mtmm) REVERT: C 121 GLU cc_start: 0.6537 (mm-30) cc_final: 0.5994 (mm-30) REVERT: C 151 ARG cc_start: 0.7901 (ttm110) cc_final: 0.7199 (mtm110) REVERT: C 185 ASP cc_start: 0.6300 (p0) cc_final: 0.5887 (p0) REVERT: C 186 PHE cc_start: 0.8106 (m-80) cc_final: 0.7733 (m-10) REVERT: C 187 GLU cc_start: 0.7096 (mp0) cc_final: 0.6391 (mp0) REVERT: C 195 PHE cc_start: 0.7959 (m-80) cc_final: 0.7434 (m-80) REVERT: C 203 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7535 (ttmm) REVERT: C 214 ASN cc_start: 0.8502 (t0) cc_final: 0.8070 (t0) REVERT: C 349 GLU cc_start: 0.8038 (pm20) cc_final: 0.7665 (mp0) REVERT: C 365 GLU cc_start: 0.7875 (tp30) cc_final: 0.7668 (tp30) REVERT: C 368 ARG cc_start: 0.7970 (mtm-85) cc_final: 0.7588 (mtm-85) REVERT: C 389 PHE cc_start: 0.8274 (m-10) cc_final: 0.8047 (m-10) REVERT: C 392 GLU cc_start: 0.7223 (mp0) cc_final: 0.6953 (mp0) REVERT: C 394 ARG cc_start: 0.6706 (ttm110) cc_final: 0.6483 (ttm110) REVERT: C 404 LYS cc_start: 0.8291 (mmmt) cc_final: 0.8027 (tppt) REVERT: C 427 ASP cc_start: 0.7153 (m-30) cc_final: 0.6888 (m-30) REVERT: C 430 LYS cc_start: 0.8196 (mtpp) cc_final: 0.7506 (mttm) REVERT: C 434 ASP cc_start: 0.7792 (m-30) cc_final: 0.7363 (m-30) REVERT: C 499 SER cc_start: 0.7827 (p) cc_final: 0.7533 (p) REVERT: C 523 GLU cc_start: 0.7532 (tp30) cc_final: 0.7250 (tp30) REVERT: C 549 ASP cc_start: 0.7154 (t0) cc_final: 0.6660 (t0) REVERT: C 593 LYS cc_start: 0.8318 (tptt) cc_final: 0.7882 (tppt) REVERT: C 602 GLU cc_start: 0.7137 (tp30) cc_final: 0.6730 (tm-30) REVERT: C 611 GLU cc_start: 0.7330 (tt0) cc_final: 0.6696 (tt0) REVERT: C 616 ILE cc_start: 0.8512 (mp) cc_final: 0.8188 (mm) REVERT: C 656 SER cc_start: 0.8567 (t) cc_final: 0.8066 (m) REVERT: C 723 VAL cc_start: 0.8373 (t) cc_final: 0.7907 (m) REVERT: C 730 SER cc_start: 0.8796 (m) cc_final: 0.8369 (t) REVERT: C 731 ARG cc_start: 0.7994 (ptp-110) cc_final: 0.7776 (ptm160) REVERT: C 734 ILE cc_start: 0.8020 (mp) cc_final: 0.7796 (pt) REVERT: C 755 LYS cc_start: 0.8476 (mmmt) cc_final: 0.8271 (mmmt) REVERT: C 785 ASP cc_start: 0.6685 (p0) cc_final: 0.6392 (p0) REVERT: C 800 MET cc_start: 0.7350 (mmp) cc_final: 0.6984 (mtp) REVERT: C 811 ASN cc_start: 0.7948 (p0) cc_final: 0.6786 (p0) REVERT: C 825 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7127 (tm-30) REVERT: C 914 LYS cc_start: 0.7885 (tppt) cc_final: 0.7548 (tppt) REVERT: C 930 ASP cc_start: 0.7838 (t0) cc_final: 0.7221 (m-30) REVERT: C 947 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7347 (tm-30) REVERT: C 948 ILE cc_start: 0.8906 (mm) cc_final: 0.8304 (mm) REVERT: C 1030 GLU cc_start: 0.7844 (tp30) cc_final: 0.7298 (tp30) REVERT: C 1035 LYS cc_start: 0.8509 (tppt) cc_final: 0.7955 (tppt) REVERT: C 1095 ASP cc_start: 0.7579 (m-30) cc_final: 0.7275 (m-30) REVERT: C 1099 ASN cc_start: 0.8047 (t0) cc_final: 0.7347 (t0) REVERT: C 1119 MET cc_start: 0.8201 (tpp) cc_final: 0.7738 (tpt) REVERT: C 1122 LYS cc_start: 0.8402 (tptm) cc_final: 0.7484 (tppp) REVERT: C 1124 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7793 (mt) REVERT: C 1126 ASP cc_start: 0.7235 (m-30) cc_final: 0.6617 (m-30) REVERT: C 1140 LYS cc_start: 0.7782 (ptpt) cc_final: 0.7386 (ptpt) REVERT: C 1146 GLN cc_start: 0.7863 (tp40) cc_final: 0.7395 (tp-100) REVERT: C 1176 LEU cc_start: 0.7881 (mp) cc_final: 0.7580 (tp) REVERT: C 1200 LYS cc_start: 0.8493 (tttt) cc_final: 0.8182 (tttt) REVERT: C 1210 ILE cc_start: 0.8145 (tt) cc_final: 0.7829 (pt) REVERT: C 1229 TYR cc_start: 0.8221 (m-80) cc_final: 0.7872 (m-10) REVERT: C 1264 GLN cc_start: 0.8351 (mp10) cc_final: 0.7945 (mp10) REVERT: C 1279 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6667 (pm20) REVERT: C 1289 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6879 (mm-30) REVERT: C 1290 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.7030 (mpp) REVERT: C 1332 SER cc_start: 0.8019 (p) cc_final: 0.7812 (p) REVERT: C 1340 GLU cc_start: 0.6413 (tp30) cc_final: 0.6107 (tp30) REVERT: D 21 LYS cc_start: 0.8108 (ptpt) cc_final: 0.7430 (ptmm) REVERT: D 33 TRP cc_start: 0.8058 (m-10) cc_final: 0.7741 (m-10) REVERT: D 44 ILE cc_start: 0.8540 (mm) cc_final: 0.7779 (mm) REVERT: D 60 ARG cc_start: 0.7514 (ttm-80) cc_final: 0.7013 (ttm-80) REVERT: D 115 TRP cc_start: 0.8559 (m-10) cc_final: 0.8299 (m-10) REVERT: D 118 LYS cc_start: 0.8179 (mmmt) cc_final: 0.7905 (mmmt) REVERT: D 141 PHE cc_start: 0.7967 (m-80) cc_final: 0.7654 (m-80) REVERT: D 148 GLU cc_start: 0.7095 (tm-30) cc_final: 0.6601 (tm-30) REVERT: D 151 MET cc_start: 0.7403 (pmm) cc_final: 0.6798 (pmm) REVERT: D 198 CYS cc_start: 0.7556 (t) cc_final: 0.7103 (t) REVERT: D 200 GLN cc_start: 0.8234 (pp30) cc_final: 0.7986 (pp30) REVERT: D 201 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8498 (mm) REVERT: D 215 LYS cc_start: 0.8838 (mtmm) cc_final: 0.8545 (ptpt) REVERT: D 219 LYS cc_start: 0.8759 (ttmt) cc_final: 0.8322 (ttpp) REVERT: D 235 GLU cc_start: 0.7251 (pm20) cc_final: 0.6875 (pm20) REVERT: D 236 TRP cc_start: 0.8382 (m-10) cc_final: 0.8026 (m-10) REVERT: D 251 PRO cc_start: 0.7867 (Cg_endo) cc_final: 0.7596 (Cg_exo) REVERT: D 282 LEU cc_start: 0.8533 (mt) cc_final: 0.8315 (tt) REVERT: D 297 ARG cc_start: 0.7919 (ttp80) cc_final: 0.7542 (tmm-80) REVERT: D 298 MET cc_start: 0.7320 (ttp) cc_final: 0.6963 (ttp) REVERT: D 332 LYS cc_start: 0.7397 (mtmm) cc_final: 0.6817 (mtpp) REVERT: D 360 TYR cc_start: 0.8283 (p90) cc_final: 0.7711 (p90) REVERT: D 399 LYS cc_start: 0.7921 (mtmt) cc_final: 0.7444 (mtmt) REVERT: D 400 MET cc_start: 0.7219 (tpp) cc_final: 0.6720 (tpp) REVERT: D 404 GLU cc_start: 0.8271 (tp30) cc_final: 0.8049 (tp30) REVERT: D 405 GLU cc_start: 0.7023 (mp0) cc_final: 0.6511 (mp0) REVERT: D 442 ILE cc_start: 0.8396 (tt) cc_final: 0.7996 (pt) REVERT: D 475 GLU cc_start: 0.7727 (mp0) cc_final: 0.7428 (mp0) REVERT: D 495 ASN cc_start: 0.7415 (m-40) cc_final: 0.7190 (m110) REVERT: D 500 ILE cc_start: 0.8296 (mm) cc_final: 0.7985 (tt) REVERT: D 549 LYS cc_start: 0.7883 (tptt) cc_final: 0.7592 (mmmt) REVERT: D 554 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7206 (tm-30) REVERT: D 555 TYR cc_start: 0.7885 (m-10) cc_final: 0.7369 (m-10) REVERT: D 573 THR cc_start: 0.8300 (p) cc_final: 0.7943 (m) REVERT: D 579 LEU cc_start: 0.8566 (tp) cc_final: 0.8238 (tp) REVERT: D 665 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7458 (mp10) REVERT: D 684 ASP cc_start: 0.7429 (m-30) cc_final: 0.7144 (m-30) REVERT: D 691 ASP cc_start: 0.7867 (m-30) cc_final: 0.7607 (m-30) REVERT: D 695 LYS cc_start: 0.8616 (tmtt) cc_final: 0.8240 (tmtt) REVERT: D 744 ARG cc_start: 0.7747 (ptm160) cc_final: 0.7487 (ttp-110) REVERT: D 781 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8228 (tptp) REVERT: D 789 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7456 (ttpp) REVERT: D 822 MET cc_start: 0.6331 (tmm) cc_final: 0.5904 (tmm) REVERT: D 870 ASP cc_start: 0.7527 (m-30) cc_final: 0.7230 (m-30) REVERT: D 913 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7101 (mm-30) REVERT: D 915 ILE cc_start: 0.8273 (tt) cc_final: 0.7949 (pt) REVERT: D 959 LYS cc_start: 0.8453 (mmtp) cc_final: 0.8251 (mmtp) REVERT: D 981 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.6100 (tm-30) REVERT: D 1020 TRP cc_start: 0.7921 (p90) cc_final: 0.7571 (p90) REVERT: D 1099 TYR cc_start: 0.7582 (m-80) cc_final: 0.6777 (m-80) REVERT: D 1146 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6528 (pp20) REVERT: D 1155 ILE cc_start: 0.8996 (mp) cc_final: 0.8775 (mp) REVERT: D 1173 ARG cc_start: 0.8257 (ptm160) cc_final: 0.7932 (ttp80) REVERT: D 1248 ILE cc_start: 0.8063 (mm) cc_final: 0.7815 (tp) REVERT: D 1250 ASP cc_start: 0.7465 (p0) cc_final: 0.7038 (p0) REVERT: D 1254 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6782 (mt-10) REVERT: D 1259 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7443 (mm-40) REVERT: D 1262 ARG cc_start: 0.7375 (ttp-110) cc_final: 0.6670 (ttp80) REVERT: D 1279 GLN cc_start: 0.7140 (pm20) cc_final: 0.6785 (pm20) REVERT: D 1327 GLU cc_start: 0.6818 (pm20) cc_final: 0.6524 (tm-30) REVERT: E 53 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7533 (mm-30) REVERT: E 55 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7165 (tp30) REVERT: G 27 ARG cc_start: 0.8125 (mtm180) cc_final: 0.7671 (mtm-85) REVERT: G 33 HIS cc_start: 0.8746 (OUTLIER) cc_final: 0.8336 (t-90) REVERT: G 72 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7785 (mm110) REVERT: G 83 VAL cc_start: 0.8940 (t) cc_final: 0.8716 (p) REVERT: G 84 ARG cc_start: 0.8093 (tpp80) cc_final: 0.7722 (tpp-160) REVERT: G 93 ILE cc_start: 0.8241 (mm) cc_final: 0.7923 (mm) outliers start: 120 outliers final: 79 residues processed: 882 average time/residue: 0.2115 time to fit residues: 276.1106 Evaluate side-chains 891 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 799 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1134 GLN Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 665 GLN Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 981 GLU Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1283 SER Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 224 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 293 optimal weight: 0.0970 chunk 188 optimal weight: 0.0020 chunk 153 optimal weight: 4.9990 chunk 297 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 44 optimal weight: 0.0170 chunk 19 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 overall best weight: 0.4226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 66 HIS ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1237 HIS D 489 ASN ** D 667 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 = 0.3808 r_free = 0.3808 target = 0.139477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.109531 restraints weight = 49377.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.113374 restraints weight = 24476.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.115891 restraints weight = 14960.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.117481 restraints weight = 10612.