Starting phenix.real_space_refine on Tue Aug 26 23:20:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hf1_34708/08_2025/8hf1_34708.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hf1_34708/08_2025/8hf1_34708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hf1_34708/08_2025/8hf1_34708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hf1_34708/08_2025/8hf1_34708.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hf1_34708/08_2025/8hf1_34708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hf1_34708/08_2025/8hf1_34708.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.053 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: 5 Type Number sf(0) Gaussians P 60 5.49 5 S 230 5.16 5 C 26898 2.51 5 N 7205 2.21 5 O 7986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42379 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 12634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1561, 12634 Classifications: {'peptide': 1561} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 65, 'TRANS': 1495} Chain breaks: 2 Chain: "B" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 144 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "C" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1027 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "D" Number of atoms: 12634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1561, 12634 Classifications: {'peptide': 1561} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 65, 'TRANS': 1495} Chain breaks: 2 Chain: "E" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 196 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna3p': 8} Chain: "F" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1027 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "G" Number of atoms: 12634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1561, 12634 Classifications: {'peptide': 1561} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 65, 'TRANS': 1495} Chain breaks: 2 Chain: "H" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 227 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 8} Link IDs: {'rna3p': 10} Chain: "I" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1010 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "J" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 196 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna3p': 8} Chain: "K" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 227 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 8} Link IDs: {'rna3p': 10} Chain: "L" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 196 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna3p': 8} Chain: "M" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 227 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 8} Link IDs: {'rna3p': 10} Time building chain proxies: 8.33, per 1000 atoms: 0.20 Number of scatterers: 42379 At special positions: 0 Unit cell: (159.84, 258.12, 189, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 230 16.00 P 60 15.00 O 7986 8.00 N 7205 7.00 C 26898 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: 3.69 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 476.8 nanoseconds 10098 Ramachandran restraints generated. 5049 Oldfield, 0 Emsley, 5049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9718 Finding SS restraints... Secondary structure from input PDB file: 228 helices and 39 sheets defined 55.0% alpha, 10.2% beta 25 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 4.93 Creating SS restraints... Processing helix chain 'A' and resid 9 through 22 removed outlier: 3.779A pdb=" N LYS A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 45 removed outlier: 4.049A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 89 through 97 removed outlier: 5.751A pdb=" N VAL A 94 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ASP A 95 " --> pdb=" O GLN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 148 through 157 removed outlier: 3.717A pdb=" N PHE A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.597A pdb=" N LYS A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 215 removed outlier: 3.773A pdb=" N TYR A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 251 removed outlier: 3.603A pdb=" N ARG A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 314 removed outlier: 7.859A pdb=" N ILE A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 9.722A pdb=" N TYR A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA A 295 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 343 Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 350 through 362 Processing helix chain 'A' and resid 364 through 378 Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.638A pdb=" N CYS A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.671A pdb=" N ALA A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 535 Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 567 through 580 removed outlier: 4.653A pdb=" N LEU A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ALA A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 607 Processing helix chain 'A' and resid 637 through 656 Processing helix chain 'A' and resid 667 through 680 removed outlier: 3.501A pdb=" N ILE A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASP A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 687 removed outlier: 3.619A pdb=" N LYS A 685 " --> pdb=" O HIS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 697 removed outlier: 3.607A pdb=" N LYS A 696 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 749 Processing helix chain 'A' and resid 792 through 809 removed outlier: 3.834A pdb=" N PHE A 807 " --> pdb=" O HIS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 852 Processing helix chain 'A' and resid 862 through 868 removed outlier: 4.751A pdb=" N GLN A 868 " --> pdb=" O GLN A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 878 removed outlier: 3.602A pdb=" N PHE A 877 " --> pdb=" O ARG A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 930 removed outlier: 6.939A pdb=" N ASN A 927 " --> pdb=" O SER A 923 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ARG A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 967 removed outlier: 3.928A pdb=" N MET A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 991 removed outlier: 3.977A pdb=" N PHE A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1016 Processing helix chain 'A' and resid 1174 through 1182 Processing helix chain 'A' and resid 1183 through 1186 Processing helix chain 'A' and resid 1190 through 1199 Processing helix chain 'A' and