Starting phenix.real_space_refine on Sun Aug 9 12:41:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gds_51277/08_2026/9gds_51277.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gds_51277/08_2026/9gds_51277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gds_51277/08_2026/9gds_51277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gds_51277/08_2026/9gds_51277.map" model { file = "/net/cci-nas-00/data/ceres_data/9gds_51277/08_2026/9gds_51277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gds_51277/08_2026/9gds_51277.cif" } resolution = 2.9 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= 0.011 sd= 1.107 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 156 5.49 5 Mg 1 5.21 5 S 125 5.16 5 C 21004 2.51 5 N 6027 2.21 5 O 6847 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34162 Number of models: 1 Model: "" Number of chains: 13 Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 928 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "K" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 898 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 100} Chain: "N" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1621 Classifications: {'DNA': 79} Link IDs: {'rna3p': 78} Chain: "T" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1603 Classifications: {'DNA': 78} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 77} Chain breaks: 1 Chain: "C" Number of atoms: 10421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1328, 10410 Classifications: {'peptide': 1328} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1272} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1328, 10410 Classifications: {'peptide': 1328} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1272} Chain breaks: 2 bond proxies already assigned to first conformer: 10562 Chain: "D" Number of atoms: 9408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1202, 9408 Classifications: {'peptide': 1202} Link IDs: {'PCIS': 2, 'PTRANS': 46, 'TRANS': 1153} Chain breaks: 4 Chain: "E" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 545 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "A" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1776 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1697 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Chain: "F" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3810 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 16, 'TRANS': 451} Chain breaks: 2 Chain: "G" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 550 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "I" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 902 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} 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 15919 SG CYS D 70 56.734 75.580 132.063 1.00 71.40 S ATOM 16041 SG CYS D 85 55.286 72.324 131.616 1.00 81.47 S ATOM 16065 SG CYS D 88 58.076 71.966 134.191 1.00 98.75 S ATOM 21775 SG CYS D 814 20.772 114.414 174.144 1.00 74.19 S ATOM 22335 SG CYS D 888 24.199 112.949 173.903 1.00 77.33 S ATOM 22384 SG CYS D 895 23.288 116.055 171.777 1.00 77.80 S ATOM 22404 SG CYS D 898 23.698 116.428 175.455 1.00 70.09 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG C 97 " occ=0.76 ... (20 atoms not shown) pdb=" NH2BARG C 97 " occ=0.24 Time building chain proxies: 9.50, per 1000 atoms: 0.28 Number of scatterers: 34162 At special positions: 0 Unit cell: (159.358, 198.832, 255.85, 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 125 16.00 P 156 15.00 Mg 1 11.99 O 6847 8.00 N 6027 7.00 C 21004 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: 2.91 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " Number of angles added : 6 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7314 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 50 sheets defined 45.1% alpha, 15.6% beta 60 base pairs and 127 stacking pairs defined. Time for finding SS restraints: 4.47 Creating SS restraints... Processing helix chain 'H' and resid 42 through 53 Processing helix chain 'H' and resid 59 through 68 Processing helix chain 'H' and resid 74 through 89 removed outlier: 3.774A pdb=" N LEU H 78 " --> pdb=" O SER H 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 54 Processing helix chain 'K' and resid 59 through 68 Processing helix chain 'K' and resid 76 through 89 removed outlier: 3.569A pdb=" N ILE K 82 " --> pdb=" O LEU K 78 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG K 86 " --> pdb=" O ILE K 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.917A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.892A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.869A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.975A pdb=" N LEU C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 242 through 247' Processing helix chain 'C' and resid 257 through 261 removed outlier: 3.913A pdb=" N VAL C 261 " --> pdb=" O ASP C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 279 Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.523A pdb=" N VAL C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.760A 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 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.774A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 410 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 480 removed outlier: 4.097A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.742A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.731A pdb=" N TYR C 555 " --> pdb=" O VAL C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 612 removed outlier: 3.684A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 612' Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 713 removed outlier: 4.035A pdb=" N GLY C 713 " --> pdb=" O ALA C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 741 removed outlier: 3.656A pdb=" N LEU C 741 " --> pdb=" O GLU C 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 738 through 741' Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 981 Processing helix chain 'C' and resid 985 through 992 removed outlier: 4.179A pdb=" N LEU C 989 " --> pdb=" O THR C 985 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 1000 removed outlier: 3.529A pdb=" N GLN C1000 " --> pdb=" O TRP C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1038 removed outlier: 3.504A pdb=" N GLN C1010 " --> pdb=" O GLU C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.266A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1164 through 1175 Processing helix chain 'C' and resid 1190 through 1201 Processing helix chain 'C' and resid 1270 through 1281 Processing helix chain 'C' and resid 1282 through 1291 Processing helix chain 'C' and resid 1296 through 1309 Processing helix chain 'C' and resid 1319 through 1332 removed outlier: 3.566A pdb=" N ASN C1323 " --> pdb=" O PRO C1319 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 77 through 81 removed outlier: 3.564A pdb=" N HIS D 80 " --> pdb=" O ARG D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.796A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 180 through 191 removed outlier: 3.810A pdb=" N ALA D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 207 Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.929A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.599A pdb=" N LEU D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.717A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.721A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.119A pdb=" N THR D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.582A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS D 781 " --> pdb=" O HIS D 777 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.578A pdb=" N LEU D 838 " --> pdb=" O ALA D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1215 through 1223 Processing helix chain 'D' and resid 1224 through 1243 removed outlier: 3.967A pdb=" N GLN D1243 " --> pdb=" O VAL D1239 " (cutoff:3.500A) Processing helix chain 'D' and resid 1248 through 1260 removed outlier: 4.310A pdb=" N ILE D1252 " --> pdb=" O ASN D1248 " (cutoff:3.500A) Processing helix chain 'D' and resid 1281 through 1295 Processing helix chain 'D' and resid 1307 through 1314 Processing helix chain 'D' and resid 1317 through 1325 removed outlier: 3.631A pdb=" N ALA D1321 " --> pdb=" O SER D1317 " (cutoff:3.500A) Processing helix chain 'D' and resid 1326 through 1338 Processing helix chain 'D' and resid 1345 through 1352 removed outlier: 3.770A pdb=" N ASN D1349 " --> pdb=" O GLY D1345 " (cutoff:3.500A) Processing helix chain 'D' and resid 1358 through 1360 No H-bonds generated for 'chain 'D' and resid 1358 through 1360' Processing helix chain 'D' and resid 1361 through 1374 removed outlier: 3.504A pdb=" N ALA D1373 " --> pdb=" O GLN D1369 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN D1374 " --> pdb=" O ALA D1370 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 14 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 74 Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.526A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 213 through 234 removed outlier: 4.255A pdb=" N ALA A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 213 through 229 removed outlier: 3.603A pdb=" N LEU B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 108 removed outlier: 3.606A pdb=" N MET F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 138 Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.803A pdb=" N TYR F 145 " --> pdb=" O GLY F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 removed outlier: 3.835A pdb=" N LEU F 163 " --> pdb=" O ARG F 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 159 through 163' Processing helix chain 'F' and resid 224 through 243 Processing helix chain 'F' and resid 250 through 266 removed outlier: 3.500A pdb=" N SER F 254 " --> pdb=" O SER F 250 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU F 266 " --> pdb=" O ASP F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 300 removed outlier: 3.529A pdb=" N THR F 280 " --> pdb=" O HIS F 276 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU F 281 " --> pdb=" O LEU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 313 Processing helix chain 'F' and resid 320 through 330 removed outlier: 3.979A pdb=" N LEU F 324 " --> pdb=" O ASN F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 360 removed outlier: 3.595A pdb=" N VAL F 338 " --> pdb=" O TYR F 334 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLU F 344 " --> pdb=" O GLU F 340 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET F 354 " --> pdb=" O GLN F 350 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE F 355 " --> pdb=" O LYS F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 401 removed outlier: 5.143A pdb=" N ARG F 393 " --> pdb=" O GLU F 389 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU F 394 " --> pdb=" O ALA F 390 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS F 401 " --> pdb=" O SER F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 425 Processing helix chain 'F' and resid 434 through 455 removed outlier: 4.019A pdb=" N TYR F 438 " --> pdb=" O LYS F 434 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TRP F 441 " --> pdb=" O THR F 437 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP F 442 " --> pdb=" O TYR