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.118405 restraints weight = 8499.241| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28014 Z= 0.119 Angle : 0.615 12.887 38147 Z= 0.315 Chirality : 0.043 0.326 4351 Planarity : 0.004 0.054 4731 Dihedral : 14.634 177.601 4488 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.41 % Allowed : 20.26 % Favored : 76.34 % 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: 1.06 (0.16), residues: 1104 sheet: -0.28 (0.26), residues: 409 loop : -1.45 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1341 TYR 0.017 0.001 TYR C 47 PHE 0.027 0.001 PHE D1319 TRP 0.014 0.001 TRP D1193 HIS 0.015 0.001 HIS G 29 Details of bonding type rmsd covalent geometry : bond 0.00263 (28008) covalent geometry : angle 0.61401 (38141) hydrogen bonds : bond 0.03698 ( 1063) hydrogen bonds : angle 4.28724 ( 2930) metal coordination : bond 0.00506 ( 6) metal coordination : angle 2.84775 ( 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 903 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 807 time to evaluate : 1.004 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 16 ILE cc_start: 0.8484 (mt) cc_final: 0.8189 (tt) REVERT: A 33 ARG cc_start: 0.7722 (ptm160) cc_final: 0.7224 (ptm160) REVERT: A 51 MET cc_start: 0.8059 (mmm) cc_final: 0.7838 (tpp) REVERT: A 58 GLU cc_start: 0.7358 (pp20) cc_final: 0.6803 (pp20) REVERT: A 59 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7612 (t) REVERT: A 74 VAL cc_start: 0.8508 (m) cc_final: 0.8034 (p) REVERT: A 80 GLU cc_start: 0.7718 (tp30) cc_final: 0.7169 (mp0) REVERT: A 104 LYS cc_start: 0.7966 (tptp) cc_final: 0.7374 (tptp) REVERT: A 170 ARG cc_start: 0.8237 (ttp-110) cc_final: 0.7393 (ttm-80) REVERT: A 171 LEU cc_start: 0.8693 (pp) cc_final: 0.8095 (pp) REVERT: A 188 GLU cc_start: 0.7735 (pm20) cc_final: 0.7124 (pm20) REVERT: A 204 GLU cc_start: 0.7720 (pt0) cc_final: 0.7406 (pt0) REVERT: A 212 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6845 (m-30) REVERT: B 16 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7737 (mt) REVERT: B 32 GLU cc_start: 0.7214 (tm-30) cc_final: 0.6905 (tm-30) REVERT: B 51 MET cc_start: 0.7419 (mmm) cc_final: 0.7196 (mmm) REVERT: B 97 GLU cc_start: 0.6941 (pm20) cc_final: 0.6482 (pm20) REVERT: B 136 GLU cc_start: 0.8796 (pm20) cc_final: 0.8189 (pp20) REVERT: B 198 LEU cc_start: 0.7097 (mt) cc_final: 0.6882 (mp) REVERT: B 205 MET cc_start: 0.7608 (ppp) cc_final: 0.6779 (ppp) REVERT: B 214 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.5893 (tm-30) REVERT: B 228 LEU cc_start: 0.7960 (tp) cc_final: 0.7556 (tt) REVERT: C 8 LYS cc_start: 0.8458 (mttt) cc_final: 0.8089 (mtpt) REVERT: C 17 LYS cc_start: 0.8016 (mptt) cc_final: 0.7512 (mmtp) REVERT: C 40 GLU cc_start: 0.5823 (tm-30) cc_final: 0.5556 (tm-30) REVERT: C 87 ILE cc_start: 0.8413 (tp) cc_final: 0.7945 (pt) REVERT: C 99 LYS cc_start: 0.8156 (ttmm) cc_final: 0.7672 (mtmm) REVERT: C 121 GLU cc_start: 0.6577 (mm-30) cc_final: 0.6097 (mm-30) REVERT: C 151 ARG cc_start: 0.7880 (ttm110) cc_final: 0.7516 (ptp-110) REVERT: C 180 ARG cc_start: 0.7381 (ttp80) cc_final: 0.7104 (ttp80) REVERT: C 183 TRP cc_start: 0.8103 (m-10) cc_final: 0.7691 (m-10) REVERT: C 185 ASP cc_start: 0.6178 (p0) cc_final: 0.5731 (p0) REVERT: C 186 PHE cc_start: 0.8047 (m-80) cc_final: 0.7652 (m-10) REVERT: C 187 GLU cc_start: 0.7095 (mp0) cc_final: 0.6547 (mp0) REVERT: C 195 PHE cc_start: 0.7935 (m-80) cc_final: 0.7446 (m-80) REVERT: C 203 LYS cc_start: 0.8264 (ttmt) cc_final: 0.7690 (ttpt) REVERT: C 211 ARG cc_start: 0.7479 (mtp85) cc_final: 0.6998 (mtp85) REVERT: C 214 ASN cc_start: 0.8568 (t0) cc_final: 0.8163 (t0) REVERT: C 349 GLU cc_start: 0.7924 (pm20) cc_final: 0.7482 (pm20) REVERT: C 368 ARG cc_start: 0.7992 (mtm-85) cc_final: 0.7474 (mtm-85) REVERT: C 389 PHE cc_start: 0.8215 (m-10) cc_final: 0.7659 (m-80) REVERT: C 392 GLU cc_start: 0.7137 (mp0) cc_final: 0.6856 (mp0) REVERT: C 394 ARG cc_start: 0.6756 (ttm110) cc_final: 0.6501 (ttm110) REVERT: C 404 LYS cc_start: 0.8220 (mmmt) cc_final: 0.8014 (tptm) REVERT: C 427 ASP cc_start: 0.7113 (m-30) cc_final: 0.6836 (m-30) REVERT: C 430 LYS cc_start: 0.8126 (mtpp) cc_final: 0.7508 (mttm) REVERT: C 434 ASP cc_start: 0.7765 (m-30) cc_final: 0.7326 (m-30) REVERT: C 499 SER cc_start: 0.7732 (p) cc_final: 0.7453 (p) REVERT: C 503 LYS cc_start: 0.8449 (mmtt) cc_final: 0.8227 (tptt) REVERT: C 523 GLU cc_start: 0.7517 (tp30) cc_final: 0.7227 (tp30) REVERT: C 549 ASP cc_start: 0.7165 (t0) cc_final: 0.6650 (t0) REVERT: C 562 GLU cc_start: 0.7400 (tm-30) cc_final: 0.6682 (tm-30) REVERT: C 593 LYS cc_start: 0.8303 (tptt) cc_final: 0.7790 (tppt) REVERT: C 611 GLU cc_start: 0.7405 (tt0) cc_final: 0.6588 (mt-10) REVERT: C 616 ILE cc_start: 0.8469 (mp) cc_final: 0.8142 (mm) REVERT: C 656 SER cc_start: 0.8538 (t) cc_final: 0.7877 (m) REVERT: C 719 LYS cc_start: 0.8079 (mtmm) cc_final: 0.7613 (mtmm) REVERT: C 730 SER cc_start: 0.8739 (m) cc_final: 0.8348 (t) REVERT: C 731 ARG cc_start: 0.7939 (ptp-110) cc_final: 0.7720 (ptm160) REVERT: C 785 ASP cc_start: 0.6645 (p0) cc_final: 0.6293 (p0) REVERT: C 788 SER cc_start: 0.8397 (m) cc_final: 0.7746 (p) REVERT: C 800 MET cc_start: 0.7308 (mmp) cc_final: 0.7101 (mmm) REVERT: C 811 ASN cc_start: 0.7901 (p0) cc_final: 0.7571 (p0) REVERT: C 914 LYS cc_start: 0.7859 (tppt) cc_final: 0.7557 (tppt) REVERT: C 930 ASP cc_start: 0.7749 (t0) cc_final: 0.7177 (m-30) REVERT: C 947 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7353 (tm-30) REVERT: C 948 ILE cc_start: 0.8838 (mm) cc_final: 0.8217 (mm) REVERT: C 1028 LYS cc_start: 0.8916 (pttt) cc_final: 0.8642 (pttp) REVERT: C 1030 GLU cc_start: 0.7950 (tp30) cc_final: 0.7345 (tp30) REVERT: C 1032 LYS cc_start: 0.8888 (mttt) cc_final: 0.8614 (mttt) REVERT: C 1035 LYS cc_start: 0.8526 (tppt) cc_final: 0.7929 (tppt) REVERT: C 1089 GLU cc_start: 0.7280 (mp0) cc_final: 0.6867 (mp0) REVERT: C 1095 ASP cc_start: 0.7526 (m-30) cc_final: 0.7149 (m-30) REVERT: C 1119 MET cc_start: 0.8138 (tpp) cc_final: 0.7715 (tpt) REVERT: C 1122 LYS cc_start: 0.8327 (tptm) cc_final: 0.7677 (tptp) REVERT: C 1126 ASP cc_start: 0.7169 (m-30) cc_final: 0.6578 (m-30) REVERT: C 1131 MET cc_start: 0.7821 (ttt) cc_final: 0.7528 (ptp) REVERT: C 1140 LYS cc_start: 0.7713 (ptpt) cc_final: 0.7321 (ptpt) REVERT: C 1142 ARG cc_start: 0.7784 (ttm-80) cc_final: 0.7361 (mtp180) REVERT: C 1146 GLN cc_start: 0.7637 (tp40) cc_final: 0.6910 (tp-100) REVERT: C 1200 LYS cc_start: 0.8399 (tttt) cc_final: 0.8095 (tttt) REVERT: C 1210 ILE cc_start: 0.8070 (tt) cc_final: 0.7736 (pt) REVERT: C 1229 TYR cc_start: 0.8193 (m-80) cc_final: 0.7719 (m-10) REVERT: C 1264 GLN cc_start: 0.8236 (mp10) cc_final: 0.7781 (mp10) REVERT: C 1274 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6276 (mp0) REVERT: C 1281 TYR cc_start: 0.7507 (m-80) cc_final: 0.6717 (m-80) REVERT: C 1332 SER cc_start: 0.7914 (p) cc_final: 0.7708 (p) REVERT: D 21 LYS cc_start: 0.8028 (ptpt) cc_final: 0.7444 (ptmm) REVERT: D 29 MET cc_start: 0.7782 (ttt) cc_final: 0.6899 (tpp) REVERT: D 33 TRP cc_start: 0.7841 (m-10) cc_final: 0.7326 (m-10) REVERT: D 115 TRP cc_start: 0.8501 (m-10) cc_final: 0.8229 (m-10) REVERT: D 118 LYS cc_start: 0.8149 (mmmt) cc_final: 0.7861 (mmmt) REVERT: D 141 PHE cc_start: 0.7843 (m-80) cc_final: 0.7415 (m-80) REVERT: D 148 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6631 (tm-30) REVERT: D 151 MET cc_start: 0.7417 (pmm) cc_final: 0.6864 (pmm) REVERT: D 158 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7857 (pp30) REVERT: D 198 CYS cc_start: 0.7577 (t) cc_final: 0.7048 (t) REVERT: D 200 GLN cc_start: 0.8336 (pp30) cc_final: 0.8050 (pp30) REVERT: D 201 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8511 (mm) REVERT: D 202 ARG cc_start: 0.8277 (mtt-85) cc_final: 0.7929 (mtt90) REVERT: D 215 LYS cc_start: 0.8835 (mtmm) cc_final: 0.8519 (ptpt) REVERT: D 219 LYS cc_start: 0.8794 (ttmt) cc_final: 0.8366 (ttpp) REVERT: D 235 GLU cc_start: 0.7288 (pm20) cc_final: 0.7003 (pm20) REVERT: D 236 TRP cc_start: 0.8366 (m-10) cc_final: 0.8065 (m-10) REVERT: D 251 PRO cc_start: 0.7750 (Cg_endo) cc_final: 0.7452 (Cg_exo) REVERT: D 275 ARG cc_start: 0.7999 (tpp-160) cc_final: 0.7198 (tpp-160) REVERT: D 282 LEU cc_start: 0.8452 (mt) cc_final: 0.8221 (tt) REVERT: D 297 ARG cc_start: 0.7878 (ttp80) cc_final: 0.7241 (tmm-80) REVERT: D 298 MET cc_start: 0.7393 (ttp) cc_final: 0.6502 (ttp) REVERT: D 332 LYS cc_start: 0.7154 (mtmm) cc_final: 0.6662 (mtpp) REVERT: D 360 TYR cc_start: 0.8244 (p90) cc_final: 0.7600 (p90) REVERT: D 399 LYS cc_start: 0.7865 (mtmt) cc_final: 0.7291 (mtmt) REVERT: D 400 MET cc_start: 0.7211 (tpp) cc_final: 0.6603 (tpp) REVERT: D 402 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6807 (tm-30) REVERT: D 405 GLU cc_start: 0.6957 (mp0) cc_final: 0.6369 (mp0) REVERT: D 442 ILE cc_start: 0.8424 (tt) cc_final: 0.8017 (pt) REVERT: D 475 GLU cc_start: 0.7679 (mp0) cc_final: 0.7388 (mp0) REVERT: D 489 ASN cc_start: 0.7504 (m110) cc_final: 0.7034 (m-40) REVERT: D 500 ILE cc_start: 0.8296 (mm) cc_final: 0.7992 (tt) REVERT: D 512 TYR cc_start: 0.8131 (t80) cc_final: 0.7914 (t80) REVERT: D 532 GLU cc_start: 0.6851 (mp0) cc_final: 0.6526 (mp0) REVERT: D 549 LYS cc_start: 0.7852 (tptt) cc_final: 0.7591 (mmmt) REVERT: D 554 GLU cc_start: 0.7387 (tm-30) cc_final: 0.7138 (tm-30) REVERT: D 555 TYR cc_start: 0.7813 (m-10) cc_final: 0.7249 (m-10) REVERT: D 573 THR cc_start: 0.8304 (p) cc_final: 0.8050 (m) REVERT: D 579 LEU cc_start: 0.8315 (tp) cc_final: 0.7971 (tp) REVERT: D 652 GLU cc_start: 0.8368 (mp0) cc_final: 0.7884 (mp0) REVERT: D 665 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7535 (mp10) REVERT: D 667 GLN cc_start: 0.7544 (tm-30) cc_final: 0.7319 (pp30) REVERT: D 684 ASP cc_start: 0.7378 (m-30) cc_final: 0.7120 (m-30) REVERT: D 691 ASP cc_start: 0.7850 (m-30) cc_final: 0.7552 (m-30) REVERT: D 695 LYS cc_start: 0.8541 (tmtt) cc_final: 0.8222 (tmtt) REVERT: D 723 TYR cc_start: 0.7978 (t80) cc_final: 0.7639 (t80) REVERT: D 744 ARG cc_start: 0.7737 (ptm160) cc_final: 0.7231 (ttm170) REVERT: D 770 LEU cc_start: 0.7877 (mm) cc_final: 0.7381 (mt) REVERT: D 781 LYS cc_start: 0.8491 (ttmt) cc_final: 0.8210 (tptm) REVERT: D 789 LYS cc_start: 0.7930 (ttpt) cc_final: 0.7417 (ttpp) REVERT: D 822 MET cc_start: 0.6364 (tmm) cc_final: 0.5948 (tmm) REVERT: D 870 ASP cc_start: 0.7476 (m-30) cc_final: 0.7188 (m-30) REVERT: D 913 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7095 (mm-30) REVERT: D 915 ILE cc_start: 0.8225 (tt) cc_final: 0.7916 (pt) REVERT: D 922 SER cc_start: 0.8308 (m) cc_final: 0.7776 (p) REVERT: D 959 LYS cc_start: 0.8464 (mmtp) cc_final: 0.8129 (mmtp) REVERT: D 981 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.6024 (tm-30) REVERT: D 992 LYS cc_start: 0.7737 (mmmm) cc_final: 0.7320 (mmmt) REVERT: D 1020 TRP cc_start: 0.7927 (p90) cc_final: 0.7663 (p90) REVERT: D 1099 TYR cc_start: 0.7598 (m-80) cc_final: 0.6774 (m-80) REVERT: D 1146 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6436 (pp20) REVERT: D 1155 ILE cc_start: 0.8983 (mp) cc_final: 0.8727 (mp) REVERT: D 1173 ARG cc_start: 0.8255 (ptm160) cc_final: 0.7994 (ptm160) REVERT: D 1188 GLU cc_start: 0.6372 (pm20) cc_final: 0.5097 (pm20) REVERT: D 1248 ILE cc_start: 0.7975 (mm) cc_final: 0.7692 (tp) REVERT: D 1250 ASP cc_start: 0.7512 (p0) cc_final: 0.7032 (p0) REVERT: D 1254 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6760 (mt-10) REVERT: D 1259 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7491 (mm-40) REVERT: D 1262 ARG cc_start: 0.6958 (ttp-110) cc_final: 0.6562 (ttp80) REVERT: D 1327 GLU cc_start: 0.6652 (pm20) cc_final: 0.5843 (mp0) REVERT: E 52 ARG cc_start: 0.7971 (ttp80) cc_final: 0.7739 (ttp80) REVERT: E 53 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7463 (mm-30) REVERT: E 55 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7085 (tp30) REVERT: E 62 GLN cc_start: 0.8334 (tp40) cc_final: 0.7783 (tp40) REVERT: G 27 ARG cc_start: 0.8131 (mtm180) cc_final: 0.7711 (mtm-85) REVERT: G 33 HIS cc_start: 0.8803 (OUTLIER) cc_final: 0.8420 (t-90) REVERT: G 43 MET cc_start: 0.7446 (tmm) cc_final: 0.6583 (tmm) REVERT: G 80 TRP cc_start: 0.7898 (t60) cc_final: 0.7298 (t60) REVERT: G 83 VAL cc_start: 0.8873 (t) cc_final: 0.8651 (p) REVERT: G 84 ARG cc_start: 0.8108 (tpp80) cc_final: 0.7831 (tpt170) outliers start: 96 outliers final: 67 residues processed: 857 average time/residue: 0.2109 time to fit residues: 268.6095 Evaluate side-chains 867 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 789 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1048 LYS Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 665 GLN Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 981 GLU Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1235 ASN Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 65 PHE Chi-restraints excluded: chain G residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 162 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 139 optimal weight: 30.0000 chunk 297 optimal weight: 1.9990 chunk 174 optimal weight: 0.1980 chunk 311 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN C 219 GLN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C1237 HIS ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.109549 restraints weight = 49150.