resid 1209 through 1232 removed outlier: 3.748A pdb=" N LEU A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1248 Processing helix chain 'A' and resid 1249 through 1259 Processing helix chain 'A' and resid 1262 through 1266 Processing helix chain 'A' and resid 1272 through 1277 removed outlier: 3.541A pdb=" N TRP A1277 " --> pdb=" O PRO A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1294 Processing helix chain 'A' and resid 1295 through 1300 removed outlier: 4.026A pdb=" N LYS A1300 " --> pdb=" O PRO A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1303 through 1309 Processing helix chain 'A' and resid 1313 through 1319 Processing helix chain 'A' and resid 1324 through 1342 Processing helix chain 'A' and resid 1347 through 1356 removed outlier: 4.253A pdb=" N GLU A1351 " --> pdb=" O PHE A1348 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN A1353 " --> pdb=" O SER A1350 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N PHE A1354 " --> pdb=" O GLU A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1394 removed outlier: 3.617A pdb=" N LEU A1370 " --> pdb=" O ILE A1366 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU A1383 " --> pdb=" O LYS A1379 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N GLN A1384 " --> pdb=" O ASN A1380 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS A1385 " --> pdb=" O TYR A1381 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS A1388 " --> pdb=" O GLN A1384 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET A1389 " --> pdb=" O HIS A1385 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A1390 " --> pdb=" O ALA A1386 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A1391 " --> pdb=" O PHE A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1410 removed outlier: 3.746A pdb=" N GLN A1406 " --> pdb=" O PRO A1403 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A1407 " --> pdb=" O LEU A1404 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU A1408 " --> pdb=" O THR A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1430 removed outlier: 4.097A pdb=" N ILE A1426 " --> pdb=" O ASN A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1441 Processing helix chain 'A' and resid 1447 through 1455 Processing helix chain 'A' and resid 1468 through 1491 removed outlier: 3.844A pdb=" N ALA A1477 " --> pdb=" O PHE A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1508 Processing helix chain 'A' and resid 1508 through 1519 Processing helix chain 'A' and resid 1520 through 1525 removed outlier: 3.722A pdb=" N PHE A1523 " --> pdb=" O ARG A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1546 Processing helix chain 'A' and resid 1609 through 1628 removed outlier: 4.494A pdb=" N GLY A1613 " --> pdb=" O PRO A1609 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1651 Proline residue: A1643 - end of helix removed outlier: 3.949A pdb=" N ARG A1650 " --> pdb=" O GLN A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1655 through 1663 Processing helix chain 'A' and resid 1701 through 1722 Processing helix chain 'C' and resid 189 through 210 removed outlier: 4.168A pdb=" N LEU C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C 201 " --> pdb=" O ARG C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 224 removed outlier: 4.129A pdb=" N HIS C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 231 through 244 Processing helix chain 'C' and resid 249 through 261 Processing helix chain 'C' and resid 295 through 310 removed outlier: 4.353A pdb=" N TYR C 299 " --> pdb=" O GLU C 295 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASP C 300 " --> pdb=" O THR C 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 22 removed outlier: 3.724A pdb=" N LYS D 21 " --> pdb=" O ASP D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 45 removed outlier: 3.913A pdb=" N THR D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 56 Processing helix chain 'D' and resid 66 through 81 Processing helix chain 'D' and resid 89 through 97 removed outlier: 5.702A pdb=" N VAL D 94 " --> pdb=" O GLU D 91 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ASP D 95 " --> pdb=" O GLN D 92 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TRP D 97 " --> pdb=" O VAL D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 109 Processing helix chain 'D' and resid 116 through 125 Processing helix chain 'D' and resid 129 through 131 No H-bonds generated for 'chain 'D' and resid 129 through 131' Processing helix chain 'D' and resid 140 through 144 Processing helix chain 'D' and resid 148 through 158 removed outlier: 3.656A pdb=" N PHE D 157 " --> pdb=" O PHE D 153 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR D 158 " --> pdb=" O MET D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 195 removed outlier: 3.638A pdb=" N LYS D 187 " --> pdb=" O ASN D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 213 Processing helix chain 'D' and resid 232 through 251 removed outlier: 3.613A pdb=" N ARG D 236 " --> pdb=" O LEU D 232 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 251 " --> pdb=" O VAL D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 292 Processing helix chain 'D' and resid 293 through 314 removed outlier: 3.728A pdb=" N ILE D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 343 Processing helix chain 'D' and resid 344 through 348 Processing helix chain 'D' and resid 350 through 362 removed outlier: 3.500A pdb=" N GLU D 356 " --> pdb=" O ASN D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 378 Processing helix chain 'D' and resid 382 through 386 removed outlier: 3.720A pdb=" N ILE D 386 " --> pdb=" O PRO D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 410 removed outlier: 3.901A pdb=" N LYS D 399 " --> pdb=" O ARG D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 484 through 495 removed outlier: 3.641A pdb=" N ALA D 495 " --> pdb=" O SER D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 535 removed outlier: 3.696A pdb=" N ARG D 535 " --> pdb=" O TYR D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 552 removed outlier: 3.805A pdb=" N PHE D 551 " --> pdb=" O ILE D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 569 No H-bonds generated for 'chain 'D' and resid 567 through 569' Processing helix chain 'D' and resid 570 through 580 removed outlier: 3.592A pdb=" N GLN D 580 " --> pdb=" O HIS D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 589 removed outlier: 4.251A pdb=" N PHE D 589 " --> pdb=" O ALA D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 607 Processing helix chain 'D' and resid 637 through 