Starting phenix.real_space_refine on Fri Mar 6 03:48:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rin_4892/03_2026/6rin_4892.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rin_4892/03_2026/6rin_4892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rin_4892/03_2026/6rin_4892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rin_4892/03_2026/6rin_4892.map" model { file = "/net/cci-nas-00/data/ceres_data/6rin_4892/03_2026/6rin_4892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rin_4892/03_2026/6rin_4892.cif" } resolution = 3.7 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= 0.008 sd= 0.074 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 58 5.49 5 Mg 1 5.21 5 S 110 5.16 5 C 17102 2.51 5 N 4878 2.21 5 O 5433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 27584 Number of models: 1 Model: "" Number of chains: 10 Chain: "N" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 392 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain breaks: 1 Chain: "T" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 550 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "F" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1292 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "B" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1772 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 219} Chain: "C" Number of atoms: 10407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10407 Classifications: {'peptide': 1319} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1263} Chain breaks: 1 Chain: "D" Number of atoms: 10545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10545 Classifications: {'peptide': 1358} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1302} 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: "R" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 273 Classifications: {'RNA': 13} Modifications used: {'5*END': 1, 'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna3p': 12} 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 16630 SG CYS D 70 25.909 113.557 81.696 1.00128.74 S ATOM 16644 SG CYS D 72 24.797 116.651 82.496 1.00136.84 S ATOM 16752 SG CYS D 85 23.214 115.722 79.449 1.00118.16 S ATOM 16776 SG CYS D 88 26.754 115.071 78.842 1.00125.83 S ATOM 22464 SG CYS D 814 39.097 46.502 76.882 1.00 84.54 S ATOM 23029 SG CYS D 888 40.073 50.366 75.923 1.00 80.97 S ATOM 23080 SG CYS D 895 39.924 48.992 79.099 1.00 61.94 S ATOM 23101 SG CYS D 898 42.377 47.050 78.005 1.00 59.82 S Time building chain proxies: 6.08, per 1000 atoms: 0.22 Number of scatterers: 27584 At special positions: 0 Unit cell: (136.4, 151.8, 166.1, 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 110 16.00 P 58 15.00 Mg 1 11.99 O 5433 8.00 N 4878 7.00 C 17102 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: 2.52 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " Number of angles added : 12 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6210 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 54 sheets defined 38.6% alpha, 13.4% beta 23 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'F' and resid 7 through 25 removed outlier: 3.702A pdb=" N GLU F 25 " --> pdb=" O LEU F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 38 removed outlier: 3.704A pdb=" N VAL F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER F 38 " --> pdb=" O THR F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 71 Processing helix chain 'F' and resid 122 through 127 Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.985A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.617A 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 157 through 162 Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 230 through 233 removed outlier: 4.150A pdb=" N ASP A 233 " --> pdb=" O ALA A 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 230 through 233' Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 154 through 161 removed outlier: 4.035A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.603A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 163 through 167 removed outlier: 4.124A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 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 281 removed outlier: 3.879A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.645A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 294' Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.536A pdb=" N ARG C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 386 Processing helix chain 'C' and resid 398 through 408 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 480 Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 removed outlier: 4.033A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 549 Processing helix chain 'C' and resid 608 through 614 Processing helix chain 'C' and resid 657 through 661 removed outlier: 4.127A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 666 removed outlier: 3.545A pdb=" N SER C 666 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.513A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 688 removed outlier: 3.589A pdb=" N ALA C 679 " --> pdb=" O ASP C 675 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 removed outlier: 3.971A pdb=" N VAL C 708 " --> pdb=" O MET C 704 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C 712 " --> pdb=" O VAL C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 826 removed outlier: 4.086A pdb=" N GLU C 825 " --> pdb=" O ARG C 821 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP C 826 " --> pdb=" O VAL C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 865 removed outlier: 3.721A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU C 865 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 980 removed outlier: 3.884A pdb=" N LEU C 946 " --> pdb=" O ASP C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 990 removed outlier: 4.257A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.840A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN C1038 " --> pdb=" O ARG C1034 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.638A pdb=" N MET C1085 " --> pdb=" O ILE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.152A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.852A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 4.084A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.886A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE C1164 " --> pdb=" O LEU C1161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1160 