Starting phenix.real_space_refine on Mon Sep 14 03:42:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rin_4892/09_2026/6rin_4892.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rin_4892/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6rin_4892/09_2026/6rin_4892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rin_4892/09_2026/6rin_4892.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6rin_4892/09_2026/6rin_4892.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rin_4892/09_2026/6rin_4892.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rin_4892/09_2026/6rin_4892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rin_4892/09_2026/6rin_4892.map" } 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): 0.14s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNAv2': 13} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 6.13, 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: 2.89 Conformation dependent library (CDL) restraints added in 1.2 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: 3.49 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: 7.22 Time building geometry restraints manager: 3.65 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=" O4' DC T 16 " pdb=" C4' DC T 16 " pdb=" C3' DC T 16 " ideal model delta sigma weight residual 106.00 102.92 3.08 6.00e-01 2.78e+00 2.64e+01 ... (remaining 38233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 16933 35.19 - 70.39: 193 70.39 - 105.58: 13 105.58 - 140.77: 1 140.77 - 175.97: 1 Dihedral angle restraints: 17141 sinusoidal: 7480 harmonic: 9661 Sorted by residual: dihedral pdb=" O5' G R 10 " pdb=" C5' G R 10 " pdb=" C4' G R 10 " pdb=" C3' G R 10 " ideal model delta sinusoidal sigma weight residual 180.00 139.16 40.84 3 6.40e+00 2.44e-02 4.00e+01 dihedral pdb=" O5' U R 13 " pdb=" C5' U R 13 " pdb=" C4' U R 13 " pdb=" C3' U R 13 " ideal model delta sinusoidal sigma weight residual -180.00 -143.12 -36.88 3 6.40e+00 2.44e-02 3.52e+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 ... (remaining 17138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.396: 4353 0.396 - 0.791: 0 0.791 - 1.187: 0 1.187 - 1.583: 0 1.583 - 1.978: 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 2.34 0.36 1.98 2.00e-01 2.50e+01 9.79e+01 chirality pdb=" P U R 13 " pdb=" OP1 U R 13 " pdb=" OP2 U R 13 " pdb=" O5' U R 13 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.57e+00 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 ... (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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 33.730 Find NCS groups from input model: 0.380 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 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= 0.457 Angle : 1.068 39.502 38250 Z= 0.574 Chirality : 0.061 1.978 4354 Planarity : 0.006 0.084 4805 Dihedral : 11.434 175.967 10931 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/Z covalent geometry : bond 0.00917 / 0.46 (28124) covalent geometry : angle 1.00279 / 0.57 (38238) hydrogen bonds : bond 0.12513 / 13.72 ( 1098) hydrogen bonds : angle 6.34439 / 6.77 ( 2997) metal coordination : bond 0.05652 / 5.65 ( 8) metal coordination : angle 20.75720 / 38.91 ( 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 : 1.066 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: 0.2189 time to fit residues: 200.9078 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 : 1.077 ------------------------------------------------------------------------------- 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... ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 23 HIS B 84 ASN C 65 ASN C 69 GLN C 150 HIS C 330 HIS C 406 ASN C 437 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 HIS C 811 ASN C1080 ASN C1116 HIS C1268 GLN C1313 HIS D 232 ASN D 266 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS D 792 ASN D 929 GLN D 936 HIS D 951 GLN D1010 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.104604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.078348 restraints weight = 64654.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.078983 restraints weight = 44056.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.079223 restraints weight = 35437.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.079529 restraints weight = 30497.