656 Processing helix chain 'D' and resid 667 through 680 removed outlier: 4.307A pdb=" N ASP D 677 " --> pdb=" O ALA D 673 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N VAL D 678 " --> pdb=" O SER D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 687 Processing helix chain 'D' and resid 693 through 697 removed outlier: 3.668A pdb=" N ALA D 697 " --> pdb=" O VAL D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 749 removed outlier: 3.532A pdb=" N GLN D 749 " --> pdb=" O TYR D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 810 removed outlier: 3.729A pdb=" N PHE D 807 " --> pdb=" O HIS D 803 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 852 Processing helix chain 'D' and resid 862 through 868 removed outlier: 4.332A pdb=" N GLN D 868 " --> pdb=" O GLN D 864 " (cutoff:3.500A) Processing helix chain 'D' and resid 873 through 878 removed outlier: 3.647A pdb=" N PHE D 877 " --> pdb=" O ARG D 873 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 930 removed outlier: 7.038A pdb=" N ASN D 927 " --> pdb=" O SER D 923 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG D 928 " --> pdb=" O LYS D 924 " (cutoff:3.500A) Processing helix chain 'D' and resid 960 through 967 removed outlier: 3.852A pdb=" N MET D 967 " --> pdb=" O SER D 963 " (cutoff:3.500A) Processing helix chain 'D' and resid 972 through 976 removed outlier: 3.711A pdb=" N CYS D 976 " --> pdb=" O PRO D 973 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 990 Processing helix chain 'D' and resid 991 through 1016 removed outlier: 3.691A pdb=" N PHE D1001 " --> pdb=" O ASN D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1021 removed outlier: 4.020A pdb=" N LEU D1020 " --> pdb=" O ASN D1017 " (cutoff:3.500A) Processing helix chain 'D' and resid 1174 through 1182 Processing helix chain 'D' and resid 1183 through 1186 Processing helix chain 'D' and resid 1190 through 1199 Processing helix chain 'D' and resid 1209 through 1232 removed outlier: 3.819A pdb=" N LEU D1215 " --> pdb=" O ARG D1211 " (cutoff:3.500A) Processing helix chain 'D' and resid 1236 through 1249 Processing helix chain 'D' and resid 1249 through 1259 Processing helix chain 'D' and resid 1260 through 1261 No H-bonds generated for 'chain 'D' and resid 1260 through 1261' Processing helix chain 'D' and resid 1262 through 1266 Processing helix chain 'D' and resid 1285 through 1295 Processing helix chain 'D' and resid 1295 through 1301 removed outlier: 4.358A pdb=" N ILE D1301 " --> pdb=" O GLU D1297 " (cutoff:3.500A) Processing helix chain 'D' and resid 1303 through 1310 removed outlier: 3.591A pdb=" N LEU D1307 " --> pdb=" O GLY D1303 " (cutoff:3.500A) Processing helix chain 'D' and resid 1313 through 1320 Processing helix chain 'D' and resid 1324 through 1339 removed outlier: 3.658A pdb=" N GLY D1339 " --> pdb=" O CYS D1335 " (cutoff:3.500A) Processing helix chain 'D' and resid 1349 through 1351 No H-bonds generated for 'chain 'D' and resid 1349 through 1351' Processing helix chain 'D' and resid 1352 through 1357 removed outlier: 3.957A pdb=" N VAL D1356 " --> pdb=" O VAL D1352 " (cutoff:3.500A) Processing helix chain 'D' and resid 1363 through 1393 removed outlier: 7.889A pdb=" N LEU D1383 " --> pdb=" O LYS D1379 " (cutoff:3.500A) removed outlier: 9.586A pdb=" N GLN D1384 " --> pdb=" O ASN D1380 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS D1385 " --> pdb=" O TYR D1381 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS D1388 " --> pdb=" O GLN D1384 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET D1389 " --> pdb=" O HIS D1385 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU D1390 " --> pdb=" O ALA D1386 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU D1391 " --> pdb=" O PHE D1387 " (cutoff:3.500A) Processing helix chain 'D' and resid 1403 through 1410 removed outlier: 4.474A pdb=" N LEU D1408 " --> pdb=" O THR D1405 " (cutoff:3.500A) Processing helix chain 'D' and resid 1422 through 1428 removed outlier: 3.854A pdb=" N ILE D1426 " --> pdb=" O ASN D1422 " (cutoff:3.500A) Processing helix chain 'D' and resid 1432 through 1441 Processing helix chain 'D' and resid 1447 through 1454 Processing helix chain 'D' and resid 1468 through 1491 removed outlier: 3.536A pdb=" N ILE D1474 " --> pdb=" O GLU D1470 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA D1477 " --> pdb=" O PHE D1473 " (cutoff:3.500A) Processing helix chain 'D' and resid 1495 through 1508 Processing helix chain 'D' and resid 1508 through 1519 Processing helix chain 'D' and resid 1520 through 1525 removed outlier: 4.077A pdb=" N PHE D1523 " --> pdb=" O ARG D1520 " (cutoff:3.500A) Processing helix chain 'D' and resid 1529 through 1546 removed outlier: 3.536A pdb=" N SER D1533 " --> pdb=" O ASN D1529 " (cutoff:3.500A) Processing helix chain 'D' and resid 1610 through 1628 Processing helix chain 'D' and resid 1629 through 1651 Proline residue: D1643 - end of helix Processing helix chain 'D' and resid 1655 through 1663 Processing helix chain 'D' and resid 1701 through 1722 Processing helix chain 'F' and resid 189 through 210 removed outlier: 4.093A pdb=" N PHE F 201 " --> pdb=" O ARG F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 230 removed outlier: 5.816A pdb=" N HIS F 224 " --> pdb=" O CYS F 221 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE F 227 " --> pdb=" O HIS F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 244 Processing helix chain 'F' and resid 249 through 261 Processing helix chain 'F' and resid 295 through 310 removed outlier: 4.553A pdb=" N TYR F 299 " --> pdb=" O GLU F 295 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ASP F 300 " --> pdb=" O THR F 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 22 removed outlier: 4.016A pdb=" N LYS G 21 " --> pdb=" O ASP G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 45 removed outlier: 3.617A pdb=" N THR G 35 " --> pdb=" O GLY G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 81 Processing helix chain 'G' and resid 89 through 97 removed outlier: 5.490A pdb=" N VAL G 94 " --> pdb=" O GLU G 91 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ASP G 95 " --> pdb=" O GLN G 92 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP G 96 " --> pdb=" O GLY G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 109 Processing helix chain 'G' and resid 115 through 125 removed outlier: 3.543A pdb=" N PHE G 119 " --> pdb=" O THR G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 131 No H-bonds generated for 'chain 'G' and resid 129 through 131' Processing helix chain 'G' and resid 141 through 144 Processing