through 1164' Processing helix chain 'C' and resid 1167 through 1177 Processing helix chain 'C' and resid 1185 through 1189 removed outlier: 3.766A pdb=" N ASP C1188 " --> pdb=" O PRO C1185 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY C1189 " --> pdb=" O VAL C1186 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1185 through 1189' Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 removed outlier: 3.533A pdb=" N ASP C1241 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1297 through 1309 Processing helix chain 'C' and resid 1321 through 1332 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.607A pdb=" N ARG D 98 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.574A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 264 through 286 removed outlier: 4.292A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.721A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 337 through 342 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 removed outlier: 3.780A pdb=" N ALA D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 417 removed outlier: 4.310A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) 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 450 through 454 removed outlier: 3.739A pdb=" N VAL D 453 " --> pdb=" O HIS D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 485 removed outlier: 3.961A pdb=" N MET D 485 " --> pdb=" O ARG D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 489 Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.776A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 593 Processing helix chain 'D' and resid 597 through 613 removed outlier: 3.939A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY D 613 " --> pdb=" O TYR D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.909A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.348A 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 802 removed outlier: 3.765A pdb=" N TYR D 772 " --> pdb=" O ASN D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 874 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 940 through 946 removed outlier: 3.600A pdb=" N ALA D 945 " --> pdb=" O ALA D 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 1051 through 1055 removed outlier: 3.739A pdb=" N THR D1054 " --> pdb=" O ASP D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 4.083A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 Processing helix chain 'D' and resid 1282 through 1295 removed outlier: 3.666A pdb=" N ASN D1295 " --> pdb=" O GLU D1291 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1319 through 1324 Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1347 through 1354 Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 4.006A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG D1373 " --> pdb=" O ARG D1369 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.625A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 73 Processing sheet with id=AA1, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.683A pdb=" N TRP F 90 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE F 153 " --> pdb=" O TRP F 90 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU F 92 " --> pdb=" O ASN F 151 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 137 " --> pdb=" O TRP F 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 140 through 141 Processing sheet with id=AA4, first strand: chain 'A' and resid 12 through 17 removed outlier: 5.184A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 24 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 104 removed outlier: 7.613A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA7, first strand: chain 'A' and resid 108 through 111 removed outlier: 4.007A pdb=" N GLY A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 133 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.762A pdb=" N TYR A 177 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 13 through 18 removed outlier: 6.452A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU B 198 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA B 189 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 97 through 101 removed outlier: 6.906A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AB3, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AB4, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB5, first strand: chain 'C' and resid 13 through 14 removed outlier: 7.323A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 59 through 60 removed outlier: 7.048A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 59 through 60 removed outlier: 7.048A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AB9, first strand: chain 'C' and resid 451 through 453 removed outlier: 6.558A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AC2, first strand: chain 'C' and resid 195 through 196 Processing sheet with id=AC3, first strand: chain 'C' and resid 227 through 230 removed outlier: 3.633A pdb=" N VAL C 228 " --> pdb=" O THR C 335 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.459A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.808A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.808A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 623 through 624 removed outlier: 4.411A pdb=" N HIS C 628 " --> pdb=" O ASP C 624 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 716 through 717 removed outlier: 3.787A pdb=" N ALA C 784 " --> pdb=" O ALA C 716 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.006A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.731A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AD3, first strand: chain 'C' and resid 801 through 804 removed outlier: 4.717A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 818 through 819 removed outlier: 7.318A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 830 through 832 removed outlier: 3.580A pdb=" N ARG C1058 " --> pdb=" O THR C 830 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 835 through 839 Processing sheet with id=AD7, first strand: chain 'C' and resid 842 through 843 removed outlier: 3.820A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 882 through 884 removed outlier: 3.587A pdb=" N VAL C 884 " --> pdb=" O LEU C 918 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AE1, first strand: chain 'C' and resid 1066 through 1067 Processing sheet with id=AE2, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 4.046A pdb=" N GLY D 351 