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.079790 restraints weight = 26606.994| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28132 Z= 0.157 Angle : 0.765 24.353 38250 Z= 0.386 Chirality : 0.056 2.042 4354 Planarity : 0.006 0.091 4805 Dihedral : 12.439 179.731 4340 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.61 % Allowed : 8.31 % Favored : 90.09 % 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: -2.79 (0.13), residues: 3349 helix: -0.05 (0.15), residues: 1130 sheet: -1.99 (0.23), residues: 411 loop : -3.17 (0.12), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 978 TYR 0.016 0.002 TYR C1229 PHE 0.031 0.002 PHE D1037 TRP 0.012 0.002 TRP F 35 HIS 0.008 0.001 HIS D 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (28124) covalent geometry : angle 0.75332 / 0.39 (38238) hydrogen bonds : bond 0.05968 / 6.39 ( 1098) hydrogen bonds : angle 4.92132 / 5.09 ( 2997) metal coordination : bond 0.01208 / 1.16 ( 8) metal coordination : angle 7.41038 / 14.65 ( 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 383 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 337 time to evaluate : 1.141 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 69 MET cc_start: 0.8043 (tpp) cc_final: 0.7652 (mmt) REVERT: F 76 ASP cc_start: 0.7192 (t0) cc_final: 0.6946 (t0) REVERT: F 109 ASP cc_start: 0.7813 (m-30) cc_final: 0.7608 (m-30) REVERT: A 137 ASN cc_start: 0.8685 (p0) cc_final: 0.8256 (p0) REVERT: B 145 LYS cc_start: 0.8536 (ttmm) cc_final: 0.8261 (ttmm) REVERT: C 241 LEU cc_start: 0.8062 (tp) cc_final: 0.7838 (tt) REVERT: C 357 ASN cc_start: 0.8785 (t0) cc_final: 0.8288 (m110) REVERT: C 472 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8251 (tm-30) REVERT: C 515 MET cc_start: 0.8185 (ttp) cc_final: 0.7977 (ttp) REVERT: C 915 ASP cc_start: 0.8078 (t0) cc_final: 0.7725 (m-30) REVERT: C 1290 MET cc_start: 0.8751 (tpp) cc_final: 0.8175 (tpp) REVERT: D 1189 MET cc_start: 0.7975 (tmm) cc_final: 0.7745 (tmm) REVERT: E 12 LYS cc_start: 0.8394 (tppt) cc_final: 0.8090 (tppt) outliers start: 46 outliers final: 20 residues processed: 371 average time/residue: 0.1886 time to fit residues: 110.9909 Evaluate side-chains 260 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 240 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 1330 ILE Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 789 LYS Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 936 HIS Chi-restraints excluded: chain D residue 1175 LEU 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: 8.9990 chunk 217 optimal weight: 8.9990 chunk 270 optimal weight: 0.9990 chunk 15 optimal weight: 0.0770 chunk 209 optimal weight: 8.9990 chunk 51 optimal weight: 0.0970 chunk 191 optimal weight: 6.9990 chunk 228 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 271 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 overall best weight: 1.3740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN C 437 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN D 365 GLN D 792 ASN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.102936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.076275 restraints weight = 66400.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.076665 restraints weight = 45399.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.077048 restraints weight = 36916.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.077406 restraints weight = 30785.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.077604 restraints weight = 27747.293| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28132 Z= 0.148 Angle : 0.697 25.729 38250 Z= 0.352 Chirality : 0.054 1.963 4354 Planarity : 0.005 0.080 4805 Dihedral : 12.258 178.498 4340 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 1.85 % Allowed : 10.96 % Favored : 87.19 % 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: -2.17 (0.14), residues: 3349 helix: 0.59 (0.16), residues: 1139 sheet: -1.63 (0.24), residues: 420 loop : -2.91 (0.13), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 52 TYR 0.024 0.001 TYR F 77 PHE 0.019 0.001 PHE F 103 TRP 0.009 0.001 TRP D 409 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (28124) covalent geometry : angle 0.69005 / 0.35 (38238) hydrogen bonds : bond 0.05331 / 5.73 ( 1098) hydrogen bonds : angle 4.64526 / 4.81 ( 2997) metal coordination : bond 0.00801 / 0.76 ( 8) metal coordination : angle 5.46945 / 10.32 ( 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 311 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 258 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 69 MET cc_start: 0.8051 (tpp) cc_final: 0.7682 (mmt) REVERT: F 76 ASP cc_start: 0.7303 (t0) cc_final: 0.7086 (t0) REVERT: F 124 MET cc_start: 0.8472 (tmm) cc_final: 0.7707 (tmm) REVERT: A 191 ARG cc_start: 0.6138 (tpt90) cc_final: 