helix chain 'G' and resid 148 through 157 removed outlier: 3.914A pdb=" N PHE G 157 " --> pdb=" O PHE G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 165 removed outlier: 4.004A pdb=" N LYS G 164 " --> pdb=" O ASN G 161 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU G 165 " --> pdb=" O GLN G 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 161 through 165' Processing helix chain 'G' and resid 183 through 195 removed outlier: 3.765A pdb=" N LYS G 187 " --> pdb=" O ASN G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 215 removed outlier: 3.555A pdb=" N LEU G 213 " --> pdb=" O GLU G 209 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYR G 214 " --> pdb=" O ASN G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 251 removed outlier: 3.731A pdb=" N ARG G 236 " --> pdb=" O LEU G 232 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU G 251 " --> pdb=" O VAL G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 292 removed outlier: 3.592A pdb=" N VAL G 277 " --> pdb=" O LYS G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 313 Processing helix chain 'G' and resid 316 through 345 Processing helix chain 'G' and resid 346 through 348 No H-bonds generated for 'chain 'G' and resid 346 through 348' Processing helix chain 'G' and resid 350 through 362 removed outlier: 3.701A pdb=" N GLU G 356 " --> pdb=" O ASN G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 378 Processing helix chain 'G' and resid 382 through 386 Processing helix chain 'G' and resid 394 through 410 removed outlier: 3.579A pdb=" N CYS G 398 " --> pdb=" O ARG G 394 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS G 399 " --> pdb=" O ARG G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 453 Processing helix chain 'G' and resid 484 through 495 removed outlier: 3.704A pdb=" N ALA G 495 " --> pdb=" O SER G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 510 through 535 Processing helix chain 'G' and resid 543 through 550 Processing helix chain 'G' and resid 567 through 569 No H-bonds generated for 'chain 'G' and resid 567 through 569' Processing helix chain 'G' and resid 570 through 580 Processing helix chain 'G' and resid 598 through 607 Processing helix chain 'G' and resid 637 through 656 Processing helix chain 'G' and resid 667 through 680 removed outlier: 4.009A pdb=" N ILE G 675 " --> pdb=" O ARG G 671 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP G 677 " --> pdb=" O ALA G 673 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N VAL G 678 " --> pdb=" O SER G 674 " (cutoff:3.500A) Processing helix chain 'G' and resid 681 through 687 removed outlier: 3.938A pdb=" N LYS G 685 " --> pdb=" O HIS G 682 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY G 687 " --> pdb=" O ASN G 684 " (cutoff:3.500A) Processing helix chain 'G' and resid 738 through 740 No H-bonds generated for 'chain 'G' and resid 738 through 740' Processing helix chain 'G' and resid 741 through 750 removed outlier: 4.127A pdb=" N GLN G 749 " --> pdb=" O TYR G 745 " (cutoff:3.500A) Processing helix chain 'G' and resid 792 through 810 removed outlier: 3.501A pdb=" N LEU G 796 " --> pdb=" O ASN G 792 " (cutoff:3.500A) Processing helix chain 'G' and resid 845 through 852 Processing helix chain 'G' and resid 862 through 868 removed outlier: 4.231A pdb=" N GLN G 868 " --> pdb=" O GLN G 864 " (cutoff:3.500A) Processing helix chain 'G' and resid 873 through 878 removed outlier: 3.535A pdb=" N PHE G 877 " --> pdb=" O ARG G 873 " (cutoff:3.500A) Processing helix chain 'G' and resid 916 through 930 removed outlier: 7.388A pdb=" N ASN G 927 " --> pdb=" O SER G 923 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG G 928 " --> pdb=" O LYS G 924 " (cutoff:3.500A) Processing helix chain 'G' and resid 960 through 967 removed outlier: 4.150A pdb=" N MET G 967 " --> pdb=" O SER G 963 " (cutoff:3.500A) Processing helix chain 'G' and resid 972 through 974 No H-bonds generated for 'chain 'G' and resid 972 through 974' Processing helix chain 'G' and resid 983 through 990 Processing helix chain 'G' and resid 991 through 1017 removed outlier: 3.656A pdb=" N ILE G 995 " --> pdb=" O PHE G 991 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE G1001 " --> pdb=" O ASN G 997 " (cutoff:3.500A) Processing helix chain 'G' and resid 1174 through 1182 Processing helix chain 'G' and resid 1183 through 1186 removed outlier: 3.507A pdb=" N ILE G1186 " --> pdb=" O LYS G1183 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1183 through 1186' Processing helix chain 'G' and resid 1190 through 1199 Processing helix chain 'G' and resid 1209 through 1232 removed outlier: 4.198A pdb=" N LEU G1215 " --> pdb=" O ARG G1211 " (cutoff:3.500A) Processing helix chain 'G' and resid 1236 through 1249 Processing helix chain 'G' and resid 1249 through 1259 removed outlier: 3.515A pdb=" N LEU G1253 " --> pdb=" O SER G1249 " (cutoff:3.500A) Processing helix chain 'G' and resid 1260 through 1261 No H-bonds generated for 'chain 'G' and resid 1260 through 1261' Processing helix chain 'G' and resid 1262 through 1266 Processing helix chain 'G' and resid 1285 through 1294 Processing helix chain 'G' and resid 1295 through 1300 removed outlier: 3.776A pdb=" N LYS G1300 " --> pdb=" O PRO G1296 " (cutoff:3.500A) Processing helix chain 'G' and resid 1303 through 1308 Processing helix chain 'G' and resid 1313 through 1319 Processing helix chain 'G' and resid 1324 through 1338 Processing helix chain 'G' and resid 1339 through 1341 No H-bonds generated for 'chain 'G' and resid 1339 through 1341' Processing helix chain 'G' and resid 1363 through 1382 Processing helix chain 'G' and resid 1382 through 1387 Processing helix chain 'G' and resid 1387 through 1394 removed outlier: 3.984A pdb=" N GLU G1391 " --> pdb=" O PHE G1387 " (cutoff:3.500A) Processing helix chain 'G' and resid 1403 through 1407 Processing helix chain 'G' and resid 1422 through 1430 removed outlier: 4.020A pdb=" N ILE G1426 " --> pdb=" O ASN G1422 " (cutoff:3.500A) Processing helix chain 'G' and resid 1432 through 1441 Processing helix chain 'G' and resid 1447 through 1455 Processing helix chain 'G' and resid 1468 through 1491 removed outlier: 3.715A pdb=" N ILE G1474 " --> pdb=" O GLU G1470 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA G1477 " --> pdb=" O PHE G1473 " (cutoff:3.500A) Processing helix chain 'G' and resid 1495 through 1508 Processing helix chain 'G' and resid 1508 through 1519 Processing helix chain 'G' and resid 1520 through 1525 removed outlier: 3.878A pdb=" N PHE G1523 " --> pdb=" O ARG G1520 " (cutoff:3.500A) Processing