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.113213 restraints weight = 24647.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.115656 restraints weight = 15126.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.117211 restraints weight = 10665.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.118047 restraints weight = 8482.536| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 28014 Z= 0.143 Angle : 0.629 13.024 38147 Z= 0.325 Chirality : 0.043 0.337 4351 Planarity : 0.004 0.053 4731 Dihedral : 14.636 177.412 4488 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.04 % Allowed : 20.61 % Favored : 75.35 % 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: -0.65 (0.14), residues: 3285 helix: 1.04 (0.16), residues: 1102 sheet: -0.30 (0.25), residues: 445 loop : -1.48 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1341 TYR 0.021 0.001 TYR D 995 PHE 0.021 0.001 PHE D 892 TRP 0.027 0.001 TRP D1193 HIS 0.005 0.001 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00323 (28008) covalent geometry : angle 0.62824 (38141) hydrogen bonds : bond 0.03959 ( 1063) hydrogen bonds : angle 4.26065 ( 2930) metal coordination : bond 0.00664 ( 6) metal coordination : angle 3.13827 ( 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 920 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 806 time to evaluate : 0.966 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.8477 (mt) cc_final: 0.8180 (tt) REVERT: A 33 ARG cc_start: 0.7697 (ptm160) cc_final: 0.7223 (ptm160) REVERT: A 74 VAL cc_start: 0.8639 (m) cc_final: 0.8182 (p) REVERT: A 104 LYS cc_start: 0.8057 (tptp) cc_final: 0.7477 (tptp) REVERT: A 170 ARG cc_start: 0.8266 (ttp-110) cc_final: 0.7613 (ttm-80) REVERT: A 171 LEU cc_start: 0.8712 (pp) cc_final: 0.8472 (pp) REVERT: A 188 GLU cc_start: 0.7762 (pm20) cc_final: 0.7124 (pm20) REVERT: A 204 GLU cc_start: 0.7708 (pt0) cc_final: 0.7428 (pt0) REVERT: A 212 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6812 (m-30) REVERT: B 16 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7777 (mt) REVERT: B 32 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6947 (tm-30) REVERT: B 51 MET cc_start: 0.7425 (mmm) cc_final: 0.7128 (mmm) REVERT: B 97 GLU cc_start: 0.6898 (pm20) cc_final: 0.6429 (pm20) REVERT: B 136 GLU cc_start: 0.8704 (pm20) cc_final: 0.8349 (pp20) REVERT: B 198 LEU cc_start: 0.7141 (mt) cc_final: 0.6911 (mp) REVERT: B 205 MET cc_start: 0.7605 (ppp) cc_final: 0.6944 (ppp) REVERT: B 214 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.5931 (tm-30) REVERT: C 8 LYS cc_start: 0.8503 (mttt) cc_final: 0.8117 (mtpt) REVERT: C 17 LYS cc_start: 0.8008 (mptt) cc_final: 0.7472 (mmtp) REVERT: C 41 GLN cc_start: 0.6958 (mm-40) cc_final: 0.6576 (mm-40) REVERT: C 44 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.5991 (tm-30) REVERT: C 82 VAL cc_start: 0.7772 (m) cc_final: 0.7509 (p) REVERT: C 99 LYS cc_start: 0.8100 (ttmm) cc_final: 0.7784 (mtmm) REVERT: C 121 GLU cc_start: 0.6591 (mm-30) cc_final: 0.5803 (mm-30) REVERT: C 151 ARG cc_start: 0.7855 (ttm110) cc_final: 0.7498 (ptp-110) REVERT: C 180 ARG cc_start: 0.7398 (ttp80) cc_final: 0.7174 (ttp80) REVERT: C 185 ASP cc_start: 0.6191 (p0) cc_final: 0.5754 (p0) REVERT: C 186 PHE cc_start: 0.8040 (m-80) cc_final: 0.7649 (m-10) REVERT: C 187 GLU cc_start: 0.7072 (mp0) cc_final: 0.6225 (mp0) REVERT: C 195 PHE cc_start: 0.8016 (m-80) cc_final: 0.7510 (m-80) REVERT: C 203 LYS cc_start: 0.8254 (ttmt) cc_final: 0.7675 (ttpt) REVERT: C 214 ASN cc_start: 0.8546 (t0) cc_final: 0.8146 (t0) REVERT: C 262 TYR cc_start: 0.6354 (m-80) cc_final: 0.6113 (m-80) REVERT: C 349 GLU cc_start: 0.7941 (pm20) cc_final: 0.7444 (pm20) REVERT: C 368 ARG cc_start: 0.7864 (mtm-85) cc_final: 0.7357 (mtm-85) REVERT: C 389 PHE cc_start: 0.8169 (m-10) cc_final: 0.7867 (m-80) REVERT: C 392 GLU cc_start: 0.7060 (mp0) cc_final: 0.6803 (mp0) REVERT: C 394 ARG cc_start: 0.6696 (ttm110) cc_final: 0.6458 (ttm110) REVERT: C 404 LYS cc_start: 0.8287 (mmmt) cc_final: 0.7993 (ttmm) REVERT: C 427 ASP cc_start: 0.7031 (m-30) cc_final: 0.6793 (m-30) REVERT: C 430 LYS cc_start: 0.8229 (mtpp) cc_final: 0.7571 (mttm) REVERT: C 434 ASP cc_start: 0.7730 (m-30) cc_final: 0.7294 (m-30) REVERT: C 499 SER cc_start: 0.7725 (p) cc_final: 0.7457 (p) REVERT: C 503 LYS cc_start: 0.8442 (mmtt) cc_final: 0.8192 (tptt) REVERT: C 523 GLU cc_start: 0.7497 (tp30) cc_final: 0.7175 (tp30) REVERT: C 549 ASP cc_start: 0.7156 (t0) cc_final: 0.6671 (t0) REVERT: C 611 GLU cc_start: 0.7384 (tt0) cc_final: 0.6639 (mt-10) REVERT: C 616 ILE cc_start: 0.8516 (mp) cc_final: 0.8162 (mm) REVERT: C 653 MET cc_start: 0.7106 (ttp) cc_final: 0.6906 (tmm) REVERT: C 654 ASP cc_start: 0.7757 (m-30) cc_final: 0.6940 (m-30) REVERT: C 656 SER cc_start: 0.8533 (t) cc_final: 0.8048 (m) REVERT: C 694 ARG cc_start: 0.7349 (ptp90) cc_final: 0.7125 (ptp90) REVERT: C 704 MET cc_start: 0.6973 (mmp) cc_final: 0.6533 (mmm) REVERT: C 714 VAL cc_start: 0.8376 (p) cc_final: 0.8106 (t) REVERT: C 719 LYS cc_start: 0.8064 (mtmm) cc_final: 0.7632 (mtmm) REVERT: C 723 VAL cc_start: 0.8426 (t) cc_final: 0.8020 (m) REVERT: C 730 SER cc_start: 0.8787 (m) cc_final: 0.8378 (t) REVERT: C 731 ARG cc_start: 0.7953 (ptp-110) cc_final: 0.7703 (ptm160) REVERT: C 785 ASP cc_start: 0.6626 (p0) cc_final: 0.6282 (p0) REVERT: C 788 SER cc_start: 0.8404 (m) cc_final: 0.7787 (p) REVERT: C 800 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.7006 (mtp) REVERT: C 811 ASN cc_start: 0.7886 (p0) cc_final: 0.6747 (p0) REVERT: C 825 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7013 (tm-30) REVERT: C 848 GLU cc_start: 0.7414 (pt0) cc_final: 0.7174 (pt0) REVERT: C 914 LYS cc_start: 0.7810 (tppt) cc_final: 0.7529 (tppt) REVERT: C 930 ASP cc_start: 0.7718 (t0) cc_final: 0.7218 (m-30) REVERT: C 947 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7328 (tm-30) REVERT: C 948 ILE cc_start: 0.8916 (mm) cc_final: 0.8291 (mm) REVERT: C 1028 LYS cc_start: 0.8888 (pttt) cc_final: 0.8458 (pttp) REVERT: C 1032 LYS cc_start: 0.8876 (mttt) cc_final: 0.8502 (mttt) REVERT: C 1035 LYS cc_start: 0.8573 (tppt) cc_final: 0.7974 (tppt) REVERT: C 1089 GLU cc_start: 0.7226 (mp0) cc_final: 0.6840 (mp0) REVERT: C 1095 ASP cc_start: 0.7513 (m-30) cc_final: 0.7165 (m-30) REVERT: C 1099 ASN cc_start: 0.8018 (t0) cc_final: 0.7271 (t0) REVERT: C 1119 MET cc_start: 0.8154 (tpp) cc_final: 0.7721 (tpt) REVERT: C 1122 LYS cc_start: 0.8363 (tptm) cc_final: 0.7714 (tptp) REVERT: C 1126 ASP cc_start: 0.7151 (m-30) cc_final: 0.6554 (m-30) REVERT: C 1131 MET cc_start: 0.7797 (ttt) cc_final: 0.7460 (ptp) REVERT: C 1140 LYS cc_start: 0.7698 (ptpt) cc_final: 0.7304 (ptpt) REVERT: C 1142 ARG cc_start: 0.7788 (ttm-80) cc_final: 0.7383 (mtp180) REVERT: C 1143 GLU cc_start: 0.7444 (tm-30) cc_final: 0.6883 (tm-30) REVERT: C 1146 GLN cc_start: 0.7702 (tp40) cc_final: 0.7207 (tp-100) REVERT: C 1147 ARG cc_start: 0.8292 (mmm-85) cc_final: 0.7798 (ttm-80) REVERT: C 1194 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6201 (pm20) REVERT: C 1200 LYS cc_start: 0.8483 (tttt) cc_final: 0.8171 (tttt) REVERT: C 1210 ILE cc_start: 0.8096 (tt) cc_final: 0.7762 (pt) REVERT: C 1211 ARG cc_start: 0.7334 (ttt-90) cc_final: 0.6886 (ttt-90) REVERT: C 1229 TYR cc_start: 0.8197 (m-80) cc_final: 0.7773 (m-10) REVERT: C 1264 GLN cc_start: 0.8289 (mp10) cc_final: 0.7859 (mp10) REVERT: C 1274 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6288 (mp0) REVERT: C 1289 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6832 (mm-30) REVERT: C 1332 SER cc_start: 0.7982 (p) cc_final: 0.7745 (p) REVERT: D 21 LYS cc_start: 0.8083 (ptpt) cc_final: 0.7534 (ptmm) REVERT: D 29 MET cc_start: 0.7835 (ttt) cc_final: 0.7027 (tpp) REVERT: D 33 TRP cc_start: 0.7767 (m-10) cc_final: 0.7347 (m-10) REVERT: D 90 VAL cc_start: 0.7574 (t) cc_final: 0.7373 (p) REVERT: D 96 LYS cc_start: 0.8467 (mmmt) cc_final: 0.8115 (mmtm) REVERT: D 115 TRP cc_start: 0.8530 (m-10) cc_final: 0.8276 (m-10) REVERT: D 118 LYS cc_start: 0.8158 (mmmt) cc_final: 0.7884 (mmmt) REVERT: D 148 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6663 (tm-30) REVERT: D 151 MET cc_start: 0.7368 (pmm) cc_final: 0.6867 (pmm) REVERT: D 158 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7844 (pp30) REVERT: D 198 CYS cc_start: 0.7575 (t) cc_final: 0.7005 (t) REVERT: D 200 GLN cc_start: 0.8352 (pp30) cc_final: 0.8082 (pp30) REVERT: D 201 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8401 (mm) REVERT: D 219 LYS cc_start: 0.8777 (ttmt) cc_final: 0.8362 (ttpp) REVERT: D 235 GLU cc_start: 0.7217 (pm20) cc_final: 0.6919 (pm20) REVERT: D 236 TRP cc_start: 0.8402 (m-10) cc_final: 0.8091 (m-10) REVERT: D 251 PRO cc_start: 0.7813 (Cg_endo) cc_final: 0.7572 (Cg_exo) REVERT: D 275 ARG cc_start: 0.7992 (tpp-160) cc_final: 0.7050 (tpp-160) REVERT: D 279 LEU cc_start: 0.8156 (tp) cc_final: 0.7921 (tp) REVERT: D 282 LEU cc_start: 0.8478 (mt) cc_final: 0.8266 (tt) REVERT: D 297 ARG cc_start: 0.7875 (ttp80) cc_final: 0.7402 (tmm-80) REVERT: D 298 MET cc_start: 0.7351 (ttp) cc_final: 0.6344 (ttp) REVERT: D 325 LYS cc_start: 0.8252 (mmtt) cc_final: 0.7976 (mmtp) REVERT: D 332 LYS cc_start: 0.7226 (mtmm) cc_final: 0.6714 (mtpp) REVERT: D 360 TYR cc_start: 0.8252 (p90) cc_final: 0.7642 (p90) REVERT: D 368 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7858 (tp) REVERT: D 399 LYS cc_start: 0.7888 (mtmt) cc_final: 0.7397 (mtmt) REVERT: D 400 MET cc_start: 0.7252 (tpp) cc_final: 0.6615 (tpp) REVERT: D 402 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6836 (tm-30) REVERT: D 405 GLU cc_start: 0.7009 (mp0) cc_final: 0.6449 (mp0) REVERT: D 441 LEU cc_start: 0.8396 (mm) cc_final: 0.7978 (mt) REVERT: D 442 ILE cc_start: 0.8431 (tt) cc_final: 0.8046 (pt) REVERT: D 475 GLU cc_start: 0.7665 (mp0) cc_final: 0.7423 (mp0) REVERT: D 500 ILE cc_start: 0.8297 (mm) cc_final: 0.8002 (tt) REVERT: D 512 TYR cc_start: 0.8259 (t80) cc_final: 0.7975 (t80) REVERT: D 532 GLU cc_start: 0.6823 (mp0) cc_final: 0.6554 (mp0) REVERT: D 549 LYS cc_start: 0.7903 (tptt) cc_final: 0.7601 (tptt) REVERT: D 554 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7193 (tm-30) REVERT: D 573 THR cc_start: 0.8270 (p) cc_final: 0.7945 (m) REVERT: D 579 LEU cc_start: 0.8428 (tp) cc_final: 0.8056 (tp) REVERT: D 622 ASP cc_start: 0.6959 (m-30) cc_final: 0.6705 (m-30) REVERT: D 665 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7540 (mp10) REVERT: D 684 ASP cc_start: 0.7463 (m-30) cc_final: 0.7124 (m-30) REVERT: D 691 ASP cc_start: 0.7818 (m-30) cc_final: 0.7555 (m-30) REVERT: D 695 LYS cc_start: 0.8564 (tmtt) cc_final: 0.8247 (tmtt) REVERT: D 702 GLN cc_start: 0.7864 (tt0) cc_final: 0.7600 (tt0) REVERT: D 723 TYR cc_start: 0.8023 (t80) cc_final: 0.7407 (t80) REVERT: D 744 ARG cc_start: 0.7790 (ptm160) cc_final: 0.7293 (ttm170) REVERT: D 781 LYS cc_start: 0.8480 (ttmt) cc_final: 0.8234 (tptm) REVERT: D 789 LYS cc_start: 0.7914 (ttpt) cc_final: 0.7449 (ttpp) REVERT: D 822 MET cc_start: 0.6271 (tmm) cc_final: 0.5976 (tmm) REVERT: D 842 ARG cc_start: 0.6915 (mtt180) cc_final: 0.6132 (mtt180) REVERT: D 858 VAL cc_start: 0.7517 (t) cc_final: 0.7242 (p) REVERT: D 860 ARG cc_start: 0.6189 (ttt180) cc_final: 0.5891 (ttp80) REVERT: D 