0.5929 (tpt90) REVERT: B 145 LYS cc_start: 0.8563 (ttmm) cc_final: 0.8321 (ttmm) REVERT: C 239 MET cc_start: 0.8658 (tmm) cc_final: 0.8435 (ppp) REVERT: C 357 ASN cc_start: 0.8796 (t0) cc_final: 0.8365 (m-40) REVERT: C 472 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8222 (tm-30) REVERT: C 915 ASP cc_start: 0.8062 (t0) cc_final: 0.7744 (m-30) REVERT: C 997 TRP cc_start: 0.7148 (m-10) cc_final: 0.6752 (m-90) REVERT: D 114 ILE cc_start: 0.9268 (tt) cc_final: 0.9056 (tp) REVERT: D 304 ASP cc_start: 0.7761 (m-30) cc_final: 0.7508 (t0) REVERT: E 12 LYS cc_start: 0.8416 (tppt) cc_final: 0.8215 (tppt) REVERT: E 70 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8481 (tm-30) outliers start: 53 outliers final: 28 residues processed: 297 average time/residue: 0.1749 time to fit residues: 85.3605 Evaluate side-chains 255 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 82 LEU 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 247 ARG Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 43 ASN 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: 5.9990 chunk 308 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 221 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 332 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 151 ASN B 132 HIS C 618 GLN D 276 ASN D 365 GLN D 936 HIS ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.102334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.075490 restraints weight = 65954.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.075653 restraints weight = 45071.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.076172 restraints weight = 34044.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.076431 restraints weight = 30348.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.076603 restraints weight = 28058.912| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28132 Z= 0.150 Angle : 0.672 26.142 38250 Z= 0.337 Chirality : 0.053 1.941 4354 Planarity : 0.005 0.064 4805 Dihedral : 12.157 177.587 4340 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.16 % Allowed : 12.32 % Favored : 85.51 % 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: -1.75 (0.14), residues: 3349 helix: 0.91 (0.16), residues: 1144 sheet: -1.24 (0.24), residues: 406 loop : -2.68 (0.13), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 52 TYR 0.018 0.001 TYR F 64 PHE 0.021 0.001 PHE F 103 TRP 0.010 0.001 TRP D 409 HIS 0.006 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (28124) covalent geometry : angle 0.66797 / 0.34 (38238) hydrogen bonds : bond 0.04980 / 5.37 ( 1098) hydrogen bonds : angle 4.45879 / 4.63 ( 2997) metal coordination : bond 0.00805 / 0.75 ( 8) metal coordination : angle 4.23849 / 7.83 ( 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 300 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 238 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 124 MET cc_start: 0.8646 (tmm) cc_final: 0.8352 (tmm) REVERT: A 117 HIS cc_start: 0.6271 (p-80) cc_final: 0.5912 (p-80) REVERT: A 191 ARG cc_start: 0.6292 (tpt90) cc_final: 0.6058 (tpt90) REVERT: B 145 LYS cc_start: 0.8628 (ttmm) cc_final: 0.8412 (ttmm) REVERT: C 357 ASN cc_start: 0.8887 (t0) cc_final: 0.8398 (m-40) REVERT: C 370 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8115 (mtp) REVERT: C 472 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8349 (tm-30) REVERT: C 915 ASP cc_start: 0.8057 (t0) cc_final: 0.7790 (m-30) REVERT: C 997 TRP cc_start: 0.7113 (m-10) cc_final: 0.6682 (m-90) REVERT: D 995 TYR cc_start: 0.7434 (m-80) cc_final: 0.7215 (m-10) REVERT: E 68 GLU cc_start: 0.8500 (tp30) cc_final: 0.8162 (tp30) REVERT: E 70 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8507 (tm-30) outliers start: 62 outliers final: 34 residues processed: 284 average time/residue: 0.1728 time to fit residues: 80.7391 Evaluate side-chains 253 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 218 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE 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 32 LEU Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 1330 ILE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 281 ARG Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 518 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 697 MET Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 44 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 222 optimal weight: 9.9990 chunk 320 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 220 optimal weight: 0.0060 chunk 308 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 276 ASN D1249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.101104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.073624 restraints weight = 65778.