helix chain 'G' and resid 1529 through 1546 Processing helix chain 'G' and resid 1610 through 1628 Processing helix chain 'G' and resid 1629 through 1649 Proline residue: G1643 - end of helix Processing helix chain 'G' and resid 1655 through 1663 Processing helix chain 'G' and resid 1701 through 1722 Processing helix chain 'I' and resid 194 through 208 removed outlier: 3.627A pdb=" N LYS I 208 " --> pdb=" O TYR I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 219 through 227 removed outlier: 4.645A pdb=" N HIS I 224 " --> pdb=" O CYS I 221 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE I 227 " --> pdb=" O HIS I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 231 through 244 Processing helix chain 'I' and resid 249 through 261 Processing helix chain 'I' and resid 295 through 311 removed outlier: 4.536A pdb=" N TYR I 299 " --> pdb=" O GLU I 295 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASP I 300 " --> pdb=" O THR I 296 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE I 311 " --> pdb=" O ARG I 307 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 88 removed outlier: 6.305A pdb=" N ALA A 60 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLY A 114 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE A 62 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG A 59 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ILE A 137 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU A 61 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 24 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE A 25 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 220 removed outlier: 6.585A pdb=" N THR A 219 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N LEU A 504 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR A 506 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 225 " --> pdb=" O THR A 506 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 220 removed outlier: 6.585A pdb=" N THR A 219 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N LEU A 504 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL A 476 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N PHE A 505 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE A 478 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N ALA A 507 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 260 through 261 removed outlier: 4.398A pdb=" N ARG A 260 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA6, first strand: chain 'A' and resid 593 through 596 Processing sheet with id=AA7, first strand: chain 'A' and resid 702 through 706 Processing sheet with id=AA8, first strand: chain 'A' and resid 768 through 771 Processing sheet with id=AA9, first strand: chain 'A' and resid 768 through 771 removed outlier: 4.832A pdb=" N TYR A 754 " --> pdb=" O ILE A 729 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AB2, first strand: chain 'A' and resid 970 through 971 removed outlier: 3.709A pdb=" N ILE A 940 " --> pdb=" O LEU A 971 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N MET A 939 " --> pdb=" O VAL A 898 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL A 898 " --> pdb=" O MET A 939 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU A 941 " --> pdb=" O THR A 896 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 895 " --> pdb=" O LYS A 880 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS A 880 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE A 881 " --> pdb=" O PHE A 979 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1554 through 1558 removed outlier: 3.511A pdb=" N THR A1604 " --> pdb=" O ARG A1555 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET A1602 " --> pdb=" O LEU A1557 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER A1603 " --> pdb=" O PHE A1698 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1554 through 1558 removed outlier: 3.511A pdb=" N THR A1604 " --> pdb=" O ARG A1555 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET A1602 " --> pdb=" O LEU A1557 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER A1603 " --> pdb=" O PHE A1698 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 266 through 270 removed outlier: 4.303A pdb=" N LEU C 278 " --> pdb=" O VAL C 270 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 85 through 88 removed outlier: 3.635A pdb=" N THR D 115 " --> pdb=" O TYR D 88 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY D 114 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG D 59 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N ILE D 137 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU D 61 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR D 172 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE D 25 " --> pdb=" O ILE D 200 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 219 through 225 removed outlier: 3.502A pdb=" N PHE D 225 " --> pdb=" O THR D 506 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N CYS D 388 " --> pdb=" O MET D 458 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N CYS D 460 " --> pdb=" O CYS D 388 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL D 390 " --> pdb=" O CYS D 460 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLN D 422 " --> pdb=" O ILE D 459 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 558 through 559 Processing sheet with id=AB9, first strand: chain 'D' and resid 593 through 596 Processing sheet with id=AC1, first strand: chain 'D' and resid 702 through 705 Processing sheet with id=AC2, first strand: chain 'D' and resid 786 through 789 Processing sheet with id=AC3, first strand: chain 'D' and resid 729 through 733 Processing sheet with id=AC4, first strand: chain 'D' and resid 819 through 820 Processing sheet with id=AC5, first strand: chain 'D' and resid 969 through 971 removed outlier: 4.182A pdb=" N VAL D 969 " --> pdb=" O VAL D 942 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL D 942 " --> pdb=" O VAL D 969 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 971 " --> pdb=" O ILE D 940 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE D 940 " --> pdb=" O LEU D 971 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET D 939 " --> pdb=" O HIS D 899 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ARG D 943 " --> pdb=" O VAL D 895 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL D 895 " --> pdb=" O ARG D 943 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 1669 through 1670 Processing sheet with id=AC7, first strand: chain 'D' and resid 1674 through 1676 removed outlier: 3.751A pdb=" N GLY D1699 " --> pdb=" O VAL D1680 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 267 through 270 removed outlier: 4.415A pdb=" N LEU F 278 " --> pdb=" O VAL F 270 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 85 through 88 removed outlier: 5.503A pdb=" N GLY G 86 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ALA G 60 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY G 114 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N PHE G 62 " --> pdb=" O GLY G 114 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ARG G 59 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL G 135 " --> pdb=" O ARG G 59 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N SER G 134 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N VAL G 169 " --> pdb=" O SER G 134 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL G 136 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU G 171 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE G 138 " --> pdb=" O LEU G 171 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR G 172 " --> pdb=" O VAL G 26 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE G 25 " --> pdb=" O ILE G 200 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 219 through 225 removed outlier: 6.381A pdb=" N THR G 219 " --> pdb=" O PHE G 502 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU G 504 " --> pdb=" O THR G 219 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL G 221 " --> pdb=" O LEU G 504 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N THR G 506 " --> pdb=" O VAL G 221 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL G 223 " --> pdb=" O THR G 506 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU G 389 " --> pdb=" O PHE G 477 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N CYS G 388 " --> pdb=" O MET G 458 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N CYS G 460 " --> pdb=" O CYS G 388 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL G 390 " --> pdb=" O CYS G 460 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLN G 422 " --> pdb=" O ILE G 459 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 558 through 559 removed outlier: 3.718A pdb=" N PHE G 558 " --> pdb=" O LEU G 566 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 593 through 596 removed outlier: 4.092A pdb=" N TRP G 593 " --> pdb=" O ASN G 619 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 702 through 706 Processing sheet with id=AD5, first strand: chain 'G' and resid 755 through 758 removed outlier: 3.987A pdb=" N ILE G 756 " --> pdb=" O TYR G 727 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR G 727 " --> pdb=" O ILE G 756 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 755 through 758 removed outlier: 3.987A pdb=" N ILE G 756 " --> pdb=" O TYR G 727 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR G 727 " --> pdb=" O ILE G 756 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS G 724 " --> pdb=" O VAL G 788 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL G 788 " --> pdb=" O CYS G 724 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 770 through 771 Processing sheet with id=AD8, first strand: chain 'G' and resid 834 through 836 Processing sheet with id=AD9, first strand: chain 'G' and resid 892 through 895 removed outlier: 4.168A pdb=" N LYS G 880 " --> pdb=" O VAL G 895 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 1554 through 1558 removed outlier: 3.533A pdb=" N LEU G1557 " --> pdb=" O MET G1602 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N MET G1602 " --> pdb=" O LEU G1557 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN G1601 " --> pdb=" O LYS G1694 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE G1698 " --> pdb=" O SER G1603 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASN G1605 " --> pdb=" O PHE G1698 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE G1686 " --> pdb=" O ILE G1693 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 1554 through 1558 removed outlier: 3.533A pdb=" N LEU G1557 " --> pdb=" O MET G1602 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N MET G1602 " --> pdb=" O LEU G1557 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN G1601 " --> pdb=" O LYS G1694 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE G1698 " --> pdb=" O SER G1603 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASN G1605 " --> pdb=" O PHE G1698 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE G1686 " --> pdb=" O ILE G1693 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET G1681 " --> pdb=" O ILE G1674 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE G1674 " --> pdb=" O MET G1681 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 267 through 270 removed outlier: 4.212A pdb=" N LEU I 278 " --> pdb=" O VAL I 270 " (cutoff:3.500A) 2033 hydrogen bonds defined for protein. 5742 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 10.71 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13204 1.33 - 1.45: 6797 1.45 - 1.57: 22916 1.57 - 1.69: 114 1.69 - 1.81: 364 Bond restraints: 43395 Sorted by residual: bond pdb=" CG LEU I 196 " pdb=" CD1 LEU I 196 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.11e+00 bond pdb=" C SER G1672 " pdb=" N PRO G1673 " ideal model delta sigma weight residual 1.335 1.354 -0.019 8.70e-03 1.32e+04 4.87e+00 bond pdb=" N ALA I 195 " pdb=" CA ALA I 195 " ideal model delta sigma weight residual 1.468 1.442 0.026 1.24e-02 6.50e+03 4.57e+00 bond pdb=" C ALA I 195 " pdb=" O ALA I 195 " ideal model delta sigma weight residual 1.234 1.250 -0.016 8.30e-03 1.45e+04 3.50e+00 bond pdb=" C LYS A1402 " pdb=" N PRO A1403 " ideal model delta sigma weight residual 1.331 1.354 -0.023 1.21e-02 6.83e+03 3.48e+00 ... (remaining 43390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 58610 3.14 - 6.27: 334 6.27 - 9.41: 10 9.41 - 12.55: 2 12.55 - 15.69: 1 Bond angle restraints: 58957 Sorted by residual: angle pdb=" CB LYS I 199 " pdb=" CG LYS I 199 " pdb=" CD LYS I 199 " ideal model delta sigma weight residual 111.30 126.99 -15.69 2.30e+00 1.89e-01 4.65e+01 angle pdb=" N ARG I 198 " pdb=" CA ARG I 198 " pdb=" C ARG I 198 " ideal model delta sigma weight residual 110.97 105.93 5.04 1.09e+00 8.42e-01 2.14e+01 angle pdb=" N LYS I 199 " pdb=" CA LYS I 199 " pdb=" CB LYS I 199 " ideal model delta sigma weight residual 110.12 116.04 -5.92 1.47e+00 4.63e-01 1.62e+01 angle pdb=" CB LYS D 935 " pdb=" CG LYS D 935 " pdb=" CD LYS D 935 " ideal model delta sigma weight residual 111.30 120.55 -9.25 2.30e+00 1.89e-01 1.62e+01 angle pdb=" CA TYR G 519 " pdb=" CB TYR G 519 " pdb=" CG TYR