870 ASP cc_start: 0.7556 (m-30) cc_final: 0.7212 (m-30) REVERT: D 913 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7077 (mm-30) REVERT: D 915 ILE cc_start: 0.8246 (tt) cc_final: 0.7990 (pt) REVERT: D 922 SER cc_start: 0.8320 (m) cc_final: 0.7804 (p) REVERT: D 950 ILE cc_start: 0.7596 (tp) cc_final: 0.7260 (tp) REVERT: D 959 LYS cc_start: 0.8478 (mmtp) cc_final: 0.8147 (mmtp) REVERT: D 981 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.5881 (tm-30) REVERT: D 1020 TRP cc_start: 0.7840 (p90) cc_final: 0.7585 (p90) REVERT: D 1099 TYR cc_start: 0.7556 (m-80) cc_final: 0.6801 (m-80) REVERT: D 1146 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6521 (pp20) REVERT: D 1155 ILE cc_start: 0.9014 (mp) cc_final: 0.8759 (mp) REVERT: D 1250 ASP cc_start: 0.7472 (p0) cc_final: 0.7128 (p0) REVERT: D 1259 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7624 (mm-40) REVERT: D 1262 ARG cc_start: 0.6960 (ttp-110) cc_final: 0.6760 (ttp80) REVERT: D 1276 GLU cc_start: 0.6759 (mm-30) cc_final: 0.6542 (mm-30) REVERT: D 1327 GLU cc_start: 0.6641 (pm20) cc_final: 0.5864 (mp0) REVERT: E 53 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7464 (mm-30) REVERT: E 55 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7077 (tp30) REVERT: G 27 ARG cc_start: 0.8058 (mtm180) cc_final: 0.7625 (mtm-85) REVERT: G 33 HIS cc_start: 0.8816 (OUTLIER) cc_final: 0.8398 (t-90) REVERT: G 43 MET cc_start: 0.7428 (tmm) cc_final: 0.6824 (tmm) REVERT: G 80 TRP cc_start: 0.7950 (t60) cc_final: 0.7475 (t60) REVERT: G 83 VAL cc_start: 0.8893 (t) cc_final: 0.8677 (p) outliers start: 114 outliers final: 72 residues processed: 862 average time/residue: 0.2187 time to fit residues: 279.1169 Evaluate side-chains 868 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 782 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1048 LYS Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 665 GLN Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 981 GLU Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1235 ASN Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 65 PHE 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: 4.9990 chunk 334 optimal weight: 3.9990 chunk 287 optimal weight: 0.0010 chunk 332 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 217 optimal weight: 0.5980 overall best weight: 1.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C 686 GLN C1237 HIS D1114 GLN ** D1197 ASN ** 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 = 0.3760 r_free = 0.3760 target = 0.136184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.107086 restraints weight = 49233.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.110676 restraints weight = 24575.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.113067 restraints weight = 15112.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.114586 restraints weight = 10775.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.115436 restraints weight = 8614.329| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.132 28014 Z= 0.210 Angle : 0.677 13.454 38147 Z= 0.352 Chirality : 0.045 0.352 4351 Planarity : 0.005 0.068 4731 Dihedral : 14.711 177.106 4488 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.11 % Allowed : 21.36 % Favored : 74.53 % 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: -0.81 (0.14), residues: 3285 helix: 0.80 (0.16), residues: 1104 sheet: -0.38 (0.24), residues: 455 loop : -1.52 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 202 TYR 0.020 0.002 TYR A 152 PHE 0.019 0.002 PHE D 892 TRP 0.030 0.002 TRP D1193 HIS 0.045 0.002 HIS G 29 Details of bonding type rmsd covalent geometry : bond 0.00466 (28008) covalent geometry : angle 0.67541 (38141) hydrogen bonds : bond 0.04677 ( 1063) hydrogen bonds : angle 4.40750 ( 2930) metal coordination : bond 0.01534 ( 6) metal coordination : angle 3.87706 ( 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 938 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 822 time to evaluate : 0.969 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.8428 (mt) cc_final: 0.8124 (tt) REVERT: A 33 ARG cc_start: 0.7679 (ptm160) cc_final: 0.7207 (ptm160) REVERT: A 74 VAL cc_start: 0.8549 (m) cc_final: 0.8054 (p) REVERT: A 97 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6898 (tm-30) REVERT: A 101 THR cc_start: 0.8263 (m) cc_final: 0.7909 (t) REVERT: A 104 LYS cc_start: 0.8031 (tptp) cc_final: 0.7460 (tptp) REVERT: A 170 ARG cc_start: 0.8445 (ttp-110) cc_final: 0.8226 (ttm-80) REVERT: A 188 GLU cc_start: 0.7763 (pm20) cc_final: 0.7161 (pm20) REVERT: A 198 LEU cc_start: 0.7735 (mm) cc_final: 0.7365 (mm) REVERT: A 212 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6870 (m-30) REVERT: B 16 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7772 (mt) REVERT: B 32 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6921 (tm-30) REVERT: B 51 MET cc_start: 0.7483 (mmm) cc_final: 0.7274 (mmm) REVERT: B 97 GLU cc_start: 0.6931 (pm20) cc_final: 0.6453 (pm20) REVERT: B 136 GLU cc_start: 0.8711 (pm20) cc_final: 0.8468 (pp20) REVERT: B 205 MET cc_start: 0.7627 (ppp) cc_final: 0.7034 (ppp) REVERT: B 214 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.6005 (tm-30) REVERT: B 219 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7617 (mtm-85) REVERT: C 8 LYS cc_start: 0.8529 (mttt) cc_final: 0.8289 (mttm) REVERT: C 17 LYS cc_start: 0.8044 (mptt) cc_final: 0.7522 (mmtp) REVERT: C 44 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6046 (tm-30) REVERT: C 82 VAL cc_start: 0.7819 (m) cc_final: 0.7573 (p) REVERT: C 87 ILE cc_start: 0.8386 (tp) cc_final: 0.7969 (pt) REVERT: C 99 LYS cc_start: 0.8104 (ttmm) cc_final: 0.7728 (mtmm) REVERT: C 121 GLU cc_start: 0.6561 (mm-30) cc_final: 0.5751 (mm-30) REVERT: C 151 ARG cc_start: 0.7891 (ttm110) cc_final: 0.7563 (ptp-110) REVERT: C 180 ARG cc_start: 0.7402 (ttp80) cc_final: 0.7137 (ttp80) REVERT: C 185 ASP cc_start: 0.6300 (p0) cc_final: 0.5903 (p0) REVERT: C 186 PHE cc_start: 0.8096 (m-80) cc_final: 0.7774 (m-10) REVERT: C 187 GLU cc_start: 0.7081 (mp0) cc_final: 0.6280 (mp0) REVERT: C 195 PHE cc_start: 0.8050 (m-80) cc_final: 0.7569 (m-80) REVERT: C 203 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7498 (ttmm) REVERT: C 214 ASN cc_start: 0.8562 (t0) cc_final: 0.8163 (t0) REVERT: C 349 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7559 (pm20) REVERT: C 368 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7373 (mtm-85) REVERT: C 389 PHE cc_start: 0.8015 (m-10) cc_final: 0.7662 (m-80) REVERT: C 394 ARG cc_start: 0.6735 (ttm110) cc_final: 0.6515 (ttm110) REVERT: C 427 ASP cc_start: 0.7061 (m-30) cc_final: 0.6794 (m-30) REVERT: C 430 LYS cc_start: 0.8253 (mtpp) cc_final: 0.7706 (mttp) REVERT: C 434 ASP cc_start: 0.7749 (m-30) cc_final: 0.7345 (m-30) REVERT: C 496 LYS cc_start: 0.7745 (mppt) cc_final: 0.7516 (mppt) REVERT: C 499 SER cc_start: 0.7758 (p) cc_final: 0.7491 (p) REVERT: C 503 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8225 (tptt) REVERT: C 519 ASN cc_start: 0.7654 (m-40) cc_final: 0.7373 (m-40) REVERT: C 523 GLU cc_start: 0.7533 (tp30) cc_final: 0.7197 (tp30) REVERT: C 549 ASP cc_start: 0.7186 (t0) cc_final: 0.6893 (t0) REVERT: C 611 GLU cc_start: 0.7267 (tt0) cc_final: 0.6695 (tt0) REVERT: C 616 ILE cc_start: 0.8519 (mp) cc_final: 0.8316 (mm) REVERT: C 653 MET cc_start: 0.7228 (ttp) cc_final: 0.6957 (tmm) REVERT: C 654 ASP cc_start: 0.7748 (m-30) cc_final: 0.6956 (m-30) REVERT: C 656 SER cc_start: 0.8579 (t) cc_final: 0.8053 (m) REVERT: C 719 LYS cc_start: 0.8079 (mtmm) cc_final: 0.7654 (mtmm) REVERT: C 723 VAL cc_start: 0.8452 (t) cc_final: 0.8054 (m) REVERT: C 730 SER cc_start: 0.8806 (m) cc_final: 0.8404 (t) REVERT: C 731 ARG cc_start: 0.8042 (ptp-110) cc_final: 0.7825 (ptm160) REVERT: C 785 ASP cc_start: 0.6598 (p0) cc_final: 0.6235 (p0) REVERT: C 793 GLU cc_start: 0.7218 (tt0) cc_final: 0.6771 (tt0) REVERT: C 800 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.7135 (mtp) REVERT: C 811 ASN cc_start: 0.7985 (p0) cc_final: 0.6685 (p0) REVERT: C 825 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7175 (tm-30) REVERT: C 848 GLU cc_start: 0.7326 (pt0) cc_final: 0.7079 (pt0) REVERT: C 864 LYS cc_start: 0.7549 (ptpt) cc_final: 0.7322 (ptpp) REVERT: C 914 LYS cc_start: 0.7950 (tppt) cc_final: 0.7565 (tppt) REVERT: C 930 ASP cc_start: 0.7717 (t0) cc_final: 0.7230 (m-30) REVERT: C 947 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7196 (tm-30) REVERT: C 948 ILE cc_start: 0.8933 (mm) cc_final: 0.8277 (mm) REVERT: C 959 ASP cc_start: 0.6015 (m-30) cc_final: 0.5641 (m-30) REVERT: C 1028 LYS cc_start: 0.8914 (pttt) cc_final: 0.8705 (pttp) REVERT: C 1030 GLU cc_start: 0.7879 (tp30) cc_final: 0.7360 (tp30) REVERT: C 1035 LYS cc_start: 0.8618 (tppt) cc_final: 0.7980 (tppt) REVERT: C 1085 MET cc_start: 0.7560 (mmm) cc_final: 0.7219 (mmm) REVERT: C 1089 GLU cc_start: 0.7186 (mp0) cc_final: 0.6864 (mp0) REVERT: C 1095 ASP cc_start: 0.7468 (m-30) cc_final: 0.7108 (m-30) REVERT: C 1099 ASN cc_start: 0.8055 (t0) cc_final: 0.7263 (t0) REVERT: C 1119 MET cc_start: 0.8256 (tpp) cc_final: 0.7800 (tpt) REVERT: C 1122 LYS cc_start: 0.8378 (tptm) cc_final: 0.7442 (tppp) REVERT: C 1126 ASP cc_start: 0.7226 (m-30) cc_final: 0.6492 (m-30) REVERT: C 1131 MET cc_start: 0.7777 (ttt) cc_final: 0.7547 (ptp) REVERT: C 1140 LYS cc_start: 0.7803 (ptpt) cc_final: 0.7368 (ptpt) REVERT: C 1146 GLN cc_start: 0.7860 (tp40) cc_final: 0.7392 (tp-100) REVERT: C 1168 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6184 (pp20) REVERT: C 1174 GLU cc_start: 0.7495 (tp30) cc_final: 0.7252 (tp30) REVERT: C 1194 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6233 (pm20) REVERT: C 1200 LYS cc_start: 0.8536 (tttt) cc_final: 0.8252 (tttt) REVERT: C 1210 ILE cc_start: 0.8100 (tt) cc_final: 0.7801 (pt) REVERT: C 1211 ARG cc_start: 0.7352 (ttt-90) cc_final: 0.6996 (ttt-90) REVERT: C 1229 TYR cc_start: 0.8201 (m-80) cc_final: 0.7889 (m-10) REVERT: C 1264 GLN cc_start: 0.8256 (mp10) cc_final: 0.7864 (mp10) REVERT: C 1274 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6421 (mp0) REVERT: C 1285 TYR cc_start: 0.8047 (m-80) cc_final: 0.7691 (m-80) REVERT: C 1331 ARG cc_start: 0.7750 (ttm170) cc_final: 0.7549 (ttm170) REVERT: C 1332 SER cc_start: 0.8071 (p) cc_final: 0.7834 (p) REVERT: D 21 LYS cc_start: 0.8089 (ptpt) cc_final: 0.7415 (ptmm) REVERT: D 29 MET cc_start: 0.7901 (ttt) cc_final: 0.7315 (tpp) REVERT: D 33 TRP cc_start: 0.7989 (m-10) cc_final: 0.7637 (m-10) REVERT: D 50 LYS cc_start: 0.8236 (mmmt) cc_final: 0.8012 (mmmt) REVERT: D 96 LYS cc_start: 0.8533 (mmmt) cc_final: 0.8149 (mmtm) REVERT: D 115 TRP cc_start: 0.8564 (m-10) cc_final: 0.8327 (m-10) REVERT: D 118 LYS cc_start: 0.8209 (mmmt) cc_final: 0.7850 (mmmt) REVERT: D 148 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6683 (tm-30) REVERT: D 151 MET cc_start: 0.7321 (pmm) cc_final: 0.6830 (pmm) REVERT: D 158 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7803 (pp30) REVERT: D 192 MET cc_start: 0.7475 (tpp) cc_final: 0.7087 (tmm) REVERT: D 198 CYS cc_start: 0.7699 (t) cc_final: 0.7332 (t) REVERT: D 200 GLN cc_start: 0.8379 (pp30) cc_final: 0.8079 (pp30) REVERT: D 201 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8520 (mm) REVERT: D 219 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8362 (ttpp) REVERT: D 225 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7303 (mm-30) REVERT: D 235 GLU cc_start: 0.7250 (pm20) cc_final: 0.6950 (pm20) REVERT: D 236 TRP cc_start: 0.8374 (m-10) cc_final: 0.8066 (m-10) REVERT: D 279 LEU cc_start: 0.8254 (tp) cc_final: 0.8014 (tp) REVERT: D 280 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8184 (tppt) REVERT: D 282 LEU cc_start: 0.8570 (mt) cc_final: 0.8275 (tt) REVERT: D 297 ARG cc_start: 0.7841 (ttp80) cc_final: 0.7607 (tmm-80) REVERT: D 298 MET cc_start: 0.7269 (ttp) cc_final: 0.6831 (ttp) REVERT: D 332 LYS cc_start: 0.7476 (mtmm) cc_final: 0.7214 (mtmm) REVERT: D 360 TYR cc_start: 0.8309 (p90) cc_final: 0.7791 (p90) REVERT: D 363 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6417 (tp) REVERT: D 368 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7898 (tp) REVERT: D 375 GLU cc_start: 0.6926 (tm-30) cc_final: 0.6702 (tm-30) REVERT: D 399 LYS cc_start: 0.7970 (mtmt) cc_final: 0.7507 (mtmt) REVERT: D 400 MET cc_start: 0.7276 (tpp) cc_final: 0.7027 (tpp) REVERT: D 402 GLU cc_start: 0.7320 (tm-30) cc_final: 0.6857 (tm-30) REVERT: D 405 GLU cc_start: 0.7053 (mp0) cc_final: 0.6801 (mp0) REVERT: D 441 LEU cc_start: 0.8367 (mm) cc_final: 0.8028 (mt) REVERT: D 442 ILE cc_start: 0.8404 (tt) cc_final: 0.8054 (pt) REVERT: D 475 GLU cc_start: 0.7671 (mp0) cc_final: 0.7461 (mp0) REVERT: D 500 ILE cc_start: 0.8278 (mm) cc_final: 0.7973 (tt) REVERT: D 505 ASP cc_start: 0.7620 (t0) cc_final: 0.7372 (t0) REVERT: D 512 TYR cc_start: 0.8313 (t80) cc_final: 0.8066 (t80) REVERT: D 532 GLU cc_start: 0.6794 (mp0) cc_final: 0.6521 (mp0) REVERT: D 549 LYS cc_start: 0.7987 (tptt) cc_final: 0.7719 (tptt) REVERT: D 554 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7045 (tm-30) REVERT: D 573 THR cc_start: 0.8280 (p) cc_final: 0.7921 (m) REVERT: D 603 LYS cc_start: 0.7698 (tmmt) cc_final: 0.7456 (mmtm) REVERT: D 622 ASP cc_start: 0.7019 (m-30) cc_final: 0.6683 (m-30) REVERT: D 652 GLU cc_start: 0.8328 (mp0) cc_final: 0.7857 (mp0) REVERT: D 665 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7625 (mp10) REVERT: D 684 ASP cc_start: 0.7605 (m-30) cc_final: 0.7253 (m-30) REVERT: D 691 ASP cc_start: 0.7833 (m-30) cc_final: 0.7578 (m-30) REVERT: D 695 LYS cc_start: 0.8599 (tmtt) cc_final: 0.8283 (tmtt) REVERT: D 702 GLN cc_start: 0.7830 (tt0) cc_final: 0.7543 (tt0) REVERT: D 703 THR cc_start: 0.8325 (m) cc_final: 0.7668 (t) REVERT: D 723 TYR cc_start: 0.8050 (t80) cc_final: 0.7536 (t80) REVERT: D 781 LYS cc_start: 0.8495 (ttmt) cc_final: 0.8243 (tptm) REVERT: D 789 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7482 (ptmm) REVERT: D 822 MET cc_start: 0.6404 (tmm) cc_final: 0.6085 (tmm) REVERT: D 860 ARG cc_start: 0.6649 (ttt180) cc_final: 0.6141 (ttp80) REVERT: D 870 ASP cc_start: 0.7551 (m-30) cc_final: 0.7210 (m-30) REVERT: D 913 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7126 (mm-30) REVERT: D 915 ILE cc_start: 0.8192 (tt) cc_final: 0.7974 (pt) REVERT: D 922 SER cc_start: 0.8265 (m) cc_final: 0.7794 (p) REVERT: D 959 LYS cc_start: 0.8541 (mmtp) cc_final: 0.8260 (mmtp) REVERT: D 981 GLU cc_start: 0.6298 (OUTLIER) cc_final: 0.5913 (tm-30) REVERT: D 1099 TYR cc_start: 0.7565 (m-80) cc_final: 0.6789 (m-80) REVERT: D 1250 ASP cc_start: 0.7338 (p0) cc_final: 0.7107 (p0) REVERT: D 1259 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7609 (mm-40) REVERT: D 1327 GLU cc_start: 0.6796 (pm20) cc_final: 0.6028 (mp0) REVERT: E 53 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7585 (mm-30) REVERT: E 55 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7129 (tp30) REVERT: E 58 LEU cc_start: 0.8494 (pp) cc_final: 0.8280 (pp) REVERT: G 27 ARG cc_start: 0.8101 (mtm-85) cc_final: 0.7667 (mtm-85) REVERT: G 33 HIS cc_start: 0.8809 (OUTLIER) cc_final: 0.8243 (t-90) REVERT: G 43 MET cc_start: 0.7381 (tmm) cc_final: 0.6927 (tmm) REVERT: G 73 MET cc_start: 0.6418 (ppp) cc_final: 0.6033 (ppp) REVERT: G 80 TRP cc_start: 0.8038 (t60) cc_final: 0.7639 (t60) REVERT: G 83 VAL cc_start: 0.8896 (t) cc_final: 0.8689 (p) outliers start: 116 outliers final: 71 residues processed: 886 average time/residue: 0.2089 time to fit residues: 275.9589 Evaluate side-chains 884 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 796 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1168 GLU Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 665 GLN Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 981 GLU Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1235 ASN Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 65 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 233 optimal weight: 0.7980 chunk 119 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 268 optimal weight: 0.8980 chunk 217 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 282 optimal weight: 10.0000 chunk 283 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C 686 GLN C1237 HIS D 94 GLN D 489 ASN E 15 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.138155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109145 restraints weight = 49045.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.112787 restraints weight = 24354.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.115197 restraints weight = 14922.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.116713 restraints weight = 10588.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.117716 restraints weight = 8458.921| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.156 28014 Z= 0.136 Angle : 0.663 12.430 38147 Z= 0.339 Chirality : 0.044 0.365 4351 Planarity : 0.005 0.068 4731 Dihedral : 14.670 176.225 4488 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.51 % Allowed : 23.06 % Favored : 73.43 % Cbeta Deviations : 0.03 % 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: -0.74 (0.14), residues: 3285 helix: 0.86 (0.16), residues: 1101 sheet: -0.42 (0.24), residues: 462 loop : -1.45 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 54 TYR 0.019 0.001 TYR B 185 PHE 0.021 0.001 PHE D 892 TRP 0.034 0.002 TRP D1193 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00317 (28008) covalent geometry : angle 0.66219 (38141) hydrogen bonds : bond 0.03909 ( 1063) hydrogen bonds : angle 4.24645 ( 2930) metal coordination : bond 0.00500 ( 6) metal coordination : angle 3.16139 ( 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 895 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 796 time to evaluate : 0.955 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.8411 (mt) cc_final: 0.8102 (tt) REVERT: A 33 ARG cc_start: 0.7643 (ptm160) cc_final: 0.7195 (ptm160) REVERT: A 51 MET cc_start: 0.8071 (mmm) cc_final: 0.7869 (tpp) REVERT: A 68 TYR cc_start: 0.8478 (m-80) cc_final: 0.8277 (m-80) REVERT: A 74 VAL cc_start: 0.8571 (m) cc_final: 0.8140 (p) REVERT: A 101 THR cc_start: 0.8228 (m) cc_final: 0.7628 (p) REVERT: A 104 LYS cc_start: 0.8002 (tptp) cc_final: 0.7409 (tptp) REVERT: A 170 ARG cc_start: 0.8429 (ttp-110) cc_final: 0.8224 (ttm-80) REVERT: A 188 GLU cc_start: 0.7748 (pm20) cc_final: 0.7113 (pm20) REVERT: A 198 LEU cc_start: 0.7740 (mm) cc_final: 0.7331 (mm) REVERT: A 212 ASP cc_start: 0.7163 (OUTLIER) cc_final: 0.6846 (m-30) REVERT: B 16 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7751 (mt) REVERT: B 32 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6951 (tm-30) REVERT: B 51 MET cc_start: 0.7456 (mmm) cc_final: 0.7169 (mmm) REVERT: B 97 GLU cc_start: 0.6901 (pm20) cc_final: 0.6437 (pm20) REVERT: B 136 GLU cc_start: 0.8736 (pm20) cc_final: 0.8449 (pp20) REVERT: B 205 MET cc_start: 0.7562 (ppp) cc_final: 0.6994 (ppp) REVERT: B 214 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.5422 (tm-30) REVERT: B 218 ARG cc_start: 0.8082 (ttm110) cc_final: 0.7097 (ttm110) REVERT: B 219 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7579 (mtm-85) REVERT: C 8 LYS cc_start: 0.8495 (mttt) cc_final: 0.8281 (mtpt) REVERT: C 44 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.5964 (tm-30) REVERT: C 82 VAL cc_start: 0.7794 (m) cc_final: 0.7538 (p) REVERT: C 121 GLU cc_start: 0.6552 (mm-30) cc_final: 0.6235 (mm-30) REVERT: C 151 ARG cc_start: 0.7867 (ttm110) cc_final: 0.7518 (ptp-110) REVERT: C 180 ARG cc_start: 0.7358 (ttp80) cc_final: 0.7062 (ttp80) REVERT: C 185 ASP cc_start: 0.6258 (p0) cc_final: 0.5961 (p0) REVERT: C 186 PHE cc_start: 0.8065 (m-80) cc_final: 0.7728 (m-10) REVERT: C 187 GLU cc_start: 0.7077 (mp0) cc_final: 0.6532 (mp0) REVERT: C 195 PHE cc_start: 0.8000 (m-80) cc_final: 0.7504 (m-80) REVERT: C 203 LYS cc_start: 0.8223 (ttmt) cc_final: 0.7655 (ttpt) REVERT: C 214 ASN cc_start: 0.8519 (t0) cc_final: 0.8155 (t0) REVERT: C 262 TYR cc_start: 0.6401 (m-80) cc_final: 0.6149 (m-80) REVERT: C 349 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7511 (pm20) REVERT: C 368 ARG cc_start: 0.7944 (mtm-85) cc_final: 0.7691 (mtm110) REVERT: C 389 PHE cc_start: 0.7854 (m-10) cc_final: 0.7522 (m-80) REVERT: C 394 ARG cc_start: 0.6671 (ttm110) cc_final: 0.6424 (ttm110) REVERT: C 430 LYS cc_start: 0.8178 (mtpp) cc_final: 0.7499 (mttm) REVERT: C 434 ASP cc_start: 0.7676 (m-30) cc_final: 0.7307 (m-30) REVERT: C 499 SER cc_start: 0.7680 (p) cc_final: 0.7411 (p) REVERT: C 503 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8232 (tptt) REVERT: C 519 ASN cc_start: 0.7646 (m-40) cc_final: 0.7327 (m-40) REVERT: C 523 GLU cc_start: 0.7489 (tp30) cc_final: 0.7115 (tp30) REVERT: C 549 ASP cc_start: 0.7175 (t0) cc_final: 0.6852 (t0) REVERT: C 562 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6551 (tm-30) REVERT: C 611 GLU cc_start: 0.7283 (tt0) cc_final: 0.6582 (mt-10) REVERT: C 616 ILE cc_start: 0.8511 (mp) cc_final: 0.8284 (mm) REVERT: C 653 MET cc_start: 0.7159 (ttp) cc_final: 0.6934 (tmm) REVERT: C 656 SER cc_start: 0.8521 (t) cc_final: 0.8020 (m) REVERT: C 704 MET cc_start: 0.6933 (mmp) cc_final: 0.6488 (mmm) REVERT: C 719 LYS cc_start: 0.8014 (mtmm) cc_final: 0.7692 (mtmm) REVERT: C 723 VAL cc_start: 0.8454 (t) cc_final: 0.8055 (m) REVERT: C 730 SER cc_start: 0.8797 (m) cc_final: 0.8388 (t) REVERT: C 788 SER cc_start: 0.8432 (m) cc_final: 0.7725 (p) REVERT: C 793 GLU cc_start: 0.7206 (tt0) cc_final: 0.6731 (tt0) REVERT: C 811 ASN cc_start: 0.7924 (p0) cc_final: 0.6563 (p0) REVERT: C 825 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7133 (tm-30) REVERT: C 848 GLU cc_start: 0.7271 (pt0) cc_final: 0.7064 (pt0) REVERT: C 914 LYS cc_start: 0.7918 (tppt) cc_final: 0.7625 (tppt) REVERT: C 930 ASP cc_start: 0.7707 (t0) cc_final: 0.7233 (m-30) REVERT: C 947 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7239 (tm-30) REVERT: C 948 ILE cc_start: 0.8901 (mm) cc_final: 0.8271 (mm) REVERT: C 959 ASP cc_start: 0.6048 (m-30) cc_final: 0.5796 (m-30) REVERT: C 1028 LYS cc_start: 0.8881 (pttt) cc_final: 0.8409 (pttp) REVERT: C 1030 GLU cc_start: 0.7819 (tp30) cc_final: 0.7275 (tp30) REVERT: C 1032 LYS cc_start: 0.8831 (mttt) cc_final: 0.8397 (mttt) REVERT: C 1035 LYS cc_start: 0.8603 (tppt) cc_final: 0.7992 (tppt) REVERT: C 1089 GLU cc_start: 0.7219 (mp0) cc_final: 0.6900 (mp0) REVERT: C 1095 ASP cc_start: 0.7362 (m-30) cc_final: 0.7012 (m-30) REVERT: C 1099 ASN cc_start: 0.7977 (t0) cc_final: 0.7210 (t0) REVERT: C 1119 MET cc_start: 0.8189 (tpp) cc_final: 0.7763 (tpt) REVERT: C 1122 LYS cc_start: 0.8347 (tptm) cc_final: 0.7689 (tptp) REVERT: C 1126 ASP cc_start: 0.7139 (m-30) cc_final: 0.6525 (m-30) REVERT: C 1131 MET cc_start: 0.7754 (ttt) cc_final: 0.7486 (ptp) REVERT: C 1146 GLN cc_start: 0.7704 (tp40) cc_final: 0.7186 (tp-100) REVERT: C 1147 ARG cc_start: 0.8321 (mmm-85) cc_final: 0.7903 (ttm110) REVERT: C 1168 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.6107 (pp20) REVERT: C 1194 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6223 (pm20) REVERT: C 1200 LYS cc_start: 0.8484 (tttt) cc_final: 0.8199 (tttt) REVERT: C 1210 ILE cc_start: 0.8054 (tt) cc_final: 0.7769 (pt) REVERT: C 1229 TYR cc_start: 0.8185 (m-80) cc_final: 0.7737 (m-10) REVERT: C 1264 GLN cc_start: 0.8246 (mp10) cc_final: 0.7832 (mp10) REVERT: C 1274 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6462 (mp0) REVERT: C 1289 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6815 (mm-30) REVERT: C 1332 SER cc_start: 0.8010 (p) cc_final: 0.7749 (p) REVERT: C 1340 GLU cc_start: 0.6646 (tp30) cc_final: 0.6098 (tp30) REVERT: D 21 LYS cc_start: 0.8093 (ptpt) cc_final: 0.7374 (ptmm) REVERT: D 29 MET cc_start: 0.7851 (ttt) cc_final: 0.7287 (tpp) REVERT: D 33 TRP cc_start: 0.7865 (m-10) cc_final: 0.7467 (m-10) REVERT: D 52 GLU cc_start: 0.6534 (mm-30) cc_final: 0.6295 (mm-30) REVERT: D 96 LYS cc_start: 0.8525 (mmmt) cc_final: 0.8207 (mmmt) REVERT: D 118 LYS cc_start: 0.8192 (mmmt) cc_final: 0.7912 (mmmt) REVERT: D 148 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6683 (tm-30) REVERT: D 151 MET cc_start: 0.7285 (pmm) cc_final: 0.6760 (pmm) REVERT: D 158 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7861 (pp30) REVERT: D 192 MET cc_start: 0.7426 (tpp) cc_final: 0.7080 (tmm) REVERT: D 200 GLN cc_start: 0.8345 (pp30) cc_final: 0.8098 (pp30) REVERT: D 201 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8561 (mm) REVERT: D 219 LYS cc_start: 0.8741 (ttmt) cc_final: 0.8342 (ttpp) REVERT: D 225 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7273 (mm-30) REVERT: D 235 GLU cc_start: 0.7306 (pm20) cc_final: 0.7025 (pm20) REVERT: D 236 TRP cc_start: 0.8336 (m-10) cc_final: 0.8054 (m-10) REVERT: D 275 ARG cc_start: 0.8008 (tpp-160) cc_final: 0.6943 (tpp-160) REVERT: D 279 LEU cc_start: 0.8211 (tp) cc_final: 0.7964 (tp) REVERT: D 280 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8081 (tppt) REVERT: D 282 LEU cc_start: 0.8522 (mt) cc_final: 0.8230 (tt) REVERT: D 297 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7519 (tmm-80) REVERT: D 298 MET cc_start: 0.7301 (ttp) cc_final: 0.6198 (ttp) REVERT: D 325 LYS cc_start: 0.8342 (mmtt) cc_final: 0.8058 (mmtp) REVERT: D 332 LYS cc_start: 0.7267 (mtmm) cc_final: 0.6735 (mtpp) REVERT: D 360 TYR cc_start: 0.8200 (p90) cc_final: 0.7644 (p90) REVERT: D 368 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7862 (tp) REVERT: D 375 GLU cc_start: 0.6942 (tm-30) cc_final: 0.6706 (tm-30) REVERT: D 399 LYS cc_start: 0.7910 (mtmt) cc_final: 0.7477 (mtmt) REVERT: D 400 MET cc_start: 0.7277 (tpp) cc_final: 0.6975 (tpp) REVERT: D 402 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6815 (tm-30) REVERT: D 404 GLU cc_start: 0.8091 (tp30) cc_final: 0.7257 (tm-30) REVERT: D 441 LEU cc_start: 0.8327 (mm) cc_final: 0.8017 (mt) REVERT: D 442 ILE cc_start: 0.8390 (tt) cc_final: 0.8004 (pt) REVERT: D 475 GLU cc_start: 0.7664 (mp0) cc_final: 0.7432 (mp0) REVERT: D 500 ILE cc_start: 0.8272 (mm) cc_final: 0.7979 (tt) REVERT: D 505 ASP cc_start: 0.7621 (t0) cc_final: 0.7392 (t0) REVERT: D 512 TYR cc_start: 0.8278 (t80) cc_final: 0.8045 (t80) REVERT: D 532 GLU cc_start: 0.6724 (mp0) cc_final: 0.6471 (mp0) REVERT: D 549 LYS cc_start: 0.7972 (tptt) cc_final: 0.7725 (tptt) REVERT: D 554 GLU cc_start: 0.7514 (tm-30) cc_final: 0.6910 (tm-30) REVERT: D 555 TYR cc_start: 0.7889 (m-10) cc_final: 0.7436 (m-80) REVERT: D 573 THR cc_start: 0.8278 (p) cc_final: 0.7905 (m) REVERT: D 622 ASP cc_start: 0.6958 (m-30) cc_final: 0.6708 (m-30) REVERT: D 652 GLU cc_start: 0.8313 (mp0) cc_final: 0.7829 (mp0) REVERT: D 665 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7625 (mp10) REVERT: D 684 ASP cc_start: 0.7582 (m-30) cc_final: 0.7197 (m-30) REVERT: D 691 ASP cc_start: 0.7826 (m-30) cc_final: 0.7535 (m-30) REVERT: D 695 LYS cc_start: 0.8579 (tmtt) cc_final: 0.8259 (tmtt) REVERT: D 702 GLN cc_start: 0.7839 (tt0) cc_final: 0.7529 (tt0) REVERT: D 703 THR cc_start: 0.8246 (m) cc_final: 0.7569 (t) REVERT: D 723 TYR cc_start: 0.7972 (t80) cc_final: 0.7485 (t80) REVERT: D 770 LEU cc_start: 0.7868 (mm) cc_final: 0.7360 (mt) REVERT: D 781 LYS cc_start: 0.8506 (ttmt) cc_final: 0.8228 (tptm) REVERT: D 786 THR cc_start: 0.7697 (t) cc_final: 0.7492 (t) REVERT: D 789 LYS cc_start: 0.8023 (ttpt) cc_final: 0.7484 (ptmm) REVERT: D 822 MET cc_start: 0.6444 (tmm) cc_final: 0.6087 (tmm) REVERT: D 860 ARG cc_start: 0.6592 (ttt180) cc_final: 0.6321 (ttt180) REVERT: D 913 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7121 (mm-30) REVERT: D 915 ILE cc_start: 0.8262 (tt) cc_final: 0.8031 (pt) REVERT: D 922 SER cc_start: 0.8221 (m) cc_final: 0.7737 (p) REVERT: D 959 LYS cc_start: 0.8544 (mmtp) cc_final: 0.8257 (mmtp) REVERT: D 981 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.5844 (tm-30) REVERT: D 1099 TYR cc_start: 0.7534 (m-80) cc_final: 0.6769 (m-80) REVERT: D 1250 ASP cc_start: 0.7279 (p0) cc_final: 0.6981 (p0) REVERT: D 1276 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6667 (mm-30) REVERT: D 1327 GLU cc_start: 0.6719 (pm20) cc_final: 0.5963 (mp0) REVERT: E 53 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7553 (mm-30) REVERT: E 55 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7052 (tp30) REVERT: E 58 LEU cc_start: 0.8486 (pp) cc_final: 0.8265 (pp) REVERT: G 27 ARG cc_start: 0.8050 (mtm-85) cc_final: 0.7643 (mtm-85) REVERT: G 33 HIS cc_start: 0.8904 (OUTLIER) cc_final: 0.8387 (t-90) REVERT: G 43 MET cc_start: 0.7346 (tmm) cc_final: 0.7001 (tmm) REVERT: G 73 MET cc_start: 0.6222 (ppp) cc_final: 0.5807 (ppp) REVERT: G 80 TRP cc_start: 0.8004 (t60) cc_final: 0.7490 (t60) outliers start: 99 outliers final: 68 residues processed: 846 average time/residue: 0.2074 time to fit residues: 261.3895 Evaluate side-chains 868 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 785 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1160 ASP Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1168 GLU Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 665 GLN Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 981 GLU Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1235 ASN Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 65 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 217 optimal weight: 0.5980 chunk 79 optimal weight: 0.0570 chunk 88 optimal weight: 0.9990 chunk 57 optimal weight: 0.0770 chunk 234 optimal weight: 0.0970 chunk 127 optimal weight: 0.8980 chunk 202 optimal weight: 0.9980 chunk 29 optimal weight: 0.0870 chunk 136 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 240 optimal weight: 0.7980 overall best weight: 0.0830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 GLN C 490 GLN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C 686 GLN C1237 HIS ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.140985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112022 restraints weight = 49451.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.115722 restraints weight = 24549.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118158 restraints weight = 15008.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.119681 restraints weight = 10650.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.120752 restraints weight = 8485.407| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.183 28014 Z= 0.123 Angle : 0.665 13.634 38147 Z= 0.336 Chirality : 0.043 0.347 4351 Planarity : 0.005 0.091 4731 Dihedral : 14.600 175.653 4488 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.23 % Allowed : 23.84 % Favored : 72.93 % Cbeta Deviations : 0.03 % 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: -0.65 (0.14), residues: 3285 helix: 0.93 (0.16), residues: 1099 sheet: -0.41 (0.25), residues: 452 loop : -1.36 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 54 TYR 0.025 0.001 TYR D 995 PHE 0.024 0.001 PHE D 892 TRP 0.038 0.002 TRP D1193 HIS 0.005 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.00291 (28008) covalent geometry : angle 0.66413 (38141) hydrogen bonds : bond 0.03286 ( 1063) hydrogen bonds : angle 4.09141 ( 2930) metal coordination : bond 0.00229 ( 6) metal coordination : angle 2.77892 ( 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 889 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 798 time to evaluate : 0.964 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.8410 (mt) cc_final: 0.8106 (tt) REVERT: A 33 ARG cc_start: 0.7643 (ptm160) cc_final: 0.7208 (ptm160) REVERT: A 68 TYR cc_start: 0.8452 (m-80) cc_final: 0.8203 (m-80) REVERT: A 74 VAL cc_start: 0.8474 (m) cc_final: 0.8113 (p) REVERT: A 101 THR cc_start: 0.8229 (m) cc_final: 0.7560 (p) REVERT: A 104 LYS cc_start: 0.7990 (tptp) cc_final: 0.7448 (tptp) REVERT: A 170 ARG cc_start: 0.8382 (ttp-110) cc_final: 0.7682 (ttm-80) REVERT: A 187 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8233 (t) REVERT: A 188 GLU cc_start: 0.7755 (pm20) cc_final: 0.7134 (pm20) REVERT: A 198 LEU cc_start: 0.7586 (mm) cc_final: 0.7104 (mm) REVERT: A 212 ASP cc_start: 0.7064 (OUTLIER) cc_final: 0.6725 (m-30) REVERT: B 16 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7758 (mt) REVERT: B 32 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6841 (tm-30) REVERT: B 51 MET cc_start: 0.7414 (mmm) cc_final: 0.7131 (mmm) REVERT: B 97 GLU cc_start: 0.6859 (pm20) cc_final: 0.6412 (pm20) REVERT: B 136 GLU cc_start: 0.8719 (pm20) cc_final: 0.8406 (pp20) REVERT: B 205 MET cc_start: 0.7520 (ppp) cc_final: 0.6876 (ppp) REVERT: B 206 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6721 (mm-30) REVERT: B 214 GLU cc_start: 0.6250 (OUTLIER) cc_final: 0.5895 (tm-30) REVERT: B 219 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7537 (mtm-85) REVERT: C 8 LYS cc_start: 0.8498 (mttt) cc_final: 0.8175 (mtpt) REVERT: C 44 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.5813 (tm-30) REVERT: C 82 VAL cc_start: 0.7766 (m) cc_final: 0.7478 (p) REVERT: C 99 LYS cc_start: 0.8183 (mtmm) cc_final: 0.7903 (pttm) REVERT: C 151 ARG cc_start: 0.7814 (ttm110) cc_final: 0.7459 (ptp-110) REVERT: C 180 ARG cc_start: 0.7281 (ttp80) cc_final: 0.7036 (ttp80) REVERT: C 183 TRP cc_start: 0.8092 (m-10) cc_final: 0.7767 (m-10) REVERT: C 185 ASP cc_start: 0.6101 (p0) cc_final: 0.5741 (p0) REVERT: C 186 PHE cc_start: 0.8015 (m-80) cc_final: 0.7569 (m-10) REVERT: C 187 GLU cc_start: 0.6987 (mp0) cc_final: 0.6095 (mp0) REVERT: C 195 PHE cc_start: 0.7930 (m-80) cc_final: 0.7492 (m-80) REVERT: C 203 LYS cc_start: 0.8170 (ttmt) cc_final: 0.7666 (ttpt) REVERT: C 211 ARG cc_start: 0.7417 (mtp85) cc_final: 0.7162 (mmm160) REVERT: C 214 ASN cc_start: 0.8483 (t0) cc_final: 0.8143 (t0) REVERT: C 262 TYR cc_start: 0.6484 (m-80) cc_final: 0.5871 (m-80) REVERT: C 349 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7497 (pm20) REVERT: C 368 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7610 (mtm-85) REVERT: C 394 ARG cc_start: 0.6648 (ttm110) cc_final: 0.6417 (ttm110) REVERT: C 430 LYS cc_start: 0.8114 (mtpp) cc_final: 0.7877 (mttm) REVERT: C 499 SER cc_start: 0.7633 (p) cc_final: 0.7369 (p) REVERT: C 503 LYS cc_start: 0.8414 (mmtt) cc_final: 0.8171 (tptt) REVERT: C 523 GLU cc_start: 0.7363 (tp30) cc_final: 0.7091 (tp30) REVERT: C 549 ASP cc_start: 0.7173 (t0) cc_final: 0.6751 (t0) REVERT: C 593 LYS cc_start: 0.8240 (tptt) cc_final: 0.7735 (tppt) REVERT: C 611 GLU cc_start: 0.7317 (tt0) cc_final: 0.6574 (mt-10) REVERT: C 616 ILE cc_start: 0.8504 (mp) cc_final: 0.8155 (mm) REVERT: C 651 ASP cc_start: 0.7264 (m-30) cc_final: 0.7031 (m-30) REVERT: C 653 MET cc_start: 