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.074735 restraints weight = 39725.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.075300 restraints weight = 26898.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.075559 restraints weight = 25223.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.075620 restraints weight = 22841.139| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28132 Z= 0.158 Angle : 0.664 26.475 38250 Z= 0.332 Chirality : 0.053 1.933 4354 Planarity : 0.004 0.064 4805 Dihedral : 12.115 176.741 4340 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.30 % Allowed : 13.09 % Favored : 84.61 % 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: -1.49 (0.14), residues: 3349 helix: 1.06 (0.16), residues: 1151 sheet: -1.00 (0.25), residues: 403 loop : -2.51 (0.13), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 272 TYR 0.015 0.001 TYR F 64 PHE 0.024 0.001 PHE F 103 TRP 0.020 0.001 TRP F 148 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (28124) covalent geometry : angle 0.66138 / 0.33 (38238) hydrogen bonds : bond 0.04896 / 5.27 ( 1098) hydrogen bonds : angle 4.36776 / 4.53 ( 2997) metal coordination : bond 0.00797 / 0.74 ( 8) metal coordination : angle 3.46805 / 6.29 ( 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 297 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 231 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 124 MET cc_start: 0.8572 (tmm) cc_final: 0.8279 (tmm) REVERT: A 117 HIS cc_start: 0.6172 (p-80) cc_final: 0.5809 (p-80) REVERT: A 191 ARG cc_start: 0.6446 (tpt90) cc_final: 0.6216 (tpt90) REVERT: A 207 THR cc_start: 0.8465 (m) cc_final: 0.8115 (p) REVERT: B 145 LYS cc_start: 0.8649 (ttmm) cc_final: 0.8439 (ttpt) REVERT: C 108 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7880 (pm20) REVERT: C 331 LYS cc_start: 0.7139 (mmtt) cc_final: 0.6775 (mmtp) REVERT: C 357 ASN cc_start: 0.8878 (t0) cc_final: 0.8428 (m-40) REVERT: C 370 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7958 (mtp) REVERT: C 472 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8251 (tm-30) REVERT: C 915 ASP cc_start: 0.8072 (t0) cc_final: 0.7802 (m-30) REVERT: C 1170 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.8059 (tpp) REVERT: D 402 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8091 (tm-30) REVERT: D 995 TYR cc_start: 0.7382 (m-80) cc_final: 0.7166 (m-10) REVERT: E 70 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8505 (tm-30) REVERT: E 72 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8064 (tp40) outliers start: 66 outliers final: 39 residues processed: 277 average time/residue: 0.1681 time to fit residues: 76.9701 Evaluate side-chains 251 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE 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 124 VAL 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 142 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 518 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 697 MET Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain E residue 10 VAL 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: 3.9990 chunk 154 optimal weight: 0.9990 chunk 196 optimal weight: 0.0670 chunk 75 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 52 optimal weight: 0.0270 chunk 320 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 chunk 279 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 151 ASN B 117 HIS C1157 GLN D 276 ASN D 450 HIS E 43 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.102073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.073915 restraints weight = 65996.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.075268 restraints weight = 39405.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.075919 restraints weight = 25800.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.076161 restraints weight = 24427.