G 519 " ideal model delta sigma weight residual 113.90 106.85 7.05 1.80e+00 3.09e-01 1.53e+01 ... (remaining 58952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.96: 24144 19.96 - 39.92: 1873 39.92 - 59.88: 285 59.88 - 79.84: 111 79.84 - 99.80: 19 Dihedral angle restraints: 26432 sinusoidal: 11456 harmonic: 14976 Sorted by residual: dihedral pdb=" CA GLU I 194 " pdb=" C GLU I 194 " pdb=" N ALA I 195 " pdb=" CA ALA I 195 " ideal model delta harmonic sigma weight residual -180.00 -152.64 -27.36 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA GLN G1191 " pdb=" C GLN G1191 " pdb=" N GLY G1192 " pdb=" CA GLY G1192 " ideal model delta harmonic sigma weight residual 180.00 153.73 26.27 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA MET G 999 " pdb=" C MET G 999 " pdb=" N TYR G1000 " pdb=" CA TYR G1000 " ideal model delta harmonic sigma weight residual 180.00 154.15 25.85 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 26429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 5484 0.048 - 0.095: 891 0.095 - 0.143: 277 0.143 - 0.191: 9 0.191 - 0.238: 2 Chirality restraints: 6663 Sorted by residual: chirality pdb=" CB ILE G 515 " pdb=" CA ILE G 515 " pdb=" CG1 ILE G 515 " pdb=" CG2 ILE G 515 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA LYS I 199 " pdb=" N LYS I 199 " pdb=" C LYS I 199 " pdb=" CB LYS I 199 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.80e-01 chirality pdb=" CA TYR G 519 " pdb=" N TYR G 519 " pdb=" C TYR G 519 " pdb=" CB TYR G 519 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 6660 not shown) Planarity restraints: 7333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 519 " -0.025 2.00e-02 2.50e+03 2.14e-02 9.12e+00 pdb=" CG TYR G 519 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR G 519 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR G 519 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR G 519 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR G 519 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR G 519 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 519 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU I 196 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" C LEU I 196 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU I 196 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG I 197 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 735 " 0.012 2.00e-02 2.50e+03 1.58e-02 4.39e+00 pdb=" CG PHE D 735 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE D 735 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE D 735 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE D 735 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 735 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 735 " 0.000 2.00e-02 2.50e+03 ... (remaining 7330 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 380 2.49 - 3.10: 34644 3.10 - 3.70: 67885 3.70 - 4.30: 95573 4.30 - 4.90: 154069 Nonbonded interactions: 352551 Sorted by model distance: nonbonded pdb=" OG SER G 22 " pdb=" OE2 GLU G 541 " model vdw 1.893 3.040 nonbonded pdb=" OG1 THR A 896 " pdb=" OE1 GLU A 941 " model vdw 1.898 3.040 nonbonded pdb=" OG1 THR A 667 " pdb=" OE1 GLU A 670 " model vdw 1.924 3.040 nonbonded pdb=" OG1 THR A 172 " pdb=" O VAL A 174 " model vdw 1.999 3.040 nonbonded pdb=" NH2 ARG G1518 " pdb=" O HIS G1548 " model vdw 2.007 3.120 ... (remaining 352546 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' selection = chain 'D' selection = chain 'G' } ncs_group { reference = (chain 'C' and resid 188 through 311) selection = (chain 'F' and resid 188 through 311) selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 41.090 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 0.082 43395 Z= 0.189 Angle : 0.635 15.686 58957 Z= 0.357 Chirality : 0.040 0.238 6663 Planarity : 0.004 0.079 7333 Dihedral : 14.776 99.802 16714 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.75 % Favored : 95.23 % Rotamer: Outliers : 0.02 % Allowed : 0.22 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.15 (0.12), residues: 5049 helix: 0.54 (0.11), residues: 2392 sheet: -0.23 (0.22), residues: 545 loop : -0.70 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 223 TYR 0.052 0.002 TYR G 519 PHE 0.036 0.002 PHE D 735 TRP 0.021 0.001 TRP I 205 HIS 0.013 0.001 HIS G 803 Details of bonding type rmsd covalent geometry : bond 0.00381 (43395) covalent geometry : angle 0.63534 (58957) hydrogen bonds : bond 0.16617 ( 2059) hydrogen bonds : angle 6.78481 ( 5864) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10098 Ramachandran restraints generated. 5049 Oldfield, 0 Emsley, 5049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10098 Ramachandran restraints generated. 5049 Oldfield, 0 Emsley, 5049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 538 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 MET cc_start: 0.7460 (ppp) cc_final: 0.7054 (ppp) REVERT: A 566 LEU cc_start: 0.9050 (tp) cc_final: 0.8832 (tp) REVERT: A 1261 ASP cc_start: 0.8249 (t0) cc_final: 0.7980 (t0) REVERT: A 1602 MET cc_start: 0.8839 (mtt) cc_final: 0.8587 (mtt) REVERT: C 285 CYS cc_start: 0.7895 (p) cc_final: 0.7605 (p) REVERT: D 354 ASN cc_start: 0.7590 (t160) cc_final: 0.6919 (m-40) REVERT: D 487 MET cc_start: 0.8652 (tmm) cc_final: 0.8339 (tmm) REVERT: D 527 ASP cc_start: 0.8875 (m-30) cc_final: 0.8664 (m-30) REVERT: D 593 TRP cc_start: 0.7268 (m-90) cc_final: 0.7057 (m-90) REVERT: D 735 PHE cc_start: 0.6150 (t80) cc_final: 0.5908 (t80) REVERT: D 747 ASN cc_start: 0.9212 (m110) cc_final: 0.8805 (t0) REVERT: D 893 MET cc_start: 0.7150 (ptm) cc_final: 0.6713 (ptm) REVERT: D 918 TYR cc_start: 0.8017 (m-10) cc_final: 0.7429 (m-80) REVERT: D 922 MET cc_start: 0.9205 (mpp) cc_final: 0.8949 (mmt) REVERT: D 985 LEU cc_start: 0.9466 (tp) cc_final: 0.9231 (tp) REVERT: D 996 LEU cc_start: 0.9513 (mt) cc_final: 0.9023 (tt) REVERT: D 1193 GLU cc_start: 0.8966 (tp30) cc_final: 0.8471 (tp30) REVERT: D 1423 THR cc_start: 0.8790 (p) cc_final: 0.8566 (t) REVERT: D 1689 MET cc_start: 0.8070 (mpp) cc_final: 0.7500 (mpp) REVERT: F 191 GLU cc_start: 0.9071 (tt0) cc_final: 0.8509 (mp0) REVERT: F 192 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7654 (mp0) REVERT: F 218 MET cc_start: 0.7745 (ptp) cc_final: 0.7334 (ptm) REVERT: G 157 PHE cc_start: 0.7622 (m-80) cc_final: 0.7314 (m-10) REVERT: G 208 MET cc_start: 0.7837 (mmp) cc_final: 0.7391 (mmm) REVERT: G 288 MET cc_start: 0.9171 (tmm) cc_final: 0.8787 (tmm) REVERT: G 322 MET cc_start: 0.8959 (tmm) cc_final: 0.8679 (tmm) REVERT: G 616 ILE cc_start: 0.7692 (mt) cc_final: 