F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 483 Processing helix chain 'F' and resid 487 through 496 Processing helix chain 'F' and resid 498 through 508 Processing helix chain 'F' and resid 526 through 531 removed outlier: 3.657A pdb=" N ASP F 529 " --> pdb=" O HIS F 526 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE F 531 " --> pdb=" O GLY F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 557 Processing helix chain 'F' and resid 560 through 572 Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 591 through 607 removed outlier: 3.888A pdb=" N ILE F 595 " --> pdb=" O THR F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 617 removed outlier: 3.798A pdb=" N SER F 617 " --> pdb=" O GLU F 613 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 262 removed outlier: 3.856A pdb=" N GLU G 262 " --> pdb=" O ASP G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 272 Processing helix chain 'G' and resid 278 through 283 removed outlier: 3.974A pdb=" N LEU G 282 " --> pdb=" O TYR G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 293 removed outlier: 3.611A pdb=" N THR G 293 " --> pdb=" O GLU G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 311 removed outlier: 4.114A pdb=" N GLU G 303 " --> pdb=" O LYS G 299 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG G 311 " --> pdb=" O VAL G 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 49 removed outlier: 3.519A pdb=" N ARG I 49 " --> pdb=" O LEU I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 65 Processing helix chain 'I' and resid 73 through 87 removed outlier: 3.652A pdb=" N THR I 77 " --> pdb=" O ASP I 73 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 34 through 37 removed outlier: 5.107A pdb=" N LEU H 35 " --> pdb=" O TYR H 25 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR H 25 " --> pdb=" O LEU H 35 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN H 111 " --> pdb=" O GLN H 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 97 through 100 Processing sheet with id=AA3, first strand: chain 'K' and resid 35 through 37 removed outlier: 5.643A pdb=" N LEU K 35 " --> pdb=" O TYR K 25 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR K 25 " --> pdb=" O LEU K 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 97 through 100 Processing sheet with id=AA5, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.544A pdb=" N LYS C 13 " --> pdb=" O ALA C1182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.224A pdb=" N SER C 66 " --> pdb=" O PHE C 105 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LYS C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU C 126 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AA8, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.489A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 154 through 159 removed outlier: 5.085A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 284 through 285 removed outlier: 3.599A pdb=" N ILE C 285 " --> pdb=" O MET C 239 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASN C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 301 through 302 removed outlier: 4.071A pdb=" N ILE C 311 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.731A pdb=" N GLU C 602 " --> pdb=" O ARG C 593 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N THR C 600 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB5, first strand: chain 'C' and resid 615 through 616 Processing sheet with id=AB6, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.546A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.664A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AB9, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC1, first strand: chain 'C' and resid 1208 through 1209 removed outlier: 7.336A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR C1225 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.938A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AC4, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.952A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 1243 through 1245 Processing sheet with id=AC6, first strand: chain 'C' and resid 1268 through 1269 Processing sheet with id=AC7, first strand: chain 'C' and resid 1334 through 1339 removed outlier: 3.835A pdb=" N ALA D 19 " --> pdb=" O GLU C1339 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.571A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.638A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 159 through 160 removed outlier: 6.701A pdb=" N THR D 177 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AD2, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD3, first strand: chain 'D' and resid 703 through 707 Processing sheet with id=AD4, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AD5, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD6, first strand: chain 'D' and resid 825 through 826 removed outlier: 6.583A pdb=" N HIS D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 848 through 849 removed outlier: 3.548A pdb=" N ILE D 858 " --> pdb=" O ILE D 848 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 991 through 995 Processing sheet with id=AD9, first strand: chain 'D' and resid 1184 through 1189 Processing sheet with id=AE1, first strand: chain 'D' and resid 1278 through 1280 removed outlier: 6.767A pdb=" N ARG D1300 " --> pdb=" O THR D1266 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 12 through 20 removed outlier: 4.980A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N HIS A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N HIS A 23 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR A 208 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LYS A 25 " --> pdb=" O MET A 206 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N MET A 206 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N THR A 27 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE A 204 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLU A 29 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU A 202 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 98 through 106 removed outlier: 3.650A pdb=" N GLU A 58 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLU A 148 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL A 56 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY A 150 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N CYS A 54 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AE5, first strand: chain 'A' and resid 109 through 112 Processing sheet with id=AE6, first strand: chain 'A' and resid 153 through 154 Processing sheet with id=AE7, first strand: chain 'B' and resid 13 through 18 removed outlier: 5.801A pdb=" N HIS B 23 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR B 208 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N LYS B 25 " --> pdb=" O MET B 206 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N MET B 206 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N THR B 27 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE B 204 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N GLU B 29 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU B 202 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N THR B 197 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL B 193 " --> pdb=" O THR B 197 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 116 through 117 removed outlier: 3.519A pdb=" N THR B 102 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ALA B 142 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE B 61 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG B 144 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL B 59 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS B 146 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AF1, first strand: chain 'B' and resid 109 through 112 Processing sheet with id=AF2, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AF3, first strand: chain 'F' and resid 164 through 166 removed outlier: 6.667A pdb=" N ARG F 268 " --> pdb=" O SER F 165 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 32 through 33 removed outlier: 4.136A pdb=" N THR I 22 " --> pdb=" O ASP I 17 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP I 17 " --> pdb=" O THR I 22 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 97 through 100 1479 hydrogen bonds defined for protein. 4204 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 137 hydrogen bonds 274 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 127 stacking parallelities Total time for adding SS restraints: 11.04 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10982 1.34 - 1.46: 7508 1.46 - 1.58: 16005 1.58 - 1.71: 310 1.71 - 1.83: 221 Bond restraints: 35026 Sorted by residual: bond pdb=" C1' DT T 4 " pdb=" N1 DT T 4 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.41e+01 bond pdb=" C3' DT T 39 " pdb=" C2' DT T 39 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.38e+01 bond pdb=" C3' DT N -51 " pdb=" C2' DT N -51 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DT N -40 " pdb=" C2' DT N -40 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DA N -11 " pdb=" C2' DA N -11 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 ... (remaining 35021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 46801 2.07 - 4.15: 1041 4.15 - 6.22: 100 6.22 - 8.29: 21 8.29 - 10.37: 8 Bond angle restraints: 47971 Sorted by residual: angle pdb=" N ARG C 211 " pdb=" CA ARG C 211 " pdb=" C ARG C 211 " ideal model delta sigma weight residual 111.07 104.83 6.24 1.07e+00 8.73e-01 3.40e+01 angle pdb=" C LEU C 210 " pdb=" N ARG C 211 " pdb=" CA ARG C 211 " ideal model delta sigma weight residual 120.44 113.95 6.49 1.30e+00 5.92e-01 2.49e+01 angle pdb=" N LEU C 213 " pdb=" CA LEU C 213 " pdb=" C LEU C 213 " ideal model delta sigma weight residual 113.02 107.34 5.68 1.20e+00 6.94e-01 2.24e+01 angle pdb=" O4' DT T 4 " pdb=" C4' DT T 4 " pdb=" C3' DT T 4 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.17e+01 angle pdb=" N3 DT N -60 " pdb=" C4 DT N -60 " pdb=" O4 DT N -60 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 ... (remaining 47966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 19906 35.85 - 71.69: 1252 71.69 - 107.54: 38 107.54 - 143.39: 0 143.39 - 179.23: 4 Dihedral angle restraints: 21200 sinusoidal: 9886 harmonic: 11314 Sorted by residual: dihedral pdb=" CA MET F 569 " pdb=" C MET F 569 " pdb=" N ARG F 570 " pdb=" CA ARG F 570 " ideal model delta harmonic sigma weight residual 180.00 155.06 24.94 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA LYS D1296 " pdb=" C LYS D1296 " pdb=" N GLU D1297 " pdb=" CA GLU D1297 " ideal model delta harmonic sigma weight residual -180.00 -155.14 -24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ARG G 318 " pdb=" C ARG G 318 " pdb=" N LEU G 319 " pdb=" CA LEU G 319 " ideal model delta harmonic sigma weight residual -180.00 -157.50 -22.50 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 21197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4406 0.055 - 0.111: 929 0.111 - 0.166: 117 0.166 - 0.222: 4 0.222 - 0.277: 3 Chirality restraints: 5459 Sorted by residual: chirality pdb=" CB ILE D 685 " pdb=" CA ILE D 685 " pdb=" CG1 ILE D 685 " pdb=" CG2 ILE D 685 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA GLU I 52 " pdb=" N GLU I 52 " pdb=" C GLU I 52 " pdb=" CB GLU I 52 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ASN I 51 " pdb=" N ASN I 51 " pdb=" C ASN I 51 " pdb=" CB ASN I 51 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 5456 not shown) Planarity restraints: 5691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN I 21 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.79e+00 pdb=" C ASN I 21 " 0.048 2.00e-02 2.50e+03 pdb=" O ASN I 21 " -0.018 2.00e-02 2.50e+03 pdb=" N THR I 22 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 560 " 0.045 5.00e-02 4.00e+02 6.76e-02 7.31e+00 pdb=" N PRO F 561 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO F 561 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 561 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 749 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO D 750 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 750 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 750 " -0.035 5.00e-02 4.00e+02 ... (remaining 5688 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 220 2.59 - 3.17: 26974 3.17 - 3.74: 53656 3.74 - 4.32: 74272 4.32 - 4.90: 121317 Nonbonded interactions: 276439 Sorted by model distance: nonbonded pdb=" OP2 DG T 57 " pdb=" NH1 ARG I 56 " model vdw 2.012 3.120 nonbonded pdb=" OD2 ASP D 462 " pdb="MG MG D1501 " model vdw 2.020 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.020 2.170 nonbonded pdb=" OE2 GLU D1280 " pdb=" OG SER D1282 " model vdw 2.041 3.040 nonbonded pdb=" O ILE F 519 " pdb=" OG SER F 525 " model vdw 2.133 3.040 ... (remaining 276434 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 4 through 160 or resid 169 through 233)) selection = chain 'B' } ncs_group { reference = (chain 'H' and resid 6 through 114) selection = chain 'K' } 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=0.24 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 13.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.980 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 45.270 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 : 0.004 0.053 35033 Z= 0.283 Angle : 0.686 10.367 47977 Z= 0.450 Chirality : 0.045 0.277 5459 Planarity : 0.005 0.068 5691 Dihedral : 19.536 179.232 13886 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.01 % Allowed : 26.95 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.13), residues: 3884 helix: 1.48 (0.13), residues: 1611 sheet: 0.74 (0.23), residues: 477 loop : -0.10 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 403 TYR 0.025 0.001 TYR D 144 PHE 0.027 0.001 PHE C 514 TRP 0.021 0.001 TRP I 64 HIS 0.012 0.001 HIS I 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.28 (35026) covalent geometry : angle 0.68571 / 0.45 (47971) hydrogen bonds : bond 0.12108 / 8.00 ( 1614) hydrogen bonds : angle 5.42418 / 5.39 ( 4478) metal coordination : bond 0.00791 / 0.40 ( 7) metal coordination : angle 2.32841 / 1.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 3371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 709 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 30 MET cc_start: 0.5530 (tmt) cc_final: 0.5322 (tmt) REVERT: C 42 ASP cc_start: 0.7617 (p0) cc_final: 0.7141 (p0) REVERT: C 186 PHE cc_start: 0.8306 (m-10) cc_final: 0.8105 (m-10) REVERT: C 200 ARG cc_start: 0.8103 (mmt180) cc_final: 0.7706 (mmt-90) REVERT: C 299 LYS cc_start: 0.7840 (tptp) cc_final: 0.7604 (tptp) REVERT: C 340 ASP cc_start: 0.7724 (m-30) cc_final: 0.7142 (t0) REVERT: C 347 MET cc_start: 0.7279 (tpt) cc_final: 0.6982 (tpt) REVERT: C 365 GLU cc_start: 0.7779 (tp30) cc_final: 0.7554 (tp30) REVERT: C 478 ARG cc_start: 0.8083 (tmt-80) cc_final: 0.7858 (tpm170) REVERT: C 491 ASP cc_start: 0.8337 (m-30) cc_final: 0.8062 (t0) REVERT: C 859 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7200 (mm-30) REVERT: C 1140 LYS cc_start: 0.8104 (mtpp) cc_final: 0.7763 (mtmt) REVERT: C 1164 SER cc_start: 0.8127 (m) cc_final: 0.7902 (t) REVERT: D 200 GLN cc_start: 0.7921 (tm130) cc_final: 0.7705 (tm130) REVERT: D 201 MET cc_start: 0.8101 (mtm) cc_final: 0.7587 (mtm) REVERT: D 202 ARG cc_start: 0.8028 (mtp85) cc_final: 0.7787 (mtp85) REVERT: D 204 GLU cc_start: 0.8064 (tt0) cc_final: 0.7691 (tm-30) REVERT: D 662 ARG cc_start: 0.7100 (mtm-85) cc_final: 0.6830 (mtm-85) REVERT: D 833 VAL cc_start: 0.8840 (p) cc_final: 0.8469 (m) REVERT: D 1158 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7195 (pt0) REVERT: D 1223 ARG cc_start: 0.8588 (ttm170) cc_final: 0.8124 (mtt180) REVERT: B 7 GLU cc_start: 0.8072 (pp20) cc_final: 0.7656 (pp20) REVERT: B 31 LEU cc_start: 0.8581 (mt) cc_final: 0.8354 (mp) REVERT: F 464 MET cc_start: 0.8370 (tpp) cc_final: 0.8006 (tpt) REVERT: F 563 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7810 (tm-30) REVERT: F 565 LYS cc_start: 0.8337 (tppt) cc_final: 0.7990 (tppp) outliers start: 34 outliers final: 18 residues processed: 727 average time/residue: 0.8483 time to fit residues: 723.1670 Evaluate side-chains 709 residues out of total 3371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 690 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1000 GLN Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 1158 GLU Chi-restraints excluded: chain D residue 1159 HIS Chi-restraints excluded: chain D residue 1192 HIS Chi-restraints excluded: chain D residue 1313 LEU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain G residue 285 ARG Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain I residue 60 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.3980 chunk 401 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 173 ASN C 494 ASN C 513 GLN C 596 ASN C 618 GLN C 677 ASN C1136 GLN C1235 ASN D 200 GLN D 430 HIS D 805 GLN E 31 GLN F 454 GLN F 480 GLN F 579 HIS G 284 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.168594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.135186 restraints weight = 66808.521| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.58 r_work: 0.3564 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35033 Z= 0.195 Angle : 0.630 13.283 47977 Z= 0.338 Chirality : 0.045 0.304 5459 Planarity : 0.005 0.058 5691 Dihedral : 18.689 177.570 6124 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.85 % Allowed : 21.79 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.13), residues: 3884 helix: 1.46 (0.13), residues: 1645 sheet: 0.71 (0.24), residues: 482 loop : -0.10 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1329 TYR 0.018 0.002 TYR D 631 PHE 0.027 0.002 PHE C 514 TRP 0.008 0.001 TRP H 15 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (35026) covalent geometry : angle 0.62864 / 0.34 (47971) hydrogen bonds : bond 0.05006 / 3.31 ( 1614) hydrogen bonds : angle 4.54101 / 4.46 ( 4478) metal coordination : bond 0.00973 / 0.51 ( 7) metal coordination : angle 3.13527 / 1.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 3371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 712 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 30 MET cc_start: 0.5944 (tmt) cc_final: 0.5595 (tmt) REVERT: K 30 MET cc_start: 0.4843 (OUTLIER) cc_final: 0.4413 (tmt) REVERT: C 189 ASP cc_start: 0.7317 (p0) cc_final: 0.7032 (p0) REVERT: C 200 ARG cc_start: 0.7854 (mmt180) cc_final: 0.7464 (mmt-90) REVERT: C 222 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7612 (t0) REVERT: C 340 ASP cc_start: 0.7506 (m-30) cc_final: 0.7032 (t0) REVERT: C 491 ASP cc_start: 0.8253 (m-30) cc_final: 0.8040 (t0) REVERT: C 542 ARG cc_start: 0.7386 (mtp180) cc_final: 0.7181 (mtp180) REVERT: C 859 GLU cc_start: 0.7537 (mm-30) cc_final: 0.6996 (tm-30) REVERT: C 1107 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8707 (mtt) REVERT: C 1200 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8279 (tp) REVERT: C 1218 ASP cc_start: 0.8231 (m-30) cc_final: 0.7924 (m-30) REVERT: D 79 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.7105 (ttpt) REVERT: D 86 GLU cc_start: 0.7481 (pm20) cc_final: 0.7260 (pm20) REVERT: D 183 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7192 (tp30) REVERT: D 200 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7408 (tm-30) REVERT: D 202 ARG cc_start: 0.7941 (mtp85) cc_final: 0.7715 (mtp85) REVERT: D 259 ARG cc_start: 0.7933 (mmt180) cc_final: 0.7628 (mmt180) REVERT: D 418 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: D 662 ARG cc_start: 0.7029 (mtm-85) cc_final: 0.6788 (mtm-85) REVERT: D 715 LYS cc_start: 0.8544 (tptp) cc_final: 0.8286 (tptp) REVERT: D 749 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.6964 (ttp-110) REVERT: D 833 VAL cc_start: 0.8711 (p) cc_final: 0.8330 (m) REVERT: D 1156 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8104 (mt) REVERT: D 1158 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7150 (pt0) REVERT: D 1223 ARG cc_start: 0.8458 (ttm170) cc_final: 0.8035 (mtt180) REVERT: D 1246 LYS cc_start: 0.8992 (tttp) cc_final: 0.8757 (tttt) REVERT: A 33 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7963 (ttp-110) REVERT: F 296 MET cc_start: 0.6178 (tpp) cc_final: 0.5880 (tpp) REVERT: F 415 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7588 (tp30) REVERT: F 476 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7641 (ptp90) REVERT: F 484 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7895 (ptt180) REVERT: F 519 ILE cc_start: 0.7934 (mm) cc_final: 0.7663 (pp) REVERT: F 563 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7741 (tp30) outliers start: 130 outliers final: 56 residues processed: 778 average time/residue: 0.8420 time to fit residues: 767.7692 Evaluate side-chains 770 residues out of total 3371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 701 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1000 GLN Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1191 GLU Chi-restraints excluded: chain C residue 1200 LEU Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 749 ARG Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 836 THR Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 879 GLN Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1158 GLU Chi-restraints excluded: chain D residue 1159 HIS Chi-restraints excluded: chain D residue 1192 HIS Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain D residue 1270 ASP Chi-restraints excluded: chain D residue 1313 LEU Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 445 GLN Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 484 ARG Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 563 GLU Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 278 TYR Chi-restraints excluded: chain G residue 285 ARG Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 315 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 18 optimal weight: 1.9990 chunk 385 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 362 optimal weight: 0.0570 chunk 156 optimal weight: 1.9990 chunk 390 optimal weight: 0.7980 chunk 370 optimal weight: 2.9990 chunk 321 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 339 ASN C 494 ASN C 922 ASN C1243 HIS D 94 GLN D 805 GLN A 84 ASN ** G 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.166784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.134022 restraints weight = 74368.689| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.61 r_work: 0.3551 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 35033 Z= 0.230 Angle : 0.627 12.662 47977 Z= 0.339 Chirality : 0.046 0.294 5459 Planarity : 0.005 0.057 5691 Dihedral : 18.690 177.313 6113 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.30 % Allowed : 21.55 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % 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: 0.87 (0.13), residues: 3884 helix: 1.42 (0.13), residues: 1630 sheet: 0.57 (0.24), residues: 494 loop : -0.15 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 359 TYR 0.024 0.002 TYR C 73 PHE 0.029 0.002 PHE H 88 TRP 0.015 0.002 TRP I 64 HIS 0.007 0.001 HIS I 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.23 (35026) covalent geometry : angle 0.62650 / 0.34 (47971) hydrogen bonds : bond 0.05191 / 3.43 ( 1614) hydrogen bonds : angle 4.48629 / 4.40 ( 4478) metal coordination : bond 0.01057 / 0.56 ( 7) metal coordination : angle 3.14683 / 1.