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.076246 restraints weight = 22079.099| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28132 Z= 0.122 Angle : 0.633 26.459 38250 Z= 0.316 Chirality : 0.052 1.935 4354 Planarity : 0.004 0.062 4805 Dihedral : 12.055 175.904 4340 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.16 % Allowed : 14.00 % Favored : 83.84 % 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: -1.32 (0.14), residues: 3349 helix: 1.13 (0.16), residues: 1157 sheet: -0.82 (0.25), residues: 404 loop : -2.40 (0.13), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 52 TYR 0.014 0.001 TYR F 11 PHE 0.018 0.001 PHE F 103 TRP 0.010 0.001 TRP F 148 HIS 0.004 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (28124) covalent geometry : angle 0.63022 / 0.32 (38238) hydrogen bonds : bond 0.04508 / 4.86 ( 1098) hydrogen bonds : angle 4.23026 / 4.37 ( 2997) metal coordination : bond 0.00617 / 0.59 ( 8) metal coordination : angle 3.15555 / 5.79 ( 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 291 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 229 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 124 MET cc_start: 0.8679 (tmm) cc_final: 0.8367 (tmm) REVERT: A 117 HIS cc_start: 0.6332 (p-80) cc_final: 0.5986 (p-80) REVERT: A 207 THR cc_start: 0.8513 (m) cc_final: 0.8091 (p) REVERT: B 145 LYS cc_start: 0.8690 (ttmm) cc_final: 0.8470 (ttpt) REVERT: C 108 GLU cc_start: 0.8549 (tm-30) cc_final: 0.7982 (pm20) REVERT: C 331 LYS cc_start: 0.7279 (mmtt) cc_final: 0.6828 (mmtp) REVERT: C 357 ASN cc_start: 0.8935 (t0) cc_final: 0.8459 (m-40) REVERT: C 370 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7951 (mtp) REVERT: C 472 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8385 (tm-30) REVERT: C 915 ASP cc_start: 0.8078 (t0) cc_final: 0.7822 (m-30) REVERT: C 1290 MET cc_start: 0.8599 (tpp) cc_final: 0.8295 (tpp) REVERT: D 151 MET cc_start: 0.7604 (ppp) cc_final: 0.7101 (pmm) REVERT: D 402 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8110 (tm-30) REVERT: D 995 TYR cc_start: 0.7455 (m-80) cc_final: 0.7184 (m-10) REVERT: E 70 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8494 (tm-30) outliers start: 62 outliers final: 41 residues processed: 267 average time/residue: 0.1731 time to fit residues: 76.5450 Evaluate side-chains 248 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 151 ASN 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 B residue 124 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 219 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 283 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 312 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 280 optimal weight: 6.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 151 ASN C 406 ASN C1209 GLN D 276 ASN D 792 ASN ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.101150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.073600 restraints weight = 66001.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.074363 restraints weight = 41107.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.074947 restraints weight = 28748.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.075211 restraints weight = 26242.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.075317 restraints weight = 24147.952| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28132 Z= 0.155 Angle : 0.653 26.510 38250 Z= 0.325 Chirality : 0.052 1.935 4354 Planarity : 0.004 0.061 4805 Dihedral : 12.066 175.801 4340 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.48 % Allowed : 14.07 % Favored : 83.46 % 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: -1.28 (0.14), residues: 3349 helix: 1.14 (0.16), residues: 1157 sheet: -0.77 (0.25), residues: 405 loop : -2.36 (0.13), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 166 TYR 0.013 0.001 TYR F 11 PHE 0.014 0.001 PHE F 103 TRP 0.009 0.001 TRP C 183 HIS 0.006 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (28124) covalent geometry : angle 0.65141 / 0.32 (38238) hydrogen bonds : bond 0.04616 / 4.98 ( 1098) hydrogen bonds : angle 4.21991 / 4.36 ( 2997) metal coordination : bond 0.00743 / 0.70 ( 8) metal coordination : angle 2.87256 / 5.20 ( 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 284 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 213 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 124 MET cc_start: 0.8654 (tmm) cc_final: 0.8324 (tmm) REVERT: A 117 HIS cc_start: 0.6221 (p-80) cc_final: 0.5890 (p-80) REVERT: A 207 THR cc_start: 0.8499 (m) cc_final: 0.8035 (p) REVERT: C 108 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8016 (pm20) REVERT: C 331 LYS cc_start: 0.7218 (mmtt) cc_final: 0.6898 (mmtp) REVERT: C 357 ASN cc_start: 0.8913 (t0) cc_final: 0.8470 (m-40) REVERT: C 472 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8340 (tm-30) REVERT: C 915 ASP cc_start: 0.7996 (t0) cc_final: 0.7792 (m-30) REVERT: C 1170 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.8016 (tpp) REVERT: C 1290 MET cc_start: 0.8621 (tpp) cc_final: 0.8327 (tpp) REVERT: D 151 MET cc_start: 0.7620 (ppp) cc_final: 0.7117 (pmm) REVERT: D 402 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8102 (tm-30) REVERT: D 532 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: D 995 TYR cc_start: 0.7416 (m-80) cc_final: 0.7158 (m-10) REVERT: D 1184 ASP cc_start: 0.7405 (m-30) cc_final: 0.6998 (m-30) REVERT: D 1189 MET cc_start: 0.8165 (tmm) cc_final: 0.7880 (tpp) REVERT: E 70 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8561 (tm-30) REVERT: E 72 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8201 (tp40) outliers start: 71 outliers final: 52 residues processed: 263 average time/residue: 0.1719 time to fit residues: 75.4346 Evaluate side-chains 260 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 206 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain A residue 172 LEU 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 98 VAL Chi-restraints excluded: chain B residue 124 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 142 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 596 ASP 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 992 LEU Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 803 VAL 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 1175 LEU Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 ILE 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: 2.9990 chunk 91 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.0070 chunk 248 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 240 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN D 792 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.100929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.073199 restraints weight = 66204.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.074200 restraints weight = 39971.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.074745 restraints weight = 27441.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.075003 restraints weight = 25605.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.075103 restraints weight = 23370.498| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28132 Z= 0.145 Angle : 0.652 26.581 38250 Z= 0.323 Chirality : 0.052 1.934 4354 Planarity : 0.004 0.060 4805 Dihedral : 12.056 175.312 4340 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.20 % Allowed : 14.17 % Favored : 83.63 % 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: -1.17 (0.14), residues: 3349 helix: 1.19 (0.16), residues: 1156 sheet: -0.71 (0.25), residues: 405 loop : -2.26 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 170 TYR 0.013 0.001 TYR F 11 PHE 0.014 0.001 PHE F 103 TRP 0.012 0.001 TRP D1193 HIS 0.006 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (28124) covalent geometry : angle 0.65015 / 0.32 (38238) hydrogen bonds : bond 0.04583 / 4.95 ( 1098) hydrogen bonds : angle 4.17437 / 4.32 ( 2997) metal coordination : bond 0.00714 / 0.68 ( 8) metal coordination : angle 2.51819 / 4.58 ( 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 279 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 216 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 124 MET cc_start: 0.8628 (tmm) cc_final: 0.8252 (tmm) REVERT: A 117 HIS cc_start: 0.6218 (p-80) cc_final: 0.5918 (p-80) REVERT: A 207 THR cc_start: 0.8462 (m) cc_final: 0.8056 (p) REVERT: C 108 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8028 (pm20) REVERT: C 331 LYS cc_start: 0.7201 (mmtt) cc_final: 0.6919 (mmtp) REVERT: C 357 ASN cc_start: 0.8964 (t0) cc_final: 0.8500 (m-40) REVERT: C 472 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8371 (tm-30) REVERT: C 492 MET cc_start: 0.8229 (pmm) cc_final: 0.7965 (pmm) REVERT: C 915 ASP cc_start: 0.8000 (t0) cc_final: 0.7797 (m-30) REVERT: C 1290 MET cc_start: 0.8685 (tpp) cc_final: 0.8354 (tpp) REVERT: D 402 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8096 (tm-30) REVERT: D 532 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: D 995 TYR cc_start: 0.7446 (m-80) cc_final: 0.7123 (m-10) REVERT: D 1184 ASP cc_start: 0.7568 (m-30) cc_final: 0.7306 (m-30) REVERT: D 1189 MET cc_start: 0.8209 (tmm) cc_final: 0.7865 (tpp) REVERT: E 70 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8595 (tm-30) outliers start: 63 outliers final: 51 residues processed: 260 average time/residue: 0.1625 time to fit residues: 70.8110 Evaluate side-chains 258 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 206 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain A residue 172 LEU 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 124 VAL 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 