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AE4, first strand: chain 'C' and resid 1335 through 1338 Processing sheet with id=AE5, first strand: chain 'D' and resid 36 through 37 removed outlier: 7.035A pdb=" N GLY D 36 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N GLU D 106 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 242 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.848A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AE7, first strand: chain 'D' and resid 366 through 369 removed outlier: 6.436A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'D' and resid 526 through 527 removed outlier: 7.382A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 706 through 707 removed outlier: 3.739A pdb=" N ILE D 707 " --> pdb=" O GLU D 714 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AF2, first strand: chain 'D' and resid 825 through 826 removed outlier: 7.199A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 848 through 849 removed outlier: 6.719A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 991 through 995 removed outlier: 4.230A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 965 through 967 removed outlier: 3.988A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 1098 through 1100 removed outlier: 3.562A pdb=" N GLY D1033 " --> pdb=" O ILE D1115 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 1046 through 1047 Processing sheet with id=AF8, first strand: chain 'D' and resid 1162 through 1164 Processing sheet with id=AF9, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.914A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 1050 hydrogen bonds defined for protein. 2877 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 6.50 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7233 1.33 - 1.45: 4756 1.45 - 1.57: 15831 1.57 - 1.69: 113 1.69 - 1.81: 191 Bond restraints: 28124 Sorted by residual: bond pdb=" C SER A 178 " pdb=" N PRO A 179 " ideal model delta sigma weight residual 1.334 1.277 0.057 8.40e-03 1.42e+04 4.60e+01 bond pdb=" CA LEU C 448 " pdb=" C LEU C 448 " ideal model delta sigma weight residual 1.523 1.449 0.074 1.34e-02 5.57e+03 3.08e+01 bond pdb=" C MET C1085 " pdb=" N PRO C1086 " ideal model delta sigma weight residual 1.332 1.281 0.051 1.12e-02 7.97e+03 2.07e+01 bond pdb=" CA CYS D 454 " pdb=" C CYS D 454 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.34e-02 5.57e+03 2.02e+01 bond pdb=" CA MET D 581 " pdb=" C MET D 581 " ideal model delta sigma weight residual 1.523 1.444 0.079 1.80e-02 3.09e+03 1.93e+01 ... (remaining 28119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.33: 38130 5.33 - 10.66: 98 10.66 - 15.99: 8 15.99 - 21.32: 0 21.32 - 26.66: 2 Bond angle restraints: 38238 Sorted by residual: angle pdb=" O3' DC T 2 " pdb=" P DA T 3 " pdb=" OP2 DA T 3 " ideal model delta sigma weight residual 108.00 81.34 26.66 3.00e+00 1.11e-01 7.89e+01 angle pdb=" O3' DC T 2 " pdb=" P DA T 3 " pdb=" OP1 DA T 3 " ideal model delta sigma weight residual 108.00 84.53 23.47 3.00e+00 1.11e-01 6.12e+01 angle pdb=" C GLY D 586 " pdb=" N LEU D 587 " pdb=" CA LEU D 587 " ideal model delta sigma weight residual 122.48 111.16 11.32 1.62e+00 3.81e-01 4.88e+01 angle pdb=" C SER D 503 " pdb=" N GLN D 504 " pdb=" CA GLN D 504 " ideal model delta sigma weight residual 121.63 108.42 13.21 1.91e+00 2.74e-01 4.79e+01 angle pdb=" OP1 DA T 3 " pdb=" P DA T 3 " pdb=" OP2 DA T 3 " ideal model delta sigma weight residual 120.00 134.57 -14.57 3.00e+00 1.11e-01 2.36e+01 ... (remaining 38233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 16966 35.19 - 70.39: 206 70.39 - 105.58: 17 105.58 - 140.77: 1 140.77 - 175.97: 1 Dihedral angle restraints: 17191 sinusoidal: 7530 harmonic: 9661 Sorted by residual: dihedral pdb=" O4' U R 13 " pdb=" C1' U R 13 " pdb=" N1 U R 13 " pdb=" C2 U R 13 " ideal model delta sinusoidal sigma weight residual -160.00 -68.41 -91.59 1 1.50e+01 4.44e-03 4.38e+01 dihedral pdb=" CA THR C 757 " pdb=" C THR C 757 " pdb=" N ARG C 758 " pdb=" CA ARG C 758 " ideal model delta harmonic sigma weight residual -180.00 -152.13 -27.87 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual -180.00 -153.43 -26.57 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 17188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.398: 4353 0.398 - 0.796: 0 0.796 - 1.193: 0 1.193 - 1.591: 0 1.591 - 1.989: 1 Chirality restraints: 4354 Sorted by residual: chirality pdb=" P DA T 3 " pdb=" OP1 DA T 3 " pdb=" OP2 DA T 3 " pdb=" O5' DA T 3 " both_signs ideal model delta sigma weight residual True 2.35 0.36 1.99 2.00e-01 2.50e+01 9.89e+01 chirality pdb=" CA GLN C 659 " pdb=" N GLN C 659 " pdb=" C GLN C 659 " pdb=" CB GLN C 659 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB ILE C 11 " pdb=" CA ILE C 11 " pdb=" CG1 ILE C 11 " pdb=" CG2 ILE C 11 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 4351 not shown) Planarity restraints: 4805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 368 " 0.055 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO D 369 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO D 369 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 369 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 29 " 0.051 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO A 30 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 589 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO C 590 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 590 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 590 " 0.039 5.00e-02 4.00e+02 ... (remaining 4802 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 271 2.58 - 3.16: 24745 3.16 - 3.74: 38814 3.74 - 4.32: 52856 4.32 - 4.90: 84516 Nonbonded interactions: 201202 Sorted by model distance: nonbonded pdb=" N2 DG N 38 " pdb=" O2 DC T 2 " model vdw 1.995 3.120 nonbonded pdb=" OP1 U R 11 " pdb="MG MG D1503 " model vdw 2.002 2.170 nonbonded pdb=" OG1 THR D 790 " pdb=" O2' U R 12 " model vdw 2.069 3.040 nonbonded pdb=" O GLY C 747 " pdb=" NH2 ARG C 974 " model vdw 2.090 3.120 nonbonded pdb=" OG SER C 318 " pdb=" OD1 ASP C 320 " model vdw 2.104 3.040 ... (remaining 201197 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 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 31.300 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 : 0.009 0.125 28132 Z= 0.423 Angle : 1.057 39.502 38250 Z= 0.547 Chirality : 0.059 1.989 4354 Planarity : 0.006 0.084 4805 Dihedral : 11.714 175.967 10981 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 