0.7085 (ttp) cc_final: 0.6845 (tmm) REVERT: C 654 ASP cc_start: 0.7663 (m-30) cc_final: 0.6858 (m-30) REVERT: C 656 SER cc_start: 0.8429 (t) cc_final: 0.7903 (m) REVERT: C 704 MET cc_start: 0.6894 (mmp) cc_final: 0.6420 (mmm) REVERT: C 723 VAL cc_start: 0.8435 (t) cc_final: 0.8051 (m) REVERT: C 730 SER cc_start: 0.8670 (m) cc_final: 0.8276 (t) REVERT: C 788 SER cc_start: 0.8396 (m) cc_final: 0.7723 (p) REVERT: C 793 GLU cc_start: 0.7326 (tt0) cc_final: 0.6804 (tt0) REVERT: C 800 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.6908 (mtp) REVERT: C 811 ASN cc_start: 0.7863 (p0) cc_final: 0.7453 (p0) REVERT: C 825 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7087 (tm-30) REVERT: C 848 GLU cc_start: 0.7312 (pt0) cc_final: 0.7073 (pt0) REVERT: C 849 GLU cc_start: 0.7397 (tp30) cc_final: 0.7044 (tp30) REVERT: C 914 LYS cc_start: 0.7848 (tppt) cc_final: 0.7542 (tppt) REVERT: C 930 ASP cc_start: 0.7682 (t0) cc_final: 0.7138 (m-30) REVERT: C 948 ILE cc_start: 0.8871 (mm) cc_final: 0.8334 (mm) REVERT: C 959 ASP cc_start: 0.5960 (m-30) cc_final: 0.5655 (m-30) REVERT: C 1028 LYS cc_start: 0.8862 (pttt) cc_final: 0.8350 (pttp) REVERT: C 1030 GLU cc_start: 0.7839 (tp30) cc_final: 0.7297 (tp30) REVERT: C 1032 LYS cc_start: 0.8898 (mttt) cc_final: 0.8457 (mttt) REVERT: C 1035 LYS cc_start: 0.8568 (tppt) cc_final: 0.7988 (tppt) REVERT: C 1095 ASP cc_start: 0.7226 (m-30) cc_final: 0.6952 (m-30) REVERT: C 1122 LYS cc_start: 0.8338 (tptm) cc_final: 0.7594 (tptp) REVERT: C 1126 ASP cc_start: 0.7106 (m-30) cc_final: 0.6487 (m-30) REVERT: C 1131 MET cc_start: 0.7777 (ttt) cc_final: 0.7449 (ptp) REVERT: C 1146 GLN cc_start: 0.7564 (tp40) cc_final: 0.6649 (tp-100) REVERT: C 1147 ARG cc_start: 0.8208 (mmm-85) cc_final: 0.7702 (ttm-80) REVERT: C 1194 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6182 (pm20) REVERT: C 1197 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7171 (tp30) REVERT: C 1200 LYS cc_start: 0.8469 (tttt) cc_final: 0.8204 (tttt) REVERT: C 1210 ILE cc_start: 0.8013 (tt) cc_final: 0.7595 (pt) REVERT: C 1229 TYR cc_start: 0.8015 (m-80) cc_final: 0.7609 (m-80) REVERT: C 1243 MET cc_start: 0.7853 (tmm) cc_final: 0.7652 (tmm) REVERT: C 1264 GLN cc_start: 0.8286 (mp10) cc_final: 0.7881 (mp10) REVERT: C 1274 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6419 (mp0) REVERT: C 1289 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6710 (mm-30) REVERT: C 1319 MET cc_start: 0.7199 (ttm) cc_final: 0.6895 (ttt) REVERT: C 1332 SER cc_start: 0.7911 (p) cc_final: 0.7616 (p) REVERT: D 21 LYS cc_start: 0.8052 (ptpt) cc_final: 0.7398 (ptmm) REVERT: D 29 MET cc_start: 0.7727 (ttt) cc_final: 0.7385 (tpp) REVERT: D 52 GLU cc_start: 0.6535 (mm-30) cc_final: 0.6221 (mm-30) REVERT: D 118 LYS cc_start: 0.8149 (mmmt) cc_final: 0.7875 (mmmt) REVERT: D 128 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7579 (mt) REVERT: D 142 GLU cc_start: 0.7731 (mp0) cc_final: 0.7445 (mp0) REVERT: D 148 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6687 (tm-30) REVERT: D 151 MET cc_start: 0.7265 (pmm) cc_final: 0.6781 (pmm) REVERT: D 158 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7858 (pp30) REVERT: D 192 MET cc_start: 0.7416 (tpp) cc_final: 0.7120 (tmm) REVERT: D 200 GLN cc_start: 0.8269 (pp30) cc_final: 0.7999 (pp30) REVERT: D 201 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8540 (mm) REVERT: D 215 LYS cc_start: 0.8947 (pttt) cc_final: 0.8602 (mmtm) REVERT: D 219 LYS cc_start: 0.8748 (ttmt) cc_final: 0.8343 (ttpp) REVERT: D 225 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7227 (mm-30) REVERT: D 235 GLU cc_start: 0.7298 (pm20) cc_final: 0.7055 (pm20) REVERT: D 280 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8058 (tppt) REVERT: D 282 LEU cc_start: 0.8454 (mt) cc_final: 0.8210 (tt) REVERT: D 325 LYS cc_start: 0.8305 (mmtt) cc_final: 0.8071 (mmtp) REVERT: D 332 LYS cc_start: 0.6834 (mtmm) cc_final: 0.6391 (mtpp) REVERT: D 340 GLN cc_start: 0.8074 (mm110) cc_final: 0.7833 (mm-40) REVERT: D 375 GLU cc_start: 0.6981 (tm-30) cc_final: 0.6751 (tm-30) REVERT: D 398 LYS cc_start: 0.8184 (ttmm) cc_final: 0.7980 (ttmm) REVERT: D 399 LYS cc_start: 0.7883 (mtmt) cc_final: 0.7398 (mtmt) REVERT: D 400 MET cc_start: 0.7261 (tpp) cc_final: 0.6169 (tpp) REVERT: D 402 GLU cc_start: 0.7233 (tm-30) cc_final: 0.6838 (tm-30) REVERT: D 404 GLU cc_start: 0.8059 (tp30) cc_final: 0.7265 (tm-30) REVERT: D 405 GLU cc_start: 0.6981 (mp0) cc_final: 0.6244 (mp0) REVERT: D 441 LEU cc_start: 0.8331 (mm) cc_final: 0.8019 (mp) REVERT: D 442 ILE cc_start: 0.8412 (tt) cc_final: 0.8026 (pt) REVERT: D 475 GLU cc_start: 0.7652 (mp0) cc_final: 0.7439 (mp0) REVERT: D 500 ILE cc_start: 0.8270 (mm) cc_final: 0.7986 (tt) REVERT: D 512 TYR cc_start: 0.8321 (t80) cc_final: 0.8045 (t80) REVERT: D 532 GLU cc_start: 0.6765 (mp0) cc_final: 0.6537 (mp0) REVERT: D 549 LYS cc_start: 0.7950 (tptt) cc_final: 0.7645 (tptt) REVERT: D 554 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7260 (tm-30) REVERT: D 557 LYS cc_start: 0.6871 (tppt) cc_final: 0.6354 (tppt) REVERT: D 573 THR cc_start: 0.8283 (p) cc_final: 0.7909 (m) REVERT: D 622 ASP cc_start: 0.6939 (m-30) cc_final: 0.6613 (m-30) REVERT: D 652 GLU cc_start: 0.8285 (mp0) cc_final: 0.7802 (mp0) REVERT: D 665 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7579 (mp10) REVERT: D 684 ASP cc_start: 0.7583 (m-30) cc_final: 0.7149 (m-30) REVERT: D 691 ASP cc_start: 0.7798 (m-30) cc_final: 0.7496 (m-30) REVERT: D 695 LYS cc_start: 0.8531 (tmtt) cc_final: 0.8232 (tmtt) REVERT: D 723 TYR cc_start: 0.7907 (t80) cc_final: 0.7183 (t80) REVERT: D 770 LEU cc_start: 0.7772 (mm) cc_final: 0.7331 (mt) REVERT: D 781 LYS cc_start: 0.8506 (ttmt) cc_final: 0.8190 (tptm) REVERT: D 789 LYS cc_start: 0.7989 (ttpt) cc_final: 0.7450 (ptmm) REVERT: D 858 VAL cc_start: 0.7063 (t) cc_final: 0.6804 (p) REVERT: D 860 ARG cc_start: 0.6250 (ttt180) cc_final: 0.6005 (ttt-90) REVERT: D 913 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7056 (mm-30) REVERT: D 922 SER cc_start: 0.8219 (m) cc_final: 0.7759 (p) REVERT: D 959 LYS cc_start: 0.8544 (mmtp) cc_final: 0.8293 (mmtp) REVERT: D 981 GLU cc_start: 0.6287 (OUTLIER) cc_final: 0.5831 (tm-30) REVERT: D 1099 TYR cc_start: 0.7479 (m-80) cc_final: 0.6843 (m-80) REVERT: D 1231 ARG cc_start: 0.8105 (mtp-110) cc_final: 0.7897 (mtp85) REVERT: D 1250 ASP cc_start: 0.7258 (p0) cc_final: 0.6950 (p0) REVERT: D 1260 MET cc_start: 0.7277 (mtt) cc_final: 0.7066 (mtp) REVERT: D 1327 GLU cc_start: 0.6547 (pm20) cc_final: 0.5696 (mp0) REVERT: D 1345 ARG cc_start: 0.8186 (mtp85) cc_final: 0.7838 (mtp-110) REVERT: E 53 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7515 (mm-30) REVERT: E 55 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6954 (tp30) REVERT: E 58 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8276 (pp) REVERT: E 62 GLN cc_start: 0.8278 (tp40) cc_final: 0.7748 (tp40) REVERT: G 27 ARG cc_start: 0.8012 (mtm-85) cc_final: 0.7636 (mtm-85) REVERT: G 33 HIS cc_start: 0.8810 (OUTLIER) cc_final: 0.8259 (t-90) REVERT: G 43 MET cc_start: 0.7338 (tmm) cc_final: 0.7065 (tmm) REVERT: G 73 MET cc_start: 0.6052 (ppp) cc_final: 0.5579 (ppp) REVERT: G 76 ASN cc_start: 0.5764 (p0) cc_final: 0.5425 (p0) REVERT: G 80 TRP cc_start: 0.7975 (t60) cc_final: 0.7618 (t60) outliers start: 91 outliers final: 56 residues processed: 844 average time/residue: 0.2126 time to fit residues: 267.1332 Evaluate side-chains 848 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 775 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 665 GLN Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 981 GLU Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1235 ASN Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 65 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 0.0980 chunk 23 optimal weight: 0.2980 chunk 212 optimal weight: 5.9990 chunk 314 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 165 optimal weight: 0.9980 chunk 267 optimal weight: 0.0670 chunk 282 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 308 optimal weight: 2.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN ** C1237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.140460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.111609 restraints weight = 49232.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.115282 restraints weight = 24461.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.117697 restraints weight = 14959.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.119280 restraints weight = 10569.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.120234 restraints weight = 8380.780| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.186 28014 Z= 0.124 Angle : 0.680 15.558 38147 Z= 0.341 Chirality : 0.043 0.363 4351 Planarity : 0.004 0.084 4731 Dihedral : 14.566 175.995 4488 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.55 % Allowed : 25.36 % Favored : 72.08 % Cbeta Deviations : 0.03 % 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: -0.58 (0.14), residues: 3285 helix: 0.97 (0.16), residues: 1101 sheet: -0.39 (0.26), residues: 411 loop : -1.29 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 322 TYR 0.021 0.001 TYR D 995 PHE 0.023 0.001 PHE D 892 TRP 0.039 0.002 TRP D1193 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00301 (28008) covalent geometry : angle 0.67902 (38141) hydrogen bonds : bond 0.03373 ( 1063) hydrogen bonds : angle 4.06568 ( 2930) metal coordination : bond 0.00285 ( 6) metal coordination : angle 2.76582 ( 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 848 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 776 time to evaluate : 0.910 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.8395 (mt) cc_final: 0.8109 (tt) REVERT: A 33 ARG cc_start: 0.7637 (ptm160) cc_final: 0.7195 (ptm160) REVERT: A 68 TYR cc_start: 0.8468 (m-80) cc_final: 0.8266 (m-80) REVERT: A 104 LYS cc_start: 0.8038 (tptp) cc_final: 0.7384 (tptp) REVERT: A 140 ILE cc_start: 0.6074 (mm) cc_final: 0.5724 (tp) REVERT: A 170 ARG cc_start: 0.8363 (ttp-110) cc_final: 0.7649 (ttm-80) REVERT: A 187 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8222 (t) REVERT: A 188 GLU cc_start: 0.7751 (pm20) cc_final: 0.7142 (pm20) REVERT: A 198 LEU cc_start: 0.7564 (mm) cc_final: 0.7058 (mm) REVERT: A 212 ASP cc_start: 0.7059 (OUTLIER) cc_final: 0.6712 (m-30) REVERT: B 16 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7776 (mt) REVERT: B 17 GLU cc_start: 0.7233 (tm-30) cc_final: 0.7007 (tm-30) REVERT: B 32 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6841 (tm-30) REVERT: B 51 MET cc_start: 0.7458 (mmm) cc_final: 0.7172 (mmm) REVERT: B 97 GLU cc_start: 0.6837 (pm20) cc_final: 0.6394 (pm20) REVERT: B 136 GLU cc_start: 0.8718 (pm20) cc_final: 0.8413 (pp20) REVERT: B 205 MET cc_start: 0.7523 (ppp) cc_final: 0.6967 (ppp) REVERT: B 214 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5906 (tm-30) REVERT: B 219 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7547 (mtm-85) REVERT: C 8 LYS cc_start: 0.8509 (mttt) cc_final: 0.8085 (mtpp) REVERT: C 44 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.5672 (tm-30) REVERT: C 82 VAL cc_start: 0.7780 (m) cc_final: 0.7506 (p) REVERT: C 99 LYS cc_start: 0.8007 (mtmm) cc_final: 0.7710 (mtmm) REVERT: C 151 ARG cc_start: 0.7822 (ttm110) cc_final: 0.7425 (ptp-110) REVERT: C 180 ARG cc_start: 0.7310 (ttp80) cc_final: 0.7033 (ttp80) REVERT: C 185 ASP cc_start: 0.6103 (p0) cc_final: 0.5669 (p0) REVERT: C 186 PHE cc_start: 0.7963 (m-80) cc_final: 