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 3371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 713 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 30 MET cc_start: 0.6022 (tmt) cc_final: 0.5685 (tmt) REVERT: K 30 MET cc_start: 0.4832 (OUTLIER) cc_final: 0.4320 (tmt) REVERT: C 176 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7111 (mt) REVERT: C 189 ASP cc_start: 0.7388 (p0) cc_final: 0.7116 (p0) REVERT: C 200 ARG cc_start: 0.7900 (mmt180) cc_final: 0.7484 (mmt-90) REVERT: C 222 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7642 (t0) REVERT: C 340 ASP cc_start: 0.7514 (m-30) cc_final: 0.7036 (t0) REVERT: C 491 ASP cc_start: 0.8260 (m-30) cc_final: 0.8058 (t0) REVERT: C 542 ARG cc_start: 0.7507 (mtp180) cc_final: 0.7290 (mtp180) REVERT: C 859 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7137 (tm-30) REVERT: C 1030 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7508 (mm-30) REVERT: C 1032 LYS cc_start: 0.8473 (tppp) cc_final: 0.8215 (mmmm) REVERT: C 1107 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8669 (mtt) REVERT: C 1162 GLU cc_start: 0.7882 (pp20) cc_final: 0.7653 (pp20) REVERT: C 1200 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8315 (tp) REVERT: C 1218 ASP cc_start: 0.8241 (m-30) cc_final: 0.7959 (m-30) REVERT: D 79 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.7113 (ttmt) REVERT: D 86 GLU cc_start: 0.7423 (pm20) cc_final: 0.7183 (pm20) REVERT: D 414 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: D 418 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7640 (mt-10) REVERT: D 607 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: D 715 LYS cc_start: 0.8530 (tptp) cc_final: 0.8278 (tptp) REVERT: D 749 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7729 (ttp-110) REVERT: D 833 VAL cc_start: 0.8715 (p) cc_final: 0.8312 (m) REVERT: D 1156 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8150 (mt) REVERT: D 1158 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7186 (pt0) REVERT: D 1223 ARG cc_start: 0.8508 (ttm170) cc_final: 0.8067 (mtt180) REVERT: D 1246 LYS cc_start: 0.9017 (tttp) cc_final: 0.8790 (tttt) REVERT: A 33 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.8030 (ttp-110) REVERT: A 76 GLU cc_start: 0.7934 (mp0) cc_final: 0.7381 (mp0) REVERT: B 144 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8202 (ttt90) REVERT: F 107 MET cc_start: 0.7110 (ppp) cc_final: 0.6838 (pp-130) REVERT: F 296 MET cc_start: 0.6236 (tpp) cc_final: 0.5872 (tpp) REVERT: F 415 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7675 (tp30) REVERT: F 476 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7679 (ptp90) REVERT: F 490 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7775 (mt-10) REVERT: F 519 ILE cc_start: 0.7964 (mm) cc_final: 0.7453 (pp) REVERT: F 563 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7878 (tp30) REVERT: F 593 GLU cc_start: 0.6457 (tp30) cc_final: 0.4492 (tp30) REVERT: I 86 MET cc_start: 0.3168 (ptm) cc_final: 0.2859 (ptp) outliers start: 145 outliers final: 78 residues processed: 776 average time/residue: 0.8434 time to fit residues: 766.8882 Evaluate side-chains 784 residues out of total 3371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 690 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 639 LYS Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 739 GLU Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1000 GLN Chi-restraints excluded: chain C residue 1034 ARG Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1191 GLU Chi-restraints excluded: chain C residue 1200 LEU Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 749 ARG Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 836 THR Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 879 GLN Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1158 GLU Chi-restraints excluded: chain D residue 1159 HIS Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain D residue 1270 ASP Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 445 GLN Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 515 MET Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 563 GLU Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 278 TYR Chi-restraints excluded: chain G residue 285 ARG Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 321 ASN Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 52 GLU Chi-restraints excluded: chain I residue 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 224 optimal weight: 0.9990 chunk 345 optimal weight: 20.0000 chunk 362 optimal weight: 0.9990 chunk 391 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 193 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 922 ASN C1243 HIS D 94 GLN D 430 HIS D 665 GLN D 805 GLN A 75 GLN A 84 ASN A 104 ASN ** F 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 480 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.165919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.133535 restraints weight = 69534.980| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.56 r_work: 0.3543 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 35033 Z= 0.233 Angle : 0.628 15.538 47977 Z= 0.337 Chirality : 0.046 0.299 5459 Planarity : 0.005 0.060 5691 Dihedral : 18.739 177.637 6106 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.57 % Allowed : 21.17 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.13), residues: 3884 helix: 1.39 (0.13), residues: 1634 sheet: 0.54 (0.24), residues: 472 loop : -0.20 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1329 TYR 0.020 0.002 TYR D 631 PHE 0.030 0.002 PHE C 514 TRP 0.014 0.002 TRP H 15 HIS 0.006 0.001 HIS K 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.23 (35026) covalent geometry : angle 0.62750 / 0.34 (47971) hydrogen bonds : bond 0.05111 / 3.38 ( 1614) hydrogen bonds : angle 4.44097 / 4.37 ( 4478) metal coordination : bond 0.01037 / 0.56 ( 7) metal coordination : angle 3.13143 / 1.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 3371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 713 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 ARG cc_start: 0.4057 (ptm-80) cc_final: 0.0228 (pmm150) REVERT: H 30 MET cc_start: 0.6254 (tmt) cc_final: 0.5872 (tmt) REVERT: H 36 ILE cc_start: 0.7425 (pp) cc_final: 0.7185 (pp) REVERT: K 30 MET cc_start: 0.4793 (OUTLIER) cc_final: 0.4343 (tmt) REVERT: C 189 ASP cc_start: 0.7396 (p0) cc_final: 0.7111 (p0) REVERT: C 193 ASN cc_start: 0.7296 (m-40) cc_final: 0.6943 (m-40) REVERT: C 200 ARG cc_start: 0.7806 (mmt180) cc_final: 0.7392 (mmt-90) REVERT: C 542 ARG cc_start: 0.7525 (mtp180) cc_final: 0.7285 (mtp180) REVERT: C 859 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7155 (tm-30) REVERT: C 903 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7833 (mtt90) REVERT: C 968 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6159 (pt0) REVERT: C 1032 LYS cc_start: 0.8481 (tppp) cc_final: 0.8227 (mmmm) REVERT: C 1107 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8646 (mtt) REVERT: C 1162 GLU cc_start: 0.7887 (pp20) cc_final: 0.7678 (pp20) REVERT: C 1200 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8333 (tp) REVERT: C 1218 ASP cc_start: 0.8227 (m-30) cc_final: 0.7939 (m-30) REVERT: D 79 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.7142 (ttmt) REVERT: D 86 GLU cc_start: 0.7419 (pm20) cc_final: 0.7181 (pm20) REVERT: D 301 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7250 (tm-30) REVERT: D 414 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7609 (tt0) REVERT: D 418 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7698 (mt-10) REVERT: D 478 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8253 (mt) REVERT: D 607 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: D 749 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7943 (ttp-110) REVERT: D 833 VAL cc_start: 0.8710 (p) cc_final: 0.8332 (m) REVERT: D 872 ILE cc_start: 0.8303 (mt) cc_final: 0.8068 (mm) REVERT: D 1156 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8160 (mt) REVERT: D 1158 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7229 (pt0) REVERT: D 1214 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7496 (mt-10) REVERT: D 1223 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8037 (mtt180) REVERT: A 33 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.8042 (ttp-110) REVERT: B 49 SER cc_start: 0.8710 (OUTLIER) cc_final: 0.8434 (p) REVERT: B 144 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8221 (ttt90) REVERT: F 107 MET cc_start: 0.7129 (ppp) cc_final: 0.6862 (pp-130) REVERT: F 387 MET cc_start: 0.7949 (tpt) cc_final: 0.7744 (tpp) REVERT: F 400 LYS cc_start: 0.8053 (tppt) cc_final: 0.7637 (pttt) REVERT: F 415 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7671 (tp30) REVERT: F 476 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7681 (ptp90) REVERT: F 484 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7864 (ptt180) REVERT: F 490 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7868 (mt-10) REVERT: F 511 GLU cc_start: 0.7324 (tp30) cc_final: 0.7021 (tp30) REVERT: F 563 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7852 (tp30) outliers start: 154 outliers final: 85 residues processed: 781 average time/residue: 0.8527 time to fit residues: 780.6063 Evaluate side-chains 806 residues out of total 3371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 701 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 639 LYS Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 739 GLU Chi-restraints excluded: chain C residue 837 SER Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 903 ARG Chi-restraints excluded: chain C residue 968 GLU Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1000 GLN Chi-restraints excluded: chain C residue 1034 ARG Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1191 GLU Chi-restraints excluded: chain C residue 1200 LEU Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 653 GLU Chi-restraints excluded: chain D residue 749 ARG Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 807 VAL Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 836 THR Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 879 GLN Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1158 GLU Chi-restraints excluded: chain D residue 1159 HIS Chi-restraints excluded: chain D residue 1192 HIS Chi-restraints excluded: chain D residue 1223 ARG Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain D residue 1270 ASP Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain F residue 425 ASP Chi-restraints excluded: chain F residue 445 GLN Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 484 ARG Chi-restraints excluded: chain F residue 515 MET Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 563 GLU Chi-restraints excluded: chain F residue 575 MET Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 278 TYR Chi-restraints excluded: chain G residue 285 ARG Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 321 ASN Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 52 GLU Chi-restraints excluded: chain I residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 120 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 302 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 282 optimal weight: 2.9990 chunk 344 optimal weight: 50.0000 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 20 GLN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN C 922 ASN C1243 HIS D 805 GLN A 84 ASN F 579 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.166190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.133636 restraints weight = 68645.630| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.53 r_work: 0.3547 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 35033 Z= 0.206 Angle : 0.612 16.132 47977 Z= 0.328 Chirality : 0.045 0.299 5459 Planarity : 0.005 0.060 5691 Dihedral : 18.716 178.354 6106 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.42 % Allowed : 21.43 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % 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: 0.82 (0.13), residues: 3884 helix: 1.43 (0.13), residues: 1639 sheet: 0.52 (0.24), residues: 469 loop : -0.23 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 34 TYR 0.024 0.002 TYR C 73 PHE 0.030 0.002 PHE C 514 TRP 0.012 0.001 TRP H 15 HIS 0.006 0.001 HIS F 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (35026) covalent geometry : angle 0.61106 / 0.33 (47971) hydrogen bonds : bond 0.04871 / 3.22 ( 1614) hydrogen bonds : angle 4.39810 / 4.32 ( 4478) metal coordination : bond 0.00922 / 0.49 ( 7) metal coordination : angle 2.66230 / 1.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 3371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 715 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 ARG cc_start: 0.4014 (ptm-80) cc_final: 0.0089 (ptt-90) REVERT: H 30 MET cc_start: 0.6332 (tmt) cc_final: 0.5932 (tmt) REVERT: K 30 MET cc_start: 0.4747 (OUTLIER) cc_final: 0.4374 (tmt) REVERT: C 187 GLU cc_start: 0.7873 (pm20) cc_final: 0.7582 (pm20) REVERT: C 189 ASP cc_start: 0.7387 (p0) cc_final: 0.7090 (p0) REVERT: C 200 ARG cc_start: 0.7792 (mmt180) cc_final: 0.7375 (mmt-90) REVERT: C 255 ILE cc_start: 0.6823 (OUTLIER) cc_final: 0.6593 (tt) REVERT: C 542 ARG cc_start: 0.7558 (mtp180) cc_final: 0.7310 (mpp-170) REVERT: C 859 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7154 (tm-30) REVERT: C 903 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7854 (mtt90) REVERT: C 968 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6145 (pt0) REVERT: C 1032 LYS cc_start: 0.8442 (tppp) cc_final: 0.8196 (mmmm) REVERT: C 1107 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8644 (mtt) REVERT: C 1200 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8341 (tp) REVERT: C 1218 ASP cc_start: 0.8224 (m-30) cc_final: 0.7936 (m-30) REVERT: D 79 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.7115 (ttmt) REVERT: D 86 GLU cc_start: 0.7412 (pm20) cc_final: 0.7168 (pm20) REVERT: D 161 THR cc_start: 0.7908 (m) cc_final: 0.7339 (p) REVERT: D 183 GLU cc_start: 0.7566 (tp30) cc_final: 0.7348 (tp30) REVERT: D 201 MET cc_start: 0.8005 (mtm) cc_final: 0.7409 (mtm) REVERT: D 301 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7262 (tm-30) REVERT: D 418 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7705 (mt-10) REVERT: D 478 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8223 (mt) REVERT: D 569 MET cc_start: 0.8939 (mmm) cc_final: 0.8336 (mmt) REVERT: D 607 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: D 653 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7218 (mt-10) REVERT: D 712 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6828 (tm-30) REVERT: D 749 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7973 (ttp-110) REVERT: D 833 VAL cc_start: 0.8708 (p) cc_final: 0.8336 (m) REVERT: D 872 ILE cc_start: 0.8352 (mt) cc_final: 0.8118 (mm) REVERT: D 1156 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8164 (mt) REVERT: D 1158 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7274 (pt0) REVERT: D 1214 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7473 (mt-10) REVERT: D 1219 ILE cc_start: 0.8635 (tt) cc_final: 0.8256 (mp) REVERT: D 1223 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8015 (mtt180) REVERT: A 33 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.8037 (ttp-110) REVERT: B 64 VAL cc_start: 0.8999 (t) cc_final: 0.8658 (m) REVERT: B 144 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8236 (ttt90) REVERT: F 107 MET cc_start: 0.7140 (ppp) cc_final: 0.6884 (pp-130) REVERT: F 387 MET cc_start: 0.7947 (tpt) cc_final: 0.7746 (tpp) REVERT: F 389 GLU cc_start: 0.7281 (mm-30) cc_final: 0.7040 (mm-30) REVERT: F 400 LYS cc_start: 0.8077 (tppt) cc_final: 0.7681 (pttt) REVERT: F 415 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7630 (mm-30) REVERT: F 464 MET cc_start: 0.8336 (tpp) cc_final: 0.7999 (tpt) REVERT: F 484 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7854 (ptt180) REVERT: F 490 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7826 (mt-10) REVERT: F 555 VAL cc_start: 0.8354 (t) cc_final: 0.8037 (t) REVERT: F 563 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7722 (tm-30) REVERT: F 583 GLU cc_start: 0.8186 (pm20) cc_final: 0.7833 (pm20) outliers start: 149 outliers final: 89 residues processed: 777 average time/residue: 0.8393 time to fit residues: 766.1311 Evaluate side-chains 810 residues out of total 3371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 701 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 42 MET Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 639 LYS Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 739 GLU Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 903 ARG Chi-restraints excluded: chain C residue 968 GLU Chi-restraints excluded: chain C residue 1000 GLN Chi-restraints excluded: chain C residue 1034 ARG Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1191 GLU Chi-restraints excluded: chain C residue 1200 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 653 GLU Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 749 ARG Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 807 VAL Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 836 THR Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1158 GLU Chi-restraints excluded: chain D residue 1159 HIS Chi-restraints excluded: chain D residue 1192 HIS Chi-restraints excluded: chain D residue 1215 SER Chi-restraints excluded: chain D residue 1223 ARG Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain D residue 1242 LEU Chi-restraints excluded: chain D residue 1270 ASP Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain F residue 425 ASP Chi-restraints excluded: chain F residue 484 ARG Chi-restraints excluded: chain F residue 515 MET Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 563 GLU Chi-restraints excluded: chain F residue 575 MET Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 278 TYR Chi-restraints excluded: chain G residue 285 ARG Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 321 ASN Chi-restraints excluded: chain I residue 52 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 7 optimal weight: 0.2980 chunk 18 optimal weight: 0.0270 chunk 21 optimal weight: 20.0000 chunk 194 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 263 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 380 optimal weight: 0.0980 chunk 339 optimal weight: 0.7980 chunk 346 optimal weight: 30.0000 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 60 GLN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 922 ASN C1243 HIS D 424 ASN D 805 GLN A 84 ASN ** F 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 480 GLN F 579 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.167788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.134914 restraints weight = 71045.882| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.63 r_work: 0.3550 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35033 Z= 0.125 Angle : 0.568 16.231 47977 Z= 0.306 Chirality : 0.042 0.302 5459 Planarity : 0.004 0.074 5691 Dihedral : 18.604 179.980 6102 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.35 % Allowed : 22.77 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % 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: 1.03 (0.13), residues: 3884 helix: 1.62 (0.13), residues: 1642 sheet: 0.64 (0.25), residues: 447 loop : -0.12 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 403 TYR 0.018 0.001 TYR D 631 PHE 0.016 0.001 PHE C 346 TRP 0.009 0.001 TRP K 15 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (35026) covalent geometry : angle 0.56793 / 0.31 (47971) hydrogen bonds : bond 0.04167 / 2.74 ( 1614) hydrogen bonds : angle 4.25059 / 4.18 ( 4478) metal coordination : bond 0.00456 / 0.23 ( 7) metal coordination : angle 2.07548 / 1.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 3371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 707 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 ARG cc_start: 0.3989 (ptm-80) cc_final: 0.0522 (pmm150) REVERT: H 30 MET cc_start: 0.6156 (tmt) cc_final: 0.5740 (tmt) REVERT: H 36 ILE cc_start: 0.7333 (pp) cc_final: 0.7062 (pt) REVERT: K 65 LYS cc_start: 0.7668 (mttt) cc_final: 0.7444 (mptt) REVERT: C 101 ARG cc_start: 0.8068 (mtt90) cc_final: 0.7830 (mtm-85) REVERT: C 189 ASP cc_start: 0.7417 (p0) cc_final: 0.7173 (p0) REVERT: C 200 ARG cc_start: 0.7791 (mmt180) cc_final: 0.7393 (mmt-90) REVERT: C 255 ILE cc_start: 0.6810 (OUTLIER) cc_final: 0.6558 (tt) REVERT: C 542 ARG cc_start: 0.7503 (mtp180) cc_final: 0.7254 (mpp-170) REVERT: C 859 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7121 (tm-30) REVERT: C 968 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6117 (pt0) REVERT: C 1032 LYS cc_start: 0.8444 (tppp) cc_final: 0.8177 (mmmm) REVERT: C 1106 ARG cc_start: 0.8651 (mtt180) cc_final: 0.8328 (mtt180) REVERT: C 1107 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8645 (mtt) REVERT: C 1200 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8313 (tp) REVERT: C 1218 ASP cc_start: 0.8231 (m-30) cc_final: 0.7930 (m-30) REVERT: D 86 GLU cc_start: 0.7417 (pm20) cc_final: 0.7185 (pm20) REVERT: D 161 THR cc_start: 0.7852 (m) cc_final: 0.7278 (p) REVERT: D 183 GLU cc_start: 0.7556 (tp30) cc_final: 0.7348 (tp30) REVERT: D 192 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8638 (ttp) REVERT: D 201 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7458 (mtm) REVERT: D 301 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7261 (tm-30) REVERT: D 569 MET cc_start: 0.8912 (mmm) cc_final: 0.8706 (mmt) REVERT: D 653 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7249 (mt-10) REVERT: D 712 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6892 (tm-30) REVERT: D 715 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8280 (tptp) REVERT: D 833 VAL cc_start: 0.8703 (p) cc_final: 0.8441 (m) REVERT: D 872 ILE cc_start: 0.8352 (mt) cc_final: 0.8117 (mm) REVERT: D 1156 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8151 (mt) REVERT: D 1158 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7223 (pt0) REVERT: D 1214 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7476 (mt-10) REVERT: D 1219 ILE cc_start: 0.8612 (tt) cc_final: 0.8249 (mp) REVERT: D 1223 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8030 (mtt180) REVERT: D 1366 GLN cc_start: 0.8136 (mt0) cc_final: 0.7877 (mt0) REVERT: A 22 THR cc_start: 0.8831 (p) cc_final: 0.8620 (p) REVERT: B 49 SER cc_start: 0.8708 (m) cc_final: 0.8443 (p) REVERT: B 64 VAL cc_start: 0.8979 (t) cc_final: 0.8635 (m) REVERT: F 107 MET cc_start: 0.7156 (ppp) cc_final: 0.6899 (pp-130) REVERT: F 389 GLU cc_start: 0.7301 (mm-30) cc_final: 0.7048 (mm-30) REVERT: F 415 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7611 (mm-30) REVERT: F 484 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7931 (ptt180) REVERT: F 490 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7884 (mt-10) REVERT: F 529 ASP cc_start: 0.7530 (p0) cc_final: 0.7298 (p0) REVERT: F 563 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: F 583 GLU cc_start: 0.8178 (pm20) cc_final: 0.7926 (mp0) outliers start: 113 outliers final: 70 residues processed: 750 average time/residue: 0.8532 time to fit residues: 748.8560 Evaluate side-chains 775 residues out of total 3371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 691 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 739 GLU Chi-restraints excluded: chain C residue 968 GLU Chi-restraints excluded: chain C residue 1000 GLN Chi-restraints excluded: chain C residue 1034 ARG Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1185 VAL Chi-restraints excluded: chain C residue 1191 GLU Chi-restraints excluded: chain C residue 1200 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 653 GLU Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 807 VAL Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 836 THR Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1158 GLU Chi-restraints excluded: chain D residue 1159 HIS Chi-restraints excluded: chain D residue 1192 HIS Chi-restraints excluded: chain D residue 1223 ARG Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain F residue 425 ASP Chi-restraints excluded: chain F residue 484 ARG Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 563 GLU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 278 TYR Chi-restraints excluded: chain G residue 285 ARG Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 321 ASN Chi-restraints excluded: chain I residue 52 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 393 optimal weight: 0.5980 chunk 381 optimal weight: 0.5980 chunk 359 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 355 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 0.0020 chunk 95 optimal weight: 0.9980 chunk 288 optimal weight: 5.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 922 ASN C1243 HIS D 94 GLN D 805 GLN D 961 HIS A 84 ASN A 104 ASN F 154 GLN F 579 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.167566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.134424 restraints weight = 74970.260| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.76 r_work: 0.3556 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35033 Z= 0.138 Angle : 0.572 16.564 47977 Z= 0.307 Chirality : 0.042 0.304 5459 Planarity : 0.004 0.071 5691 Dihedral : 18.557 178.680 6102 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.38 % Allowed : 22.86 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % 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: 1.08 (0.14), residues: 3884 helix: 1.69 (0.13), residues: 1642 sheet: 0.61 (0.25), residues: 451 loop : -0.11 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 431 TYR 0.020 0.001 TYR C 73 PHE 0.020 0.001 PHE C 906 TRP 0.007 0.001 TRP K 15 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (35026) covalent geometry : angle 0.57152 / 0.31 (47971) hydrogen bonds : bond 0.04186 / 2.76 ( 1614) hydrogen bonds : angle 4.19853 / 4.11 ( 4478) metal coordination : bond 0.00602 / 0.32 ( 7) metal coordination : angle 1.99813 / 1.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 3371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 710 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 ARG cc_start: 0.4030 (ptm-80) cc_final: 0.0252 (pmm150) REVERT: H 30 MET cc_start: 0.6136 (tmt) cc_final: 0.5751 (tmt) REVERT: C 189 ASP cc_start: 0.7436 (p0) cc_final: 0.7209 (p0) REVERT: C 200 ARG cc_start: 0.7820 (mmt180) cc_final: 0.7408 (mmt-90) REVERT: C 255 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6526 (tt) REVERT: C 365 GLU cc_start: 0.7878 (tp30) cc_final: 0.7595 (tp30) REVERT: C 484 LEU cc_start: 0.8569 (mt) cc_final: 0.8337 (mp) REVERT: C 542 ARG cc_start: 0.7559 (mtp180) cc_final: 0.7314 (mtp180) REVERT: C 859 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7139 (tm-30) REVERT: C 937 ASP cc_start: 0.7352 (t0) cc_final: 0.7081 (t0) REVERT: C 968 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.6125 (pt0) REVERT: C 1032 LYS cc_start: 0.8416 (tppp) cc_final: 0.8150 (mmmm) REVERT: C 1107 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8622 (mtt) REVERT: C 1200 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8324 (tp) REVERT: C 1218 ASP cc_start: 0.8254 (m-30) cc_final: 0.7946 (m-30) REVERT: D 86 GLU cc_start: 0.7411 (pm20) cc_final: 0.7187 (pm20) REVERT: D 161 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7331 (p) REVERT: D 183 GLU cc_start: 0.7593 (tp30) cc_final: 0.7272 (tp30) REVERT: D 192 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8622 (ttp) REVERT: D 201 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7452 (mtm) REVERT: D 301 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7283 (tm-30) REVERT: D 569 MET cc_start: 0.8882 (mmm) cc_final: 0.8495 (mmt) REVERT: D 607 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: D 653 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: D 710 GLN cc_start: 0.7764 (mp10) cc_final: 0.7497 (mp10) REVERT: D 712 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6884 (tm-30) REVERT: D 715 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8288 (tptp) REVERT: D 749 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7900 (ttp-110) REVERT: D 817 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8835 (mt) REVERT: D 833 VAL cc_start: 0.8702 (p) cc_final: 0.8409 (m) REVERT: D 872 ILE cc_start: 0.8333 (mt) cc_final: 0.8091 (mm) REVERT: D 1156 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8178 (mt) REVERT: D 1158 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7277 (pt0) REVERT: D 1214 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7472 (mt-10) REVERT: D 1223 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8030 (mtt180) REVERT: D 1366 GLN cc_start: 0.8174 (mt0) cc_final: 0.7915 (mt0) REVERT: D 1371 LYS cc_start: 0.8480 (mmtm) cc_final: 0.8149 (tppp) REVERT: A 22 THR cc_start: 0.8831 (p) cc_final: 0.8611 (p) REVERT: A 33 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.8020 (ttp-110) REVERT: B 64 VAL cc_start: 0.8958 (t) cc_final: 0.8645 (m) REVERT: F 107 MET cc_start: 0.7142 (ppp) cc_final: 0.6891 (pp-130) REVERT: F 389 GLU cc_start: 0.7299 (mm-30) cc_final: 0.7075 (mm-30) REVERT: F 400 LYS cc_start: 0.8008 (tppt) cc_final: 0.7606 (pttt) REVERT: F 415 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7603 (mm-30) REVERT: F 464 MET cc_start: 0.8253 (tpp) cc_final: 0.7996 (tpt) REVERT: F 484 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7961 (ptt180) REVERT: F 490 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7893 (mt-10) REVERT: F 529 ASP cc_start: 0.7569 (p0) cc_final: 0.7340 (p0) REVERT: F 563 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: F 583 GLU cc_start: 0.8163 (pm20) cc_final: 0.7915 (pm20) outliers start: 114 outliers final: 68 residues processed: 755 average time/residue: 0.8345 time to fit residues: 737.1934 Evaluate side-chains 786 residues out of total 3371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 699 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 739 GLU Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 968 GLU Chi-restraints excluded: chain C residue 1000 GLN Chi-restraints excluded: chain C residue 1034 ARG Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1162 GLU Chi-restraints excluded: chain C residue 1185 VAL Chi-restraints excluded: chain C residue 1191 GLU Chi-restraints excluded: chain C residue 1200 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 653 GLU Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 749 ARG Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 807 VAL Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 836 THR Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 879 GLN Chi-restraints excluded: chain D residue 891 ASP Chi-restraints excluded: chain D residue 992 LYS Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1158 GLU Chi-restraints excluded: chain D residue 1159 HIS Chi-restraints excluded: chain D residue 1188 MET Chi-restraints excluded: chain D residue 1192 HIS Chi-restraints excluded: chain D residue 1223 ARG Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain F residue 425 ASP Chi-restraints excluded: chain F residue 445 GLN Chi-restraints excluded: chain F residue 484 ARG Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 563 GLU Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 278 TYR Chi-restraints excluded: chain G residue 285 ARG Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 321 ASN Chi-restraints excluded: chain I residue 52 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 0.3980 chunk 369 optimal weight: 1.9990 chunk 314 optimal weight: 2.9990 chunk 327 optimal weight: 5.9990 chunk 187 optimal weight: 0.4980 chunk 348 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 284 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 46 GLN C 173 ASN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 922 ASN C1243 HIS D 94 GLN D 805 GLN A 84 ASN F 579 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.167344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.134562 restraints weight = 79853.570| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.83 r_work: 0.3548 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35033 Z= 0.139 Angle : 0.573 16.647 47977 Z= 0.307 Chirality : 0.042 0.307 5459 Planarity : 0.004 0.105 5691 Dihedral : 18.525 177.373 6102 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.50 % Allowed : 23.07 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % 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: 1.09 (0.14), residues: 3884 helix: 1.70 (0.13), residues: 1645 sheet: 0.63 (0.25), residues: 452 loop : -0.11 (0.15), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG D1329 TYR 0.017 0.001 TYR D 631 PHE 0.024 0.001 PHE C 514 TRP 0.007 0.001 TRP K 15 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (35026) covalent geometry : angle 0.57308 / 0.31 (47971) hydrogen bonds : bond 0.04106 / 2.71 ( 1614) hydrogen bonds : angle 4.17891 / 4.08 ( 4478) metal coordination : bond 0.00592 / 0.31 ( 7) metal coordination : angle 1.98751 / 1.