13.65 % Favored : 86.32 % Rotamer: Outliers : 0.07 % Allowed : 1.05 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.38 (0.12), residues: 3349 helix: -1.90 (0.13), residues: 1125 sheet: -2.52 (0.22), residues: 404 loop : -3.83 (0.11), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 10 TYR 0.029 0.003 TYR C1053 PHE 0.030 0.003 PHE C 828 TRP 0.026 0.003 TRP C 183 HIS 0.009 0.002 HIS C1070 Details of bonding type rmsd covalent geometry : bond 0.00911 (28124) covalent geometry : angle 0.99129 (38238) hydrogen bonds : bond 0.12513 ( 1098) hydrogen bonds : angle 6.34439 ( 2997) metal coordination : bond 0.05652 ( 8) metal coordination : angle 20.75720 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 605 time to evaluate : 1.156 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: F 76 ASP cc_start: 0.7156 (t0) cc_final: 0.6933 (t0) REVERT: B 66 HIS cc_start: 0.6972 (t70) cc_final: 0.5720 (t-90) REVERT: C 241 LEU cc_start: 0.8021 (tp) cc_final: 0.7804 (tt) REVERT: C 247 ARG cc_start: 0.7742 (ttm-80) cc_final: 0.7492 (ptt90) REVERT: C 357 ASN cc_start: 0.8911 (t0) cc_final: 0.8320 (m-40) REVERT: D 137 ARG cc_start: 0.8231 (mtp85) cc_final: 0.7934 (mtp85) REVERT: D 564 VAL cc_start: 0.8781 (t) cc_final: 0.8581 (t) REVERT: D 1121 LEU cc_start: 0.8316 (mt) cc_final: 0.8051 (mt) outliers start: 2 outliers final: 0 residues processed: 606 average time/residue: 0.2165 time to fit residues: 197.7337 Evaluate side-chains 282 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.0980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.0870 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 20.0000 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 84 ASN B 132 HIS C 65 ASN C 69 GLN C 150 HIS C 330 HIS C 437 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C 811 ASN C1116 HIS C1157 GLN C1268 GLN C1313 HIS D 232 ASN D 266 ASN D 365 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN D 929 GLN D1010 GLN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.105509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.078740 restraints weight = 64741.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.079542 restraints weight = 39102.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.079819 restraints weight = 28504.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.080139 restraints weight = 26947.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.080321 restraints weight = 23290.884| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28132 Z= 0.131 Angle : 0.698 26.153 38250 Z= 0.348 Chirality : 0.053 1.982 4354 Planarity : 0.005 0.062 4805 Dihedral : 12.846 179.241 4390 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.05 % Allowed : 8.66 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.14), residues: 3349 helix: 0.27 (0.15), residues: 1135 sheet: -1.95 (0.24), residues: 402 loop : -3.07 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 388 TYR 0.016 0.001 TYR D 679 PHE 0.034 0.001 PHE D1037 TRP 0.012 0.001 TRP F 35 HIS 0.005 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00277 (28124) covalent geometry : angle 0.68882 (38238) hydrogen bonds : bond 0.04912 ( 1098) hydrogen bonds : angle 4.61368 ( 2997) metal coordination : bond 0.00767 ( 8) metal coordination : angle 6.57121 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 358 time to evaluate : 1.208 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: F 76 ASP cc_start: 0.7387 (t0) cc_final: 0.7119 (t0) REVERT: F 109 ASP cc_start: 0.7958 (m-30) cc_final: 0.7714 (m-30) REVERT: B 145 LYS cc_start: 0.8555 (ttmm) cc_final: 0.8295 (ttmm) REVERT: C 239 MET cc_start: 0.8577 (tmm) cc_final: 0.8297 (ppp) REVERT: C 247 ARG cc_start: 0.7851 (ttm-80) cc_final: 0.7642 (ptm160) REVERT: C 357 ASN cc_start: 0.8830 (t0) cc_final: 0.8388 (m-40) REVERT: C 915 ASP cc_start: 0.8194 (t0) cc_final: 0.7706 (m-30) REVERT: C 997 TRP cc_start: 0.7099 (m-10) cc_final: 0.6681 (m-90) REVERT: D 1189 MET cc_start: 0.8037 (tmm) cc_final: 0.7762 (tmm) REVERT: E 12 LYS cc_start: 0.8458 (tppt) cc_final: 0.8184 (tppt) outliers start: 30 outliers final: 15 residues processed: 378 average time/residue: 0.1949 time to fit residues: 116.6096 Evaluate side-chains 259 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 244 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 797 THR Chi-restraints excluded: chain D residue 936 HIS Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 32 optimal weight: 7.9990 chunk 217 optimal weight: 7.9990 chunk 270 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 209 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 228 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 271 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 151 ASN C 437 ASN C 580 GLN ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 GLN D 365 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN D 936 HIS ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.099385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.072090 restraints weight = 66353.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.072520 restraints weight = 43531.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.072830 restraints weight = 32836.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.073465 restraints weight = 29609.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.073512 restraints weight = 26164.167| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 28132 Z= 0.238 Angle : 0.736 27.729 38250 Z= 0.368 Chirality : 0.054 1.912 4354 Planarity : 0.005 0.096 4805 Dihedral : 12.888 177.847 4390 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.79 % Allowed : 10.86 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.14), residues: 3349 helix: 0.74 (0.16), residues: 1143 sheet: -1.41 (0.24), residues: 431 loop : -2.91 (0.13), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 542 TYR 0.019 0.002 TYR D 723 PHE 0.018 0.002 PHE F 112 TRP 0.020 0.002 TRP C 183 HIS 0.009 0.001 HIS D 545 Details of bonding type rmsd covalent geometry : bond 0.00557 (28124) covalent geometry : angle 0.73078 (38238) hydrogen bonds : bond 0.05860 ( 1098) hydrogen bonds : angle 4.65585 ( 2997) metal coordination : bond 0.01292 ( 8) metal coordination : angle 4.87671 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 226 time to evaluate : 1.078 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: F 72 LEU cc_start: 0.9020 (mt) cc_final: 0.8466 (mt) REVERT: A 117 HIS cc_start: 0.6286 (p-80) cc_final: 