142 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 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 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 D residue 139 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 803 VAL 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 1175 LEU Chi-restraints excluded: chain D residue 1243 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 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: 7.9990 chunk 115 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 296 optimal weight: 1.9990 chunk 335 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 153 optimal weight: 0.0970 chunk 48 optimal weight: 10.0000 chunk 203 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 276 ASN D 792 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.100461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.072641 restraints weight = 66252.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.073805 restraints weight = 40905.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.074326 restraints weight = 27263.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.074638 restraints weight = 25427.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.074709 restraints weight = 22939.320| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28132 Z= 0.155 Angle : 0.656 26.643 38250 Z= 0.324 Chirality : 0.052 1.932 4354 Planarity : 0.004 0.060 4805 Dihedral : 12.057 175.327 4340 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.09 % Allowed : 14.45 % Favored : 83.46 % 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: -1.10 (0.14), residues: 3349 helix: 1.21 (0.16), residues: 1156 sheet: -0.61 (0.26), residues: 401 loop : -2.20 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 88 TYR 0.014 0.001 TYR F 11 PHE 0.018 0.001 PHE F 112 TRP 0.014 0.001 TRP D1193 HIS 0.007 0.001 HIS D 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (28124) covalent geometry : angle 0.65433 / 0.32 (38238) hydrogen bonds : bond 0.04649 / 5.00 ( 1098) hydrogen bonds : angle 4.18129 / 4.33 ( 2997) metal coordination : bond 0.00767 / 0.73 ( 8) metal coordination : angle 2.34935 / 4.21 ( 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 271 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 211 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 72 LEU cc_start: 0.8943 (mt) cc_final: 0.8394 (mt) REVERT: F 124 MET cc_start: 0.8620 (tmm) cc_final: 0.8274 (tmm) REVERT: A 207 THR cc_start: 0.8505 (m) cc_final: 0.8162 (p) REVERT: C 108 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8038 (pm20) REVERT: C 331 LYS cc_start: 0.7148 (mmtt) cc_final: 0.6880 (mmtp) REVERT: C 357 ASN cc_start: 0.8967 (t0) cc_final: 0.8485 (m-40) REVERT: C 472 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8375 (tm-30) REVERT: C 1290 MET cc_start: 0.8726 (tpp) cc_final: 0.8347 (tpp) REVERT: D 402 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8106 (tm-30) REVERT: D 532 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: D 995 TYR cc_start: 0.7465 (m-80) cc_final: 0.7145 (m-10) REVERT: D 1184 ASP cc_start: 0.7587 (m-30) cc_final: 0.7304 (m-30) REVERT: D 1189 MET cc_start: 0.8219 (tmm) cc_final: 0.7948 (tpp) REVERT: E 68 GLU cc_start: 0.8622 (tp30) cc_final: 0.8286 (tp30) REVERT: E 70 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8565 (tm-30) outliers start: 60 outliers final: 46 residues processed: 255 average time/residue: 0.1647 time to fit residues: 70.6964 Evaluate side-chains 249 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 202 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain A residue 172 LEU 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 124 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 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 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 1233 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 803 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 1175 LEU Chi-restraints excluded: chain D residue 1243 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 44 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 276 ASN D 792 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.101044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.073488 restraints weight = 66070.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.074380 restraints weight = 40597.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.074927 restraints weight = 27923.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.075236 restraints weight = 25593.