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 3371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 709 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 ARG cc_start: 0.4130 (ptm-80) cc_final: 0.0314 (pmm150) REVERT: H 30 MET cc_start: 0.6055 (tmt) cc_final: 0.5676 (tmt) REVERT: K 65 LYS cc_start: 0.7696 (mttt) cc_final: 0.7485 (mptt) REVERT: K 82 ILE cc_start: 0.8640 (mp) cc_final: 0.8373 (mt) REVERT: C 101 ARG cc_start: 0.8079 (mtt90) cc_final: 0.7859 (mtm-85) REVERT: C 119 GLU cc_start: 0.7999 (tp30) cc_final: 0.7793 (tp30) REVERT: C 189 ASP cc_start: 0.7451 (p0) cc_final: 0.7230 (p0) REVERT: C 200 ARG cc_start: 0.7807 (mmt180) cc_final: 0.7393 (mmt-90) REVERT: C 255 ILE cc_start: 0.6736 (OUTLIER) cc_final: 0.6481 (tt) REVERT: C 484 LEU cc_start: 0.8537 (mt) cc_final: 0.8307 (mp) REVERT: C 542 ARG cc_start: 0.7504 (mtp180) cc_final: 0.7263 (mtp180) REVERT: C 859 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7133 (tm-30) REVERT: C 937 ASP cc_start: 0.7346 (t0) cc_final: 0.7086 (t0) REVERT: C 968 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6159 (pt0) REVERT: C 1032 LYS cc_start: 0.8469 (tppp) cc_final: 0.8195 (mmmm) REVERT: C 1106 ARG cc_start: 0.8670 (mtt180) cc_final: 0.8393 (mtt-85) REVERT: C 1107 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8609 (mtt) REVERT: C 1200 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8382 (tp) REVERT: C 1218 ASP cc_start: 0.8244 (m-30) cc_final: 0.7956 (m-30) REVERT: D 86 GLU cc_start: 0.7400 (pm20) cc_final: 0.7185 (pm20) REVERT: D 161 THR cc_start: 0.7943 (OUTLIER) cc_final: 0.7384 (p) REVERT: D 183 GLU cc_start: 0.7619 (tp30) cc_final: 0.7406 (tp30) REVERT: D 192 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8629 (ttp) REVERT: D 201 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7493 (mtm) REVERT: D 301 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7327 (tm-30) REVERT: D 569 MET cc_start: 0.8845 (mmm) cc_final: 0.8520 (mmt) REVERT: D 607 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: D 653 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7272 (mt-10) REVERT: D 710 GLN cc_start: 0.7775 (mp10) cc_final: 0.7465 (mp10) REVERT: D 712 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6931 (tm-30) REVERT: D 715 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8288 (tptp) REVERT: D 749 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7881 (ttp-110) REVERT: D 817 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8834 (mt) REVERT: D 833 VAL cc_start: 0.8714 (p) cc_final: 0.8426 (m) REVERT: D 1156 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8191 (mt) REVERT: D 1158 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7263 (pt0) REVERT: D 1163 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.8119 (p) REVERT: D 1214 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7503 (mt-10) REVERT: D 1219 ILE cc_start: 0.8667 (tt) cc_final: 0.8280 (mp) REVERT: D 1223 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8051 (mtt180) REVERT: D 1366 GLN cc_start: 0.8155 (mt0) cc_final: 0.7900 (mt0) REVERT: D 1371 LYS cc_start: 0.8501 (mmtm) cc_final: 0.8171 (tppp) REVERT: A 22 THR cc_start: 0.8848 (p) cc_final: 0.8621 (p) REVERT: A 33 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7948 (ttp-110) REVERT: B 64 VAL cc_start: 0.8949 (t) cc_final: 0.8640 (m) REVERT: B 151 ARG cc_start: 0.8904 (mtm-85) cc_final: 0.8673 (mtm-85) REVERT: F 107 MET cc_start: 0.7175 (ppp) cc_final: 0.6927 (pp-130) REVERT: F 296 MET cc_start: 0.6420 (tpp) cc_final: 0.5863 (tpp) REVERT: F 389 GLU cc_start: 0.7309 (mm-30) cc_final: 0.7092 (mm-30) REVERT: F 415 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7648 (tp30) REVERT: F 464 MET cc_start: 0.8299 (tpp) cc_final: 0.7987 (tpt) REVERT: F 477 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7936 (tm-30) REVERT: F 484 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8003 (ptt180) REVERT: F 490 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7695 (mt-10) REVERT: F 529 ASP cc_start: 0.7578 (p0) cc_final: 0.7346 (p0) REVERT: F 563 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7730 (tp30) REVERT: F 583 GLU cc_start: 0.8192 (pm20) cc_final: 0.7991 (pm20) outliers start: 118 outliers final: 71 residues processed: 754 average time/residue: 0.8594 time to fit residues: 767.4518 Evaluate side-chains 793 residues out of total 3371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 702 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 42 MET Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 739 GLU Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 968 GLU Chi-restraints excluded: chain C residue 1000 GLN Chi-restraints excluded: chain C residue 1034 ARG Chi-restraints excluded: chain C residue 1036 ILE Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1162 GLU Chi-restraints excluded: chain C residue 1185 VAL Chi-restraints excluded: chain C residue 1191 GLU Chi-restraints excluded: chain C residue 1200 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 653 GLU Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 749 ARG Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 807 VAL Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 836 THR Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 879 GLN Chi-restraints excluded: chain D residue 992 LYS Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1158 GLU Chi-restraints excluded: chain D residue 1159 HIS Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1188 MET Chi-restraints excluded: chain D residue 1192 HIS Chi-restraints excluded: chain D residue 1223 ARG Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain F residue 425 ASP Chi-restraints excluded: chain F residue 445 GLN Chi-restraints excluded: chain F residue 484 ARG Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 563 GLU Chi-restraints excluded: chain F residue 575 MET Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 278 TYR Chi-restraints excluded: chain G residue 285 ARG Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 321 ASN Chi-restraints excluded: chain I residue 52 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 270 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 316 optimal weight: 0.0170 chunk 58 optimal weight: 0.0870 chunk 138 optimal weight: 0.7980 chunk 154 optimal weight: 0.6980 chunk 282 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 269 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 357 optimal weight: 9.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 173 ASN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN C 922 ASN C1243 HIS D 94 GLN D 805 GLN A 84 ASN F 579 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.167596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.134912 restraints weight = 84463.647| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.77 r_work: 0.3555 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35033 Z= 0.130 Angle : 0.573 16.760 47977 Z= 0.306 Chirality : 0.042 0.308 5459 Planarity : 0.004 0.057 5691 Dihedral : 18.501 176.593 6100 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.14 % Allowed : 23.54 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % 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: 1.12 (0.14), residues: 3884 helix: 1.73 (0.13), residues: 1647 sheet: 0.64 (0.25), residues: 452 loop : -0.10 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 403 TYR 0.021 0.001 TYR C 73 PHE 0.022 0.001 PHE C 906 TRP 0.007 0.001 TRP K 15 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (35026) covalent geometry : angle 0.57257 / 0.31 (47971) hydrogen bonds : bond 0.04019 / 2.64 ( 1614) hydrogen bonds : angle 4.15108 / 4.06 ( 4478) metal coordination : bond 0.00531 / 0.28 ( 7) metal coordination : angle 1.87341 / 1.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 3371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 698 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 ARG cc_start: 0.4122 (ptm-80) cc_final: 0.0308 (pmm150) REVERT: H 30 MET cc_start: 0.5995 (tmt) cc_final: 0.5624 (tmt) REVERT: K 65 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7481 (mptt) REVERT: C 101 ARG cc_start: 0.8106 (mtt90) cc_final: 0.7875 (mtm-85) REVERT: C 119 GLU cc_start: 0.7992 (tp30) cc_final: 0.7792 (tp30) REVERT: C 189 ASP cc_start: 0.7445 (p0) cc_final: 0.7227 (p0) REVERT: C 200 ARG cc_start: 0.7768 (mmt180) cc_final: 0.7377 (mmt-90) REVERT: C 255 ILE cc_start: 0.6716 (OUTLIER) cc_final: 0.6496 (tt) REVERT: C 382 GLU cc_start: 0.8035 (tp30) cc_final: 0.7763 (tm-30) REVERT: C 484 LEU cc_start: 0.8514 (mt) cc_final: 0.8291 (mp) REVERT: C 542 ARG cc_start: 0.7515 (mtp180) cc_final: 0.7285 (mtp180) REVERT: C 859 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7146 (tm-30) REVERT: C 937 ASP cc_start: 0.7350 (t0) cc_final: 0.7089 (t0) REVERT: C 968 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.6209 (pt0) REVERT: C 1032 LYS cc_start: 0.8471 (tppp) cc_final: 0.8203 (mmmm) REVERT: C 1106 ARG cc_start: 0.8656 (mtt180) cc_final: 0.8380 (mtt-85) REVERT: C 1107 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8602 (mtt) REVERT: C 1200 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8393 (tp) REVERT: C 1218 ASP cc_start: 0.8233 (m-30) cc_final: 0.7945 (m-30) REVERT: D 86 GLU cc_start: 0.7396 (pm20) cc_final: 0.7183 (pm20) REVERT: D 161 THR cc_start: 0.7955 (OUTLIER) cc_final: 0.7371 (p) REVERT: D 183 GLU cc_start: 0.7627 (tp30) cc_final: 0.7412 (tp30) REVERT: D 201 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7487 (mtm) REVERT: D 301 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7337 (tm-30) REVERT: D 484 MET cc_start: 0.8658 (mtp) cc_final: 0.8176 (mtp) REVERT: D 607 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: D 710 GLN cc_start: 0.7798 (mp10) cc_final: 0.7533 (mp10) REVERT: D 712 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6953 (tm-30) REVERT: D 715 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8308 (tptp) REVERT: D 749 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7854 (ttp-110) REVERT: D 817 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8830 (mt) REVERT: D 833 VAL cc_start: 0.8708 (p) cc_final: 0.8422 (m) REVERT: D 1156 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8214 (mt) REVERT: D 1158 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7231 (pt0) REVERT: D 1163 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8136 (p) REVERT: D 1214 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7518 (mt-10) REVERT: D 1219 ILE cc_start: 0.8670 (tt) cc_final: 0.8294 (mp) REVERT: D 1223 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8069 (mtt180) REVERT: D 1366 GLN cc_start: 0.8166 (mt0) cc_final: 0.7908 (mt0) REVERT: A 22 THR cc_start: 0.8855 (p) cc_final: 0.8619 (p) REVERT: A 33 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7945 (ttp-110) REVERT: B 64 VAL cc_start: 0.8942 (t) cc_final: 0.8641 (m) REVERT: F 107 MET cc_start: 0.7199 (ppp) cc_final: 0.6955 (pp-130) REVERT: F 296 MET cc_start: 0.6409 (tpp) cc_final: 0.5824 (tpp) REVERT: F 389 GLU cc_start: 0.7308 (mm-30) cc_final: 0.7102 (mm-30) REVERT: F 400 LYS cc_start: 0.7994 (tppt) cc_final: 0.7566 (pttt) REVERT: F 415 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7660 (tp30) REVERT: F 464 MET cc_start: 0.8299 (tpp) cc_final: 0.7995 (tpt) REVERT: F 476 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7924 (ptp90) REVERT: F 477 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7940 (tm-30) REVERT: F 490 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7622 (mt-10) REVERT: F 529 ASP cc_start: 0.7585 (p0) cc_final: 0.7354 (p0) REVERT: F 563 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7732 (tp30) REVERT: F 583 GLU cc_start: 0.8185 (pm20) cc_final: 0.7834 (pm20) outliers start: 106 outliers final: 71 residues processed: 742 average time/residue: 0.8101 time to fit residues: 703.2447 Evaluate side-chains 783 residues out of total 3371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 693 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 739 GLU Chi-restraints excluded: chain C residue 968 GLU Chi-restraints excluded: chain C residue 1000 GLN Chi-restraints excluded: chain C residue 1034 ARG Chi-restraints excluded: chain C residue 1036 ILE Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1162 GLU Chi-restraints excluded: chain C residue 1185 VAL Chi-restraints excluded: chain C residue 1191 GLU Chi-restraints excluded: chain C residue 1200 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 749 ARG Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 807 VAL Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 836 THR Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 879 GLN Chi-restraints excluded: chain D residue 992 LYS Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1158 GLU Chi-restraints excluded: chain D residue 1159 HIS Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1188 MET Chi-restraints excluded: chain D residue 1192 HIS Chi-restraints excluded: chain D residue 1223 ARG Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain F residue 425 ASP Chi-restraints excluded: chain F residue 445 GLN Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 563 GLU Chi-restraints excluded: chain F residue 575 MET Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 278 TYR Chi-restraints excluded: chain G residue 285 ARG Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 321 ASN Chi-restraints excluded: chain I residue 52 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 71 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 125 optimal weight: 0.2980 chunk 238 optimal weight: 2.9990 chunk 357 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 78 optimal weight: 0.4980 chunk 283 optimal weight: 0.5980 chunk 246 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 173 ASN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 922 ASN C 950 GLN C1243 HIS D 94 GLN D 805 GLN A 84 ASN F 579 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.166899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.134486 restraints weight = 77187.360| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.65 r_work: 0.3553 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 35033 Z= 0.160 Angle : 0.588 16.822 47977 Z= 0.313 Chirality : 0.043 0.309 5459 Planarity : 0.004 0.056 5691 Dihedral : 18.502 176.103 6100 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.20 % Allowed : 23.45 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % 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: 1.07 (0.14), residues: 3884 helix: 1.68 (0.13), residues: 1645 sheet: 0.61 (0.25), residues: 456 loop : -0.11 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 403 TYR 0.019 0.001 TYR D 631 PHE 0.016 0.001 PHE H 88 TRP 0.008 0.001 TRP H 16 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (35026) covalent geometry : angle 0.58755 / 0.31 (47971) hydrogen bonds : bond 0.04263 / 2.82 ( 1614) hydrogen bonds : angle 4.18484 / 4.11 ( 4478) metal coordination : bond 0.00680 / 0.36 ( 7) metal coordination : angle 2.03897 / 1.28 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7768 Ramachandran restraints generated. 3884 Oldfield, 0 Emsley, 3884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 3371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 712 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 ARG cc_start: 0.4015 (ptm-80) cc_final: 0.0288 (pmm150) REVERT: H 30 MET cc_start: 0.6140 (tmt) cc_final: 0.5758 (tmt) REVERT: K 65 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7476 (mptt) REVERT: C 189 ASP cc_start: 0.7451 (p0) cc_final: 0.7232 (p0) REVERT: C 200 ARG cc_start: 0.7788 (mmt180) cc_final: 0.7399 (mmt-90) REVERT: C 255 ILE cc_start: 0.6717 (OUTLIER) cc_final: 0.6488 (tt) REVERT: C 365 GLU cc_start: 0.7872 (tp30) cc_final: 0.7610 (tp30) REVERT: C 382 GLU cc_start: 0.8093 (tp30) cc_final: 0.7731 (tm-30) REVERT: C 484 LEU cc_start: 0.8502 (mt) cc_final: 0.8277 (mp) REVERT: C 542 ARG cc_start: 0.7479 (mtp180) cc_final: 0.7250 (mtp180) REVERT: C 859 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7150 (tm-30) REVERT: C 949 GLU cc_start: 0.7172 (tp30) cc_final: 0.6920 (tp30) REVERT: C 968 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6199 (pt0) REVERT: C 1032 LYS cc_start: 0.8478 (tppp) cc_final: 0.8210 (mmmm) REVERT: C 1106 ARG cc_start: 0.8674 (mtt180) cc_final: 0.8356 (mtt180) REVERT: C 1107 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8610 (mtt) REVERT: C 1200 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8391 (tp) REVERT: C 1218 ASP cc_start: 0.8214 (m-30) cc_final: 0.7934 (m-30) REVERT: D 86 GLU cc_start: 0.7353 (pm20) cc_final: 0.7145 (pm20) REVERT: D 161 THR cc_start: 0.7984 (OUTLIER) cc_final: 0.7464 (p) REVERT: D 183 GLU cc_start: 0.7594 (tp30) cc_final: 0.7285 (tp30) REVERT: D 201 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7476 (mtm) REVERT: D 301 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7309 (tm-30) REVERT: D 484 MET cc_start: 0.8653 (mtp) cc_final: 0.8187 (mtp) REVERT: D 607 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: D 710 GLN cc_start: 0.7809 (mp10) cc_final: 0.7535 (mp10) REVERT: D 715 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8267 (tptp) REVERT: D 749 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7897 (ttp-110) REVERT: D 817 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8837 (mt) REVERT: D 833 VAL cc_start: 0.8706 (p) cc_final: 0.8419 (m) REVERT: D 1156 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8228 (mt) REVERT: D 1158 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7281 (pt0) REVERT: D 1214 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7486 (mt-10) REVERT: D 1219 ILE cc_start: 0.8670 (tt) cc_final: 0.8300 (mp) REVERT: D 1223 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8067 (mtt180) REVERT: A 22 THR cc_start: 0.8856 (p) cc_final: 0.8618 (p) REVERT: A 33 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7937 (ttp-110) REVERT: B 64 VAL cc_start: 0.8954 (t) cc_final: 0.8649 (m) REVERT: B 144 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8042 (ttt90) REVERT: F 107 MET cc_start: 0.7202 (ppp) cc_final: 0.6962 (pp-130) REVERT: F 296 MET cc_start: 0.6316 (tpp) cc_final: 0.5724 (tpp) REVERT: F 415 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7656 (tp30) REVERT: F 464 MET cc_start: 0.8326 (tpp) cc_final: 0.8093 (tpt) REVERT: F 476 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7899 (ptp90) REVERT: F 477 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7920 (tm-30) REVERT: F 484 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7396 (ptm-80) REVERT: F 490 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7775 (mt-10) REVERT: F 529 ASP cc_start: 0.7562 (p0) cc_final: 0.7334 (p0) REVERT: F 555 VAL cc_start: 0.8406 (t) cc_final: 0.7974 (p) REVERT: F 563 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7734 (tp30) outliers start: 108 outliers final: 75 residues processed: 755 average time/residue: 0.7596 time to fit residues: 672.5763 Evaluate side-chains 803 residues out of total 3371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 709 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 42 MET Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 739 GLU Chi-restraints excluded: chain C residue 837 SER Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 968 GLU Chi-restraints excluded: chain C residue 1000 GLN Chi-restraints excluded: chain C residue 1034 ARG Chi-restraints excluded: chain C residue 1036 ILE Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1162 GLU Chi-restraints excluded: chain C residue 1185 VAL Chi-restraints excluded: chain C residue 1191 GLU Chi-restraints excluded: chain C residue 1200 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 749 ARG Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 807 VAL Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 836 THR Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 992 LYS Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1158 GLU Chi-restraints excluded: chain D residue 1159 HIS Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1188 MET Chi-restraints excluded: chain D residue 1192 HIS Chi-restraints excluded: chain D residue 1223 ARG Chi-restraints excluded: chain D residue 1239 VAL Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain F residue 425 ASP Chi-restraints excluded: chain F residue 445 GLN Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 484 ARG Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 563 GLU Chi-restraints excluded: chain F residue 575 MET Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 278 TYR Chi-restraints excluded: chain G residue 285 ARG Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 321 ASN Chi-restraints excluded: chain I residue 52 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 100 optimal weight: 0.7980 chunk 314 optimal weight: 2.9990 chunk 106 optimal weight: 0.0980 chunk 20 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 203 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 355 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 343 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 62 GLN C 173 ASN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN C 922 ASN C1243 HIS D 94 GLN D 805 GLN A 84 ASN F 579 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.167230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.134865 restraints weight = 68753.958| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.49 r_work: 0.3572 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 35033 Z= 0.145 Angle : 0.585 16.755 47977 Z= 0.312 Chirality : 0.042 0.309 5459 Planarity : 0.005 0.097 5691 Dihedral : 18.486 175.031 6100 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.91 % Allowed : 23.90 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % 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: 1.08 (0.14), residues: 3884 helix: 1.68 (0.13), residues: 1645 sheet: 0.63 (0.25), residues: 457 loop : -0.11 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG D1329 TYR 0.019 0.001 TYR C 73 PHE 0.026 0.001 PHE C 514 TRP 0.008 0.001 TRP H 15 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (35026) covalent geometry : angle 0.58490 / 0.31 (47971) hydrogen bonds : bond 0.04125 / 2.72 ( 1614) hydrogen bonds : angle 4.17647 / 4.10 ( 4478) metal coordination : bond 0.00608 / 0.32 ( 7) metal coordination : angle 1.88143 / 1.18 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19596.29 seconds wall clock time: 332 minutes 20.55 seconds (19940.55 seconds total)