0.5901 (p-80) REVERT: A 207 THR cc_start: 0.8493 (m) cc_final: 0.8107 (p) REVERT: C 108 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8006 (pm20) REVERT: C 239 MET cc_start: 0.8278 (tmm) cc_final: 0.8039 (ppp) REVERT: C 247 ARG cc_start: 0.7904 (ttm-80) cc_final: 0.7694 (ptm160) REVERT: C 315 MET cc_start: 0.7371 (mmm) cc_final: 0.7084 (mmm) REVERT: C 357 ASN cc_start: 0.8984 (t0) cc_final: 0.8463 (m-40) REVERT: C 515 MET cc_start: 0.8358 (ttp) cc_final: 0.8075 (ttp) REVERT: C 915 ASP cc_start: 0.8110 (t0) cc_final: 0.7759 (m-30) REVERT: D 248 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8069 (t0) REVERT: D 372 MET cc_start: 0.8868 (mtp) cc_final: 0.8577 (ttm) REVERT: D 402 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8207 (tm-30) REVERT: D 449 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8170 (tp) REVERT: D 479 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7769 (mm-30) REVERT: D 736 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8403 (mp10) REVERT: D 1126 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8256 (pt0) REVERT: D 1334 GLU cc_start: 0.8258 (tp30) cc_final: 0.7848 (tm-30) REVERT: E 68 GLU cc_start: 0.8706 (tp30) cc_final: 0.8318 (tp30) outliers start: 80 outliers final: 37 residues processed: 289 average time/residue: 0.1835 time to fit residues: 85.4314 Evaluate side-chains 246 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 936 HIS Chi-restraints excluded: chain D residue 1126 GLN Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 43 optimal weight: 3.9990 chunk 308 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 214 optimal weight: 0.7980 chunk 157 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 332 optimal weight: 4.9990 chunk 88 optimal weight: 20.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN D 450 HIS ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.099755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.072498 restraints weight = 66061.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.073106 restraints weight = 45601.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.073638 restraints weight = 30732.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.074522 restraints weight = 27025.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.074527 restraints weight = 23455.324| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28132 Z= 0.158 Angle : 0.647 27.239 38250 Z= 0.321 Chirality : 0.052 1.939 4354 Planarity : 0.004 0.064 4805 Dihedral : 12.761 179.190 4390 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.55 % Allowed : 12.08 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.14), residues: 3349 helix: 1.06 (0.16), residues: 1154 sheet: -1.06 (0.25), residues: 404 loop : -2.65 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1140 TYR 0.020 0.001 TYR F 64 PHE 0.013 0.001 PHE D 620 TRP 0.010 0.001 TRP C 183 HIS 0.009 0.001 HIS D 936 Details of bonding type rmsd covalent geometry : bond 0.00365 (28124) covalent geometry : angle 0.64451 (38238) hydrogen bonds : bond 0.04885 ( 1098) hydrogen bonds : angle 4.33938 ( 2997) metal coordination : bond 0.00907 ( 8) metal coordination : angle 3.45200 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 236 time to evaluate : 1.037 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: F 72 LEU cc_start: 0.8978 (mt) cc_final: 0.8514 (mt) REVERT: A 137 ASN cc_start: 0.8662 (p0) cc_final: 0.8267 (p0) REVERT: C 239 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7940 (ppp) REVERT: C 315 MET cc_start: 0.7306 (mmm) cc_final: 0.7083 (mmm) REVERT: C 331 LYS cc_start: 0.6870 (mmtm) cc_final: 0.6662 (mmtm) REVERT: C 357 ASN cc_start: 0.8884 (t0) cc_final: 0.8417 (m-40) REVERT: C 515 MET cc_start: 0.8289 (ttp) cc_final: 0.7917 (ttp) REVERT: C 696 ASP cc_start: 0.7698 (p0) cc_final: 0.6922 (t0) REVERT: D 479 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7546 (mm-30) REVERT: D 562 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6807 (pp20) REVERT: D 1184 ASP cc_start: 0.7216 (m-30) cc_final: 0.7001 (m-30) REVERT: D 1334 GLU cc_start: 0.8196 (tp30) cc_final: 0.7731 (tm-30) REVERT: E 48 VAL cc_start: 0.9234 (OUTLIER) cc_final: 0.8963 (p) REVERT: E 68 GLU cc_start: 0.8538 (tp30) cc_final: 0.8254 (tp30) outliers start: 73 outliers final: 41 residues processed: 289 average time/residue: 0.1866 time to fit residues: 86.7910 Evaluate side-chains 249 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 604 HIS Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 562 GLU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 44 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 chunk 101 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 222 optimal weight: 9.9990 chunk 320 optimal weight: 1.9990 chunk 229 optimal weight: 0.7980 chunk 220 optimal weight: 0.0010 chunk 308 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 618 GLN C 760 ASN D 792 ASN D1238 GLN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.100903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.073130 restraints weight = 65904.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.074746 restraints weight = 38575.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.075036 restraints weight = 25375.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.075382 restraints weight = 24611.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.075398 restraints weight = 21869.603| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28132 Z= 0.118 Angle : 0.610 27.227 38250 Z= 0.301 Chirality : 0.051 1.937 4354 Planarity : 0.004 0.063 4805 Dihedral : 12.634 178.840 4390 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.44 % Allowed : 13.58 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.14), residues: 3349 helix: 1.28 (0.16), residues: 1162 sheet: -0.87 (0.25), residues: 413 loop : -2.42 (0.13), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 67 TYR 0.014 0.001 TYR F 11 PHE 0.013 0.001 PHE F 103 TRP 0.009 0.001 TRP D 115 HIS 0.005 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00262 (28124) covalent geometry : angle 0.60816 (38238) hydrogen bonds : bond 0.04217 ( 1098) hydrogen bonds : angle 4.11785 ( 2997) metal coordination : bond 0.00629 ( 8) metal coordination : angle 2.62509 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 234 time to evaluate : 1.127 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: F 72 LEU cc_start: 0.8931 (mt) cc_final: 0.8400 (mt) REVERT: F 97 ASP cc_start: 0.8258 (m-30) cc_final: 0.7939 (p0) REVERT: A 137 ASN cc_start: 0.8696 (p0) cc_final: 0.8334 (p0) REVERT: C 108 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6965 (pm20) REVERT: C 239 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7645 (ppp) REVERT: C 357 ASN cc_start: 0.8978 (t0) cc_final: 0.8494 (m-40) REVERT: C 515 MET cc_start: 0.8210 (ttp) cc_final: 0.7777 (ttp) REVERT: C 516 ASP cc_start: 0.7296 (p0) cc_final: 0.6832 (p0) REVERT: C 696 ASP cc_start: 0.7748 (p0) cc_final: 0.6855 (t0) REVERT: D 151 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7247 (ppp) REVERT: D 449 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8160 (tp) REVERT: D 562 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6910 (pp20) REVERT: D 1184 ASP cc_start: 0.7520 (m-30) cc_final: 0.7241 (m-30) REVERT: E 48 VAL cc_start: 0.9214 (OUTLIER) cc_final: 0.8970 (p) REVERT: E 68 GLU cc_start: 0.8556 (tp30) cc_final: 0.8308 (tp30) REVERT: E 70 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8662 (tm-30) outliers start: 70 outliers final: 38 residues processed: 282 average time/residue: 0.1809 time to fit residues: 83.2912 Evaluate side-chains 249 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 206 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 562 GLU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 936 HIS Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 328 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 196 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 241 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 320 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 279 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 151 ASN C1023 HIS D 792 ASN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.098215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.070538 restraints weight = 66879.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.071139 restraints weight = 44101.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.071590 restraints weight = 30730.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.072106 restraints weight = 27971.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.072140 restraints weight = 25363.447| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28132 Z= 0.168 Angle : 0.644 27.558 38250 Z= 0.318 Chirality : 0.051 1.931 4354 Planarity : 0.004 0.061 4805 Dihedral : 12.663 179.444 4390 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.55 % Allowed : 14.24 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.14), residues: 3349 helix: 1.32 (0.16), residues: 1158 sheet: -0.78 (0.25), residues: 410 loop : -2.34 (0.13), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 67 TYR 0.026 0.001 TYR C 291 PHE 0.018 0.001 PHE F 103 TRP 0.018 0.001 TRP F 148 HIS 0.007 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00393 (28124) covalent geometry : angle 0.64218 (38238) hydrogen bonds : bond 0.04803 ( 1098) hydrogen bonds : angle 4.18687 ( 2997) metal coordination : bond 0.00839 ( 8) metal coordination : angle 2.53574 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 216 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 72 LEU cc_start: 0.8932 (mt) cc_final: 0.8407 (mt) REVERT: F 97 ASP cc_start: 0.8243 (m-30) cc_final: 0.7977 (p0) REVERT: C 142 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7775 (mm-30) REVERT: C 239 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7642 (ppp) REVERT: C 357 ASN cc_start: 0.8938 (t0) cc_final: 0.8458 (m110) REVERT: C 516 ASP cc_start: 0.7367 (p0) cc_final: 0.6868 (p0) REVERT: C 696 ASP cc_start: 0.7799 (p0) cc_final: 0.6982 (t0) REVERT: D 151 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.7211 (ppp) REVERT: D 449 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8077 (tp) REVERT: D 562 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6974 (pp20) REVERT: D 1025 MET cc_start: 0.8263 (tpp) cc_final: 0.7921 (tpp) REVERT: D 1184 ASP cc_start: 0.7663 (m-30) cc_final: 0.7302 (m-30) REVERT: E 48 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.8952 (p) REVERT: E 68 GLU cc_start: 0.8540 (tp30) cc_final: 0.8210 (tp30) outliers start: 73 outliers final: 48 residues processed: 273 average time/residue: 0.1741 time to fit residues: 77.8757 Evaluate side-chains 252 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 199 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 562 GLU Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 936 HIS Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 219 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 283 optimal weight: 0.8980 chunk 211 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 312 optimal weight: 3.9990 chunk 176 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 280 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 792 ASN D 951 GLN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.099752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.071965 restraints weight = 66544.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.072795 restraints weight = 42522.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.073503 restraints weight = 29075.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.073791 restraints weight = 26096.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.073890 restraints weight = 23840.060| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28132 Z= 0.120 Angle : 0.614 27.355 38250 Z= 0.302 Chirality : 0.051 1.938 4354 Planarity : 0.004 0.060 4805 Dihedral : 12.583 178.251 4390 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.34 % Allowed : 14.76 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: -0.96 (0.15), residues: 3349 helix: 1.42 (0.16), residues: 1166 sheet: -0.64 (0.26), residues: 398 loop : -2.18 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 67 TYR 0.018 0.001 TYR C 291 PHE 0.014 0.001 PHE F 103 TRP 0.014 0.001 TRP D1193 HIS 0.007 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00271 (28124) covalent geometry : angle 0.61336 (38238) hydrogen bonds : bond 0.04142 ( 1098) hydrogen bonds : angle 4.04825 ( 2997) metal coordination : bond 0.00572 ( 8) metal coordination : angle 2.12655 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 222 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 72 LEU cc_start: 0.8919 (mt) cc_final: 0.8429 (mt) REVERT: F 96 ASP cc_start: 0.5859 (m-30) cc_final: 0.5612 (m-30) REVERT: F 97 ASP cc_start: 0.8282 (m-30) cc_final: 0.8007 (p0) REVERT: A 80 