0.7613 (m-10) REVERT: C 187 GLU cc_start: 0.6989 (mp0) cc_final: 0.6118 (mp0) REVERT: C 195 PHE cc_start: 0.7941 (m-80) cc_final: 0.7381 (m-80) REVERT: C 203 LYS cc_start: 0.8163 (ttmt) cc_final: 0.7514 (ttmt) REVERT: C 211 ARG cc_start: 0.7417 (mtp85) cc_final: 0.7168 (mmm160) REVERT: C 214 ASN cc_start: 0.8540 (t0) cc_final: 0.8059 (t0) REVERT: C 262 TYR cc_start: 0.6399 (m-80) cc_final: 0.5841 (m-80) REVERT: C 273 HIS cc_start: 0.7328 (m-70) cc_final: 0.6931 (t-90) REVERT: C 349 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7497 (pm20) REVERT: C 368 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7404 (mtm-85) REVERT: C 394 ARG cc_start: 0.6681 (ttm110) cc_final: 0.6425 (ttm110) REVERT: C 430 LYS cc_start: 0.8151 (mtpp) cc_final: 0.7866 (mttm) REVERT: C 499 SER cc_start: 0.7635 (p) cc_final: 0.7370 (p) REVERT: C 503 LYS cc_start: 0.8407 (mmtt) cc_final: 0.8177 (tptt) REVERT: C 523 GLU cc_start: 0.7347 (tp30) cc_final: 0.7081 (tp30) REVERT: C 549 ASP cc_start: 0.7196 (t0) cc_final: 0.6769 (t0) REVERT: C 593 LYS cc_start: 0.8269 (tptt) cc_final: 0.7759 (tppt) REVERT: C 611 GLU cc_start: 0.7342 (tt0) cc_final: 0.6570 (mt-10) REVERT: C 616 ILE cc_start: 0.8546 (mp) cc_final: 0.8210 (mm) REVERT: C 651 ASP cc_start: 0.7225 (m-30) cc_final: 0.6979 (m-30) REVERT: C 654 ASP cc_start: 0.7691 (m-30) cc_final: 0.6904 (m-30) REVERT: C 656 SER cc_start: 0.8437 (t) cc_final: 0.7887 (m) REVERT: C 704 MET cc_start: 0.6918 (mmp) cc_final: 0.6460 (mmm) REVERT: C 723 VAL cc_start: 0.8429 (t) cc_final: 0.8044 (m) REVERT: C 730 SER cc_start: 0.8736 (m) cc_final: 0.8336 (t) REVERT: C 788 SER cc_start: 0.8393 (m) cc_final: 0.7725 (p) REVERT: C 793 GLU cc_start: 0.7297 (tt0) cc_final: 0.6843 (tt0) REVERT: C 800 MET cc_start: 0.7131 (mtp) cc_final: 0.6924 (mtp) REVERT: C 811 ASN cc_start: 0.7842 (p0) cc_final: 0.7449 (p0) REVERT: C 825 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7157 (tm-30) REVERT: C 848 GLU cc_start: 0.7331 (pt0) cc_final: 0.6973 (pt0) REVERT: C 849 GLU cc_start: 0.7392 (tp30) cc_final: 0.7045 (tp30) REVERT: C 914 LYS cc_start: 0.7827 (tppt) cc_final: 0.7501 (tppt) REVERT: C 930 ASP cc_start: 0.7683 (t0) cc_final: 0.7142 (m-30) REVERT: C 943 LYS cc_start: 0.8106 (pttp) cc_final: 0.7902 (pttm) REVERT: C 959 ASP cc_start: 0.5937 (m-30) cc_final: 0.5636 (m-30) REVERT: C 1028 LYS cc_start: 0.8863 (pttt) cc_final: 0.8344 (pttp) REVERT: C 1030 GLU cc_start: 0.7861 (tp30) cc_final: 0.7322 (tp30) REVERT: C 1032 LYS cc_start: 0.8914 (mttt) cc_final: 0.8452 (mttt) REVERT: C 1035 LYS cc_start: 0.8590 (tppt) cc_final: 0.8002 (tppt) REVERT: C 1095 ASP cc_start: 0.7259 (m-30) cc_final: 0.6993 (m-30) REVERT: C 1122 LYS cc_start: 0.8335 (tptm) cc_final: 0.7589 (tptp) REVERT: C 1126 ASP cc_start: 0.7145 (m-30) cc_final: 0.6474 (m-30) REVERT: C 1131 MET cc_start: 0.7747 (ttt) cc_final: 0.7462 (ptp) REVERT: C 1146 GLN cc_start: 0.7636 (tp40) cc_final: 0.6803 (tp-100) REVERT: C 1194 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6232 (pm20) REVERT: C 1200 LYS cc_start: 0.8472 (tttt) cc_final: 0.8182 (tttt) REVERT: C 1210 ILE cc_start: 0.8004 (tt) cc_final: 0.7691 (pt) REVERT: C 1229 TYR cc_start: 0.7992 (m-80) cc_final: 0.7611 (m-80) REVERT: C 1243 MET cc_start: 0.7879 (tmm) cc_final: 0.7616 (tmm) REVERT: C 1264 GLN cc_start: 0.8265 (mp10) cc_final: 0.7856 (mp10) REVERT: C 1274 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6444 (mp0) REVERT: C 1289 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6685 (mm-30) REVERT: C 1319 MET cc_start: 0.7210 (ttm) cc_final: 0.6896 (ttt) REVERT: C 1324 ASN cc_start: 0.8060 (t0) cc_final: 0.7628 (t0) REVERT: C 1329 GLU cc_start: 0.6943 (tm-30) cc_final: 0.6520 (tm-30) REVERT: C 1332 SER cc_start: 0.7981 (p) cc_final: 0.7654 (p) REVERT: D 21 LYS cc_start: 0.8067 (ptpt) cc_final: 0.7400 (ptmm) REVERT: D 29 MET cc_start: 0.7536 (ttt) cc_final: 0.7295 (tpp) REVERT: D 52 GLU cc_start: 0.6500 (mm-30) cc_final: 0.6206 (mm-30) REVERT: D 118 LYS cc_start: 0.8059 (mmmt) cc_final: 0.7761 (mmmt) REVERT: D 128 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7567 (mt) REVERT: D 148 GLU cc_start: 0.7101 (tm-30) cc_final: 0.6664 (tm-30) REVERT: D 151 MET cc_start: 0.7277 (pmm) cc_final: 0.6775 (pmm) REVERT: D 157 GLN cc_start: 0.7246 (mp10) cc_final: 0.6830 (mp10) REVERT: D 158 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7874 (pp30) REVERT: D 192 MET cc_start: 0.7459 (tpp) cc_final: 0.7198 (tmm) REVERT: D 200 GLN cc_start: 0.8263 (pp30) cc_final: 0.8033 (pp30) REVERT: D 201 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8540 (mm) REVERT: D 215 LYS cc_start: 0.8947 (pttt) cc_final: 0.8621 (mmtm) REVERT: D 219 LYS cc_start: 0.8753 (ttmt) cc_final: 0.8349 (ttpp) REVERT: D 225 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7257 (mm-30) REVERT: D 235 GLU cc_start: 0.7300 (pm20) cc_final: 0.7069 (pm20) REVERT: D 280 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8042 (tppt) REVERT: D 282 LEU cc_start: 0.8470 (mt) cc_final: 0.8237 (tt) REVERT: D 298 MET cc_start: 0.7396 (ttp) cc_final: 0.7064 (ttp) REVERT: D 325 LYS cc_start: 0.8303 (mmtt) cc_final: 0.8047 (mmtp) REVERT: D 340 GLN cc_start: 0.8039 (mm110) cc_final: 0.7825 (mm110) REVERT: D 375 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6765 (tm-30) REVERT: D 399 LYS cc_start: 0.7904 (mtmt) cc_final: 0.7388 (mtmt) REVERT: D 400 MET cc_start: 0.7271 (tpp) cc_final: 0.6179 (tpp) REVERT: D 402 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6854 (tm-30) REVERT: D 404 GLU cc_start: 0.8047 (tp30) cc_final: 0.7303 (tm-30) REVERT: D 405 GLU cc_start: 0.6971 (mp0) cc_final: 0.6388 (mp0) REVERT: D 441 LEU cc_start: 0.8325 (mm) cc_final: 0.8017 (mp) REVERT: D 442 ILE cc_start: 0.8417 (tt) cc_final: 0.8035 (pt) REVERT: D 475 GLU cc_start: 0.7664 (mp0) cc_final: 0.7442 (mp0) REVERT: D 500 ILE cc_start: 0.8285 (mm) cc_final: 0.7975 (tt) REVERT: D 532 GLU cc_start: 0.6772 (mp0) cc_final: 0.6479 (mp0) REVERT: D 549 LYS cc_start: 0.7970 (tptt) cc_final: 0.7762 (tptt) REVERT: D 554 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7205 (tm-30) REVERT: D 573 THR cc_start: 0.8271 (p) cc_final: 0.7911 (m) REVERT: D 622 ASP cc_start: 0.6932 (m-30) cc_final: 0.6591 (m-30) REVERT: D 652 GLU cc_start: 0.8305 (mp0) cc_final: 0.7786 (mp0) REVERT: D 665 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7586 (mp10) REVERT: D 684 ASP cc_start: 0.7566 (m-30) cc_final: 0.7150 (m-30) REVERT: D 691 ASP cc_start: 0.7785 (m-30) cc_final: 0.7509 (m-30) REVERT: D 695 LYS cc_start: 0.8540 (tmtt) cc_final: 0.8212 (tmtt) REVERT: D 702 GLN cc_start: 0.7774 (tt0) cc_final: 0.7110 (tp40) REVERT: D 714 GLU cc_start: 0.6890 (tp30) cc_final: 0.6432 (tm-30) REVERT: D 770 LEU cc_start: 0.7903 (mm) cc_final: 0.7433 (mt) REVERT: D 781 LYS cc_start: 0.8496 (ttmt) cc_final: 0.8201 (tptm) REVERT: D 789 LYS cc_start: 0.7999 (ttpt) cc_final: 0.7482 (ptmm) REVERT: D 858 VAL cc_start: 0.7202 (t) cc_final: 0.6954 (p) REVERT: D 860 ARG cc_start: 0.6229 (ttt180) cc_final: 0.6011 (ttt-90) REVERT: D 865 HIS cc_start: 0.7095 (p-80) cc_final: 0.6368 (p-80) REVERT: D 867 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7810 (mp10) REVERT: D 913 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7054 (mm-30) REVERT: D 922 SER cc_start: 0.8215 (m) cc_final: 0.7776 (p) REVERT: D 959 LYS cc_start: 0.8544 (mmtp) cc_final: 0.8290 (mmtp) REVERT: D 981 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5812 (tm-30) REVERT: D 993 GLU cc_start: 0.6137 (mm-30) cc_final: 0.5883 (pp20) REVERT: D 1099 TYR cc_start: 0.7488 (m-80) cc_final: 0.6846 (m-80) REVERT: D 1173 ARG cc_start: 0.8240 (ptm160) cc_final: 0.7843 (ttm-80) REVERT: D 1231 ARG cc_start: 0.8114 (mtp-110) cc_final: 0.7909 (mtp85) REVERT: D 1250 ASP cc_start: 0.7258 (p0) cc_final: 0.6980 (p0) REVERT: D 1260 MET cc_start: 0.7330 (mtt) cc_final: 0.7106 (mtp) REVERT: D 1327 GLU cc_start: 0.6543 (pm20) cc_final: 0.5773 (mp0) REVERT: E 26 ARG cc_start: 0.7758 (tpt-90) cc_final: 0.7469 (tpt170) REVERT: E 52 ARG cc_start: 0.8062 (ttp80) cc_final: 0.7852 (ttp80) REVERT: E 53 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7566 (mm-30) REVERT: E 55 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6988 (tp30) REVERT: E 62 GLN cc_start: 0.8285 (tp40) cc_final: 0.7750 (tp40) REVERT: G 27 ARG cc_start: 0.8023 (mtm-85) cc_final: 0.7633 (mtm-85) REVERT: G 33 HIS cc_start: 0.8795 (OUTLIER) cc_final: 0.8249 (t-90) REVERT: G 43 MET cc_start: 0.7341 (tmm) cc_final: 0.7124 (tmm) REVERT: G 73 MET cc_start: 0.6045 (ppp) cc_final: 0.5575 (ppp) REVERT: G 76 ASN cc_start: 0.5799 (p0) cc_final: 0.5471 (p0) REVERT: G 80 TRP cc_start: 0.7924 (t60) cc_final: 0.7442 (t60) REVERT: G 83 VAL cc_start: 0.9007 (t) cc_final: 0.8798 (p) outliers start: 72 outliers final: 47 residues processed: 814 average time/residue: 0.2072 time to fit residues: 250.5884 Evaluate side-chains 830 residues out of total 2819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 768 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 941 LYS Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1140 LYS Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1279 GLU Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 665 GLN Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 981 GLU Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1235 ASN Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 29 HIS Chi-restraints excluded: chain G residue 33 HIS Chi-restraints excluded: chain G residue 65 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 311 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 300 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 195 optimal weight: 0.1980 chunk 206 optimal weight: 0.4980 chunk 185 optimal weight: 0.0770 chunk 183 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 144 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN ** C1237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN D1218 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.140957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112183 restraints weight = 48672.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.115861 restraints weight = 24442.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.118287 restraints weight = 15014.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.119809 restraints weight = 10623.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.120830 restraints weight = 8461.387| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.4310 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= 0.125 Angle : 0.678 15.118 38147 Z= 0.340 Chirality : 0.043 0.386 4351 Planarity : 0.004 0.069 4731 Dihedral : 14.550 176.118 4488 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.45 % Allowed : 26.04 % Favored : 71.51 % Cbeta Deviations : 0.03 % 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: -0.56 (0.15), residues: 3285 helix: 0.96 (0.16), residues: 1100 sheet: -0.39 (0.26), residues: 412 loop : -1.25 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 322 TYR 0.018 0.001 TYR D 995 PHE 0.028 0.001 PHE D 461 TRP 0.038 0.002 TRP D1193 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00303 (28008) covalent geometry : angle 0.67706 (38141) hydrogen bonds : bond 0.03331 ( 1063) hydrogen bonds : angle 4.06090 ( 2930) metal coordination : bond 0.00300 ( 6) metal coordination : angle 2.74418 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5869.81 seconds wall clock time: 101 minutes 26.68 seconds (6086.68 seconds total)