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.075321 restraints weight = 23313.457| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28132 Z= 0.132 Angle : 0.646 26.611 38250 Z= 0.318 Chirality : 0.052 1.934 4354 Planarity : 0.004 0.060 4805 Dihedral : 12.037 174.946 4340 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.75 % Allowed : 14.97 % Favored : 83.28 % 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: -1.00 (0.15), residues: 3349 helix: 1.28 (0.16), residues: 1157 sheet: -0.63 (0.25), residues: 413 loop : -2.11 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1142 TYR 0.014 0.001 TYR F 11 PHE 0.014 0.001 PHE F 112 TRP 0.011 0.001 TRP D1193 HIS 0.006 0.001 HIS C 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (28124) covalent geometry : angle 0.64458 / 0.32 (38238) hydrogen bonds : bond 0.04451 / 4.80 ( 1098) hydrogen bonds : angle 4.12103 / 4.27 ( 2997) metal coordination : bond 0.00639 / 0.61 ( 8) metal coordination : angle 2.26841 / 4.13 ( 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: 50 poor density : 212 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 72 LEU cc_start: 0.8917 (mt) cc_final: 0.8390 (mt) REVERT: F 124 MET cc_start: 0.8609 (tmm) cc_final: 0.8196 (tmm) REVERT: A 207 THR cc_start: 0.8508 (m) cc_final: 0.8106 (p) REVERT: C 108 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8042 (pm20) REVERT: C 331 LYS cc_start: 0.7171 (mmtt) cc_final: 0.6916 (mmtp) REVERT: C 357 ASN cc_start: 0.8978 (t0) cc_final: 0.8495 (m-40) REVERT: C 472 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8411 (tm-30) REVERT: C 1290 MET cc_start: 0.8767 (tpp) cc_final: 0.8421 (tpp) REVERT: D 402 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8109 (tm-30) REVERT: D 532 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: D 995 TYR cc_start: 0.7352 (m-80) cc_final: 0.7018 (m-10) REVERT: D 1184 ASP cc_start: 0.7577 (m-30) cc_final: 0.7367 (m-30) REVERT: D 1189 MET cc_start: 0.8207 (tmm) cc_final: 0.7914 (tpp) REVERT: E 68 GLU cc_start: 0.8570 (tp30) cc_final: 0.8303 (tp30) REVERT: E 70 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8592 (tm-30) outliers start: 50 outliers final: 40 residues processed: 249 average time/residue: 0.1669 time to fit residues: 69.2920 Evaluate side-chains 245 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain A residue 172 LEU 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 124 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 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 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 803 VAL 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 1243 LEU 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: 0.8980 chunk 107 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 208 optimal weight: 6.9990 chunk 218 optimal weight: 0.4980 chunk 210 optimal weight: 7.9990 chunk 92 optimal weight: 0.0770 chunk 102 optimal weight: 0.9990 chunk 146 optimal weight: 0.4980 chunk 264 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 276 ASN D 777 HIS D 792 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.103034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.075669 restraints weight = 65559.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.076672 restraints weight = 40618.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.077360 restraints weight = 27381.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.077627 restraints weight = 24868.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.077765 restraints weight = 22428.135| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 28132 Z= 0.110 Angle : 0.628 26.487 38250 Z= 0.308 Chirality : 0.052 1.939 4354 Planarity : 0.004 0.060 4805 Dihedral : 11.974 173.874 4340 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.40 % Allowed : 15.39 % 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: -0.83 (0.15), residues: 3349 helix: 1.40 (0.16), residues: 1160 sheet: -0.49 (0.26), residues: 409 loop : -2.01 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 195 TYR 0.015 0.001 TYR F 20 PHE 0.013 0.001 PHE F 103 TRP 0.009 0.001 TRP F 148 HIS 0.006 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (28124) covalent geometry : angle 0.62727 / 0.31 (38238) hydrogen bonds : bond 0.03965 / 4.28 ( 1098) hydrogen bonds : angle 4.02422 / 4.18 ( 2997) metal coordination : bond 0.00425 / 0.41 ( 8) metal coordination : angle 2.07390 / 3.87 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4055.40 seconds wall clock time: 71 minutes 5.14 seconds (4265.14 seconds total)