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: A 137 ASN cc_start: 0.8741 (p0) cc_final: 0.8201 (p0) REVERT: B 71 LYS cc_start: 0.7560 (mmmt) cc_final: 0.7347 (mmtt) REVERT: C 142 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7818 (mm-30) REVERT: C 239 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7634 (ppp) REVERT: C 357 ASN cc_start: 0.8983 (t0) cc_final: 0.8495 (m110) REVERT: C 515 MET cc_start: 0.8181 (ttp) cc_final: 0.7924 (ttp) REVERT: C 516 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6814 (p0) REVERT: C 696 ASP cc_start: 0.7744 (p0) cc_final: 0.6907 (t0) REVERT: C 1329 GLU cc_start: 0.7689 (tt0) cc_final: 0.7030 (tt0) REVERT: D 151 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7232 (ppp) REVERT: D 295 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7636 (tt0) REVERT: D 375 GLU cc_start: 0.7800 (tp30) cc_final: 0.7582 (tp30) REVERT: D 449 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8106 (tp) REVERT: D 479 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7538 (mm-30) REVERT: D 562 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6942 (pp20) REVERT: D 1025 MET cc_start: 0.8260 (tpp) cc_final: 0.7908 (tpp) REVERT: D 1184 ASP cc_start: 0.7666 (m-30) cc_final: 0.7346 (m-30) REVERT: E 48 VAL cc_start: 0.9244 (OUTLIER) cc_final: 0.8994 (p) REVERT: E 55 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6715 (mm-30) REVERT: E 68 GLU cc_start: 0.8546 (tp30) cc_final: 0.8197 (tp30) REVERT: E 70 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8628 (tm-30) outliers start: 67 outliers final: 46 residues processed: 274 average time/residue: 0.1725 time to fit residues: 77.8351 Evaluate side-chains 263 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 562 GLU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 936 HIS Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 42 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 240 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 overall best weight: 3.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.096638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.068712 restraints weight = 66374.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.069468 restraints weight = 44404.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.069780 restraints weight = 32395.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.070095 restraints weight = 29433.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.070246 restraints weight = 26559.946| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 28132 Z= 0.235 Angle : 0.703 27.780 38250 Z= 0.349 Chirality : 0.052 1.922 4354 Planarity : 0.004 0.059 4805 Dihedral : 12.785 179.308 4390 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.62 % Allowed : 14.87 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.14), residues: 3349 helix: 1.26 (0.16), residues: 1156 sheet: -0.82 (0.26), residues: 423 loop : -2.24 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 191 TYR 0.027 0.002 TYR C 291 PHE 0.017 0.002 PHE F 112 TRP 0.022 0.002 TRP C 183 HIS 0.008 0.001 HIS D 545 Details of bonding type rmsd covalent geometry : bond 0.00552 (28124) covalent geometry : angle 0.70179 (38238) hydrogen bonds : bond 0.05486 ( 1098) hydrogen bonds : angle 4.36213 ( 2997) metal coordination : bond 0.01125 ( 8) metal coordination : angle 2.47351 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 215 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 59 ASP cc_start: 0.8498 (t0) cc_final: 0.8115 (t0) REVERT: F 72 LEU cc_start: 0.9062 (mt) cc_final: 0.8825 (mt) REVERT: F 97 ASP cc_start: 0.8382 (m-30) cc_final: 0.8041 (p0) REVERT: A 80 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: C 239 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7682 (ppp) REVERT: C 515 MET cc_start: 0.8192 (ttp) cc_final: 0.7879 (ttp) REVERT: C 516 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.6902 (p0) REVERT: C 1329 GLU cc_start: 0.7718 (tt0) cc_final: 0.7441 (tt0) REVERT: D 151 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7287 (ppp) REVERT: D 192 MET cc_start: 0.8946 (ttm) cc_final: 0.8709 (ttm) REVERT: D 479 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7750 (mm-30) REVERT: D 562 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6886 (pp20) REVERT: D 698 MET cc_start: 0.8843 (mmm) cc_final: 0.8447 (mpp) REVERT: D 1025 MET cc_start: 0.8347 (tpp) cc_final: 0.8011 (tpp) REVERT: D 1184 ASP cc_start: 0.7667 (m-30) cc_final: 0.7368 (m-30) REVERT: E 41 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7913 (tm-30) REVERT: E 48 VAL cc_start: 0.9348 (OUTLIER) cc_final: 0.9077 (p) REVERT: E 68 GLU cc_start: 0.8626 (tp30) cc_final: 0.8257 (tp30) outliers start: 75 outliers final: 51 residues processed: 271 average time/residue: 0.1711 time to fit residues: 75.3876 Evaluate side-chains 264 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 207 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 562 GLU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 936 HIS Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 280 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 296 optimal weight: 8.9990 chunk 335 optimal weight: 10.0000 chunk 100 optimal weight: 0.4980 chunk 153 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 203 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 211 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.099490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.071493 restraints weight = 65894.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.072889 restraints weight = 40886.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.073381 restraints weight = 27143.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.073654 restraints weight = 25489.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.073737 restraints weight = 22810.942| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28132 Z= 0.121 Angle : 0.623 27.219 38250 Z= 0.306 Chirality : 0.051 1.944 4354 Planarity : 0.004 0.060 4805 Dihedral : 12.682 178.270 4390 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.92 % Allowed : 15.64 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: -0.89 (0.15), residues: 3349 helix: 1.41 (0.16), residues: 1168 sheet: -0.51 (0.27), residues: 385 loop : -2.10 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 69 TYR 0.027 0.001 TYR C 291 PHE 0.016 0.001 PHE D 176 TRP 0.011 0.001 TRP F 148 HIS 0.005 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00272 (28124) covalent geometry : angle 0.62237 (38238) hydrogen bonds : bond 0.04192 ( 1098) hydrogen bonds : angle 4.07418 ( 2997) metal coordination : bond 0.00582 ( 8) metal coordination : angle 2.13340 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 222 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 72 LEU cc_start: 0.9015 (mt) cc_final: 0.8549 (mt) REVERT: F 96 ASP cc_start: 0.5599 (m-30) cc_final: 0.5295 (m-30) REVERT: F 97 ASP cc_start: 0.8371 (m-30) cc_final: 0.8149 (p0) REVERT: A 80 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: A 137 ASN cc_start: 0.8628 (p0) cc_final: 0.8118 (p0) REVERT: C 142 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7845 (mm-30) REVERT: C 239 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7511 (ppp) REVERT: C 515 MET cc_start: 0.8143 (ttp) cc_final: 0.7846 (ttp) REVERT: C 516 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.6752 (p0) REVERT: C 696 ASP cc_start: 0.7866 (p0) cc_final: 0.7096 (t0) REVERT: C 1315 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8449 (ptp) REVERT: D 151 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7295 (ppp) REVERT: D 192 MET cc_start: 0.8996 (ttm) cc_final: 0.8717 (ttm) REVERT: D 562 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6877 (pp20) REVERT: D 709 ARG cc_start: 0.6892 (ptt90) cc_final: 0.6289 (ptt-90) REVERT: D 1025 MET cc_start: 0.8329 (tpp) cc_final: 0.8007 (tpp) REVERT: D 1184 ASP cc_start: 0.7609 (m-30) cc_final: 0.7366 (m-30) REVERT: E 41 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7860 (tm-30) REVERT: E 48 VAL cc_start: 0.9294 (OUTLIER) cc_final: 0.9040 (p) REVERT: E 68 GLU cc_start: 0.8528 (tp30) cc_final: 0.8202 (tp30) outliers start: 55 outliers final: 39 residues processed: 266 average time/residue: 0.1700 time to fit residues: 74.5586 Evaluate side-chains 255 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 209 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 562 GLU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 936 HIS Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 156 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.097320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.069559 restraints weight = 66106.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.070135 restraints weight = 44121.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.070811 restraints weight = 30573.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.071024 restraints weight = 27888.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.071152 restraints weight = 25322.808| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 28132 Z= 0.204 Angle : 0.686 27.658 38250 Z= 0.339 Chirality : 0.052 1.927 4354 Planarity : 0.004 0.059 4805 Dihedral : 12.760 179.740 4390 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.02 % Allowed : 15.46 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: -0.97 (0.15), residues: 3349 helix: 1.37 (0.16), residues: 1158 sheet: -0.77 (0.26), residues: 414 loop : -2.10 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 542 TYR 0.028 0.002 TYR C 291 PHE 0.015 0.001 PHE F 112 TRP 0.033 0.002 TRP D1193 HIS 0.007 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00478 (28124) covalent geometry : angle 0.68535 (38238) hydrogen bonds : bond 0.05102 ( 1098) hydrogen bonds : angle 4.26367 ( 2997) metal coordination : bond 0.00996 ( 8) metal coordination : angle 2.24750 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 204 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 96 ASP cc_start: 0.5613 (m-30) cc_final: 0.5310 (m-30) REVERT: F 97 ASP cc_start: 0.8186 (m-30) cc_final: 0.7906 (p0) REVERT: A 80 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: C 142 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7857 (mm-30) REVERT: C 239 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7627 (ppp) REVERT: C 515 MET cc_start: 0.8181 (ttp) cc_final: 0.7866 (ttp) REVERT: C 516 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6849 (p0) REVERT: D 151 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7295 (ppp) REVERT: D 562 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6919 (pp20) REVERT: D 1025 MET cc_start: 0.8335 (tpp) cc_final: 0.8025 (tpp) REVERT: D 1184 ASP cc_start: 0.7610 (m-30) cc_final: 0.7380 (m-30) REVERT: E 48 VAL cc_start: 0.9335 (OUTLIER) cc_final: 0.9060 (p) REVERT: E 68 GLU cc_start: 0.8631 (tp30) cc_final: 0.8378 (tp30) outliers start: 58 outliers final: 45 residues processed: 251 average time/residue: 0.1762 time to fit residues: 72.9499 Evaluate side-chains 250 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 199 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 562 GLU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 936 HIS Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1172 LYS Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 218 optimal weight: 0.0980 chunk 210 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 264 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN D 929 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.099040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.070945 restraints weight = 65740.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.072295 restraints weight = 40419.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.072738 restraints weight = 27113.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.073018 restraints weight = 26241.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.073053 restraints weight = 23565.788| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28132 Z= 0.135 Angle : 0.638 27.405 38250 Z= 0.313 Chirality : 0.051 1.939 4354 Planarity : 0.004 0.060 4805 Dihedral : 12.644 178.828 4390 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.78 % Allowed : 15.64 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: -0.80 (0.15), residues: 3349 helix: 1.49 (0.16), residues: 1158 sheet: -0.54 (0.27), residues: 401 loop : -2.02 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 69 TYR 0.033 0.001 TYR C 291 PHE 0.015 0.001 PHE D 176 TRP 0.012 0.001 TRP D1193 HIS 0.006 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00309 (28124) covalent geometry : angle 0.63682 (38238) hydrogen bonds : bond 0.04420 ( 1098) hydrogen bonds : angle 4.09955 ( 2997) metal coordination : bond 0.00632 ( 8) metal coordination : angle 2.04499 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4028.23 seconds wall clock time: 70 minutes 40.01 seconds (4240.01 seconds total)