0.7426 (mt) REVERT: G 744 MET cc_start: 0.0869 (ttt) cc_final: 0.0061 (mmp) REVERT: G 809 ASP cc_start: 0.5285 (t0) cc_final: 0.5015 (t0) REVERT: G 893 MET cc_start: 0.1909 (mpp) cc_final: 0.1317 (mpp) REVERT: G 1219 PHE cc_start: 0.7329 (t80) cc_final: 0.6957 (t80) REVERT: G 1379 LYS cc_start: 0.7141 (tptt) cc_final: 0.6675 (tppt) REVERT: G 1388 LYS cc_start: 0.7293 (tttt) cc_final: 0.5808 (tttt) REVERT: G 1391 GLU cc_start: 0.7984 (tt0) cc_final: 0.7667 (tt0) REVERT: G 1447 ARG cc_start: 0.7503 (mmt180) cc_final: 0.7278 (mmt90) REVERT: G 1525 ILE cc_start: 0.9536 (pt) cc_final: 0.9172 (pt) REVERT: I 204 TYR cc_start: 0.8332 (m-80) cc_final: 0.7791 (m-80) REVERT: I 231 TYR cc_start: 0.8770 (t80) cc_final: 0.8480 (t80) REVERT: I 252 ASP cc_start: 0.8191 (m-30) cc_final: 0.7915 (m-30) outliers start: 1 outliers final: 1 residues processed: 538 average time/residue: 0.2323 time to fit residues: 212.6724 Evaluate side-chains 373 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 372 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 198 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 432 optimal weight: 0.5980 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 0.1980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 494 optimal weight: 0.4980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 313 GLN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1286 HIS A1406 GLN D 354 ASN D 576 HIS D 734 GLN D 955 ASN D1013 ASN ** G 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 734 GLN G 774 GLN G1013 ASN G1024 ASN G1541 ASN ** G1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 301 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.082398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.062276 restraints weight = 225801.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.063913 restraints weight = 125296.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.064947 restraints weight = 83440.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.065616 restraints weight = 62749.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.066103 restraints weight = 51640.923| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 43395 Z= 0.147 Angle : 0.660 9.217 58957 Z= 0.342 Chirality : 0.044 0.235 6663 Planarity : 0.004 0.043 7333 Dihedral : 10.343 93.327 6452 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.47 % Favored : 96.51 % Rotamer: Outliers : 0.92 % Allowed : 6.89 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.09 (0.12), residues: 5049 helix: 0.67 (0.10), residues: 2465 sheet: -0.22 (0.22), residues: 524 loop : -0.49 (0.14), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1518 TYR 0.045 0.002 TYR G 519 PHE 0.044 0.002 PHE G1194 TRP 0.017 0.002 TRP G 986 HIS 0.008 0.001 HIS G 803 Details of bonding type rmsd covalent geometry : bond 0.00320 (43395) covalent geometry : angle 0.65995 (58957) hydrogen bonds : bond 0.04876 ( 2059) hydrogen bonds : angle 5.18817 ( 5864) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10098 Ramachandran restraints generated. 5049 Oldfield, 0 Emsley, 5049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10098 Ramachandran restraints generated. 5049 Oldfield, 0 Emsley, 5049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 492 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9116 (tmm) cc_final: 0.8841 (tmm) REVERT: A 209 GLU cc_start: 0.9453 (pt0) cc_final: 0.9206 (pp20) REVERT: A 424 MET cc_start: 0.7695 (ppp) cc_final: 0.7158 (ppp) REVERT: A 601 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7541 (mt-10) REVERT: A 604 ARG cc_start: 0.8593 (tmm-80) cc_final: 0.8252 (ptt-90) REVERT: A 939 MET cc_start: 0.5873 (OUTLIER) cc_final: 0.5148 (tpp) REVERT: A 1261 ASP cc_start: 0.8176 (t0) cc_final: 0.7778 (t0) REVERT: C 218 MET cc_start: 0.7427 (mtm) cc_final: 0.7030 (ptm) REVERT: C 230 PHE cc_start: 0.8710 (t80) cc_final: 0.8166 (t80) REVERT: C 304 ASP cc_start: 0.8979 (OUTLIER) cc_final: 0.8522 (p0) REVERT: D 250 ASP cc_start: 0.8757 (m-30) cc_final: 0.8543 (m-30) REVERT: D 354 ASN cc_start: 0.7471 (t0) cc_final: 0.6797 (m-40) REVERT: D 487 MET cc_start: 0.8392 (tmm) cc_final: 0.8048 (tmm) REVERT: D 744 MET cc_start: 0.9042 (tpt) cc_final: 0.8773 (tpp) REVERT: D 779 VAL cc_start: 0.9208 (t) cc_final: 0.8989 (t) REVERT: D 805 MET cc_start: 0.8898 (ppp) cc_final: 0.8356 (ppp) REVERT: D 907 TYR cc_start: 0.8374 (m-80) cc_final: 0.7993 (m-80) REVERT: D 918 TYR cc_start: 0.7610 (m-10) cc_final: 0.7188 (m-80) REVERT: D 922 MET cc_start: 0.9123 (mpp) cc_final: 0.8904 (mmt) REVERT: D 935 LYS cc_start: 0.7672 (mmmt) cc_final: 0.7195 (mmmt) REVERT: D 939 MET cc_start: 0.3141 (tpp) cc_final: 0.2686 (tpp) REVERT: D 985 LEU cc_start: 0.9412 (tp) cc_final: 0.9160 (tp) REVERT: D 996 LEU cc_start: 0.9473 (mt) cc_final: 0.8874 (tt) REVERT: D 1193 GLU cc_start: 0.9040 (tp30) cc_final: 0.8485 (tp30) REVERT: D 1237 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7696 (tm-30) REVERT: D 1389 MET cc_start: 0.8926 (mmm) cc_final: 0.8499 (mmm) REVERT: D 1689 MET cc_start: 0.8156 (mpp) cc_final: 0.7630 (mpp) REVERT: F 191 GLU cc_start: 0.8964 (tt0) cc_final: 0.8419 (mp0) REVERT: F 311 ILE cc_start: 0.7819 (mm) cc_final: 0.7459 (mt) REVERT: G 17 ASP cc_start: 0.9114 (m-30) cc_final: 0.8635 (p0) REVERT: G 75 MET cc_start: 0.8686 (mmm) cc_final: 0.8475 (mmm) REVERT: G 288 MET cc_start: 0.9207 (tmm) cc_final: 0.8803 (tmm) REVERT: G 322 MET cc_start: 0.9036 (tmm) cc_final: 0.8723 (tmm) REVERT: G 424 MET cc_start: 0.8394 (tmm) cc_final: 0.8090 (ptp) REVERT: G 458 MET cc_start: 0.8259 (tpp) cc_final: 0.8029 (tpp) REVERT: G 616 ILE cc_start: 0.7455 (mt) cc_final: 0.7090 (mt) REVERT: G 744 MET cc_start: -0.0186 (ttt) cc_final: -0.0764 (mmp) REVERT: G 893 MET cc_start: 0.0177 (mpp) cc_final: -0.0284 (mpp) REVERT: G 1379 LYS cc_start: 0.6882 (tptt) cc_final: 0.6614 (tppt) REVERT: G 1617 GLU cc_start: 0.9438 (tp30) cc_final: 0.8835 (tp30) REVERT: G 1650 ARG cc_start: 0.7674 (ptm-80) cc_final: 0.7216 (ptm-80) REVERT: G 1707 LEU cc_start: 0.9283 (tt) cc_final: 0.9030 (pp) REVERT: I 199 LYS cc_start: 0.9049 (pttt) cc_final: 0.8727 (mtmm) REVERT: I 206 GLU cc_start: 0.8171 (mp0) cc_final: 0.7930 (mp0) REVERT: I 226 TYR cc_start: 0.8774 (t80) cc_final: 0.8468 (t80) REVERT: I 231 TYR cc_start: 0.8760 (t80) cc_final: 0.8546 (t80) REVERT: I 252 ASP cc_start: 0.8061 (m-30) cc_final: 0.7854 (m-30) REVERT: I 304 ASP cc_start: 0.9272 (p0) cc_final: 0.9015 (p0) outliers start: 42 outliers final: 21 residues processed: 514 average time/residue: 0.2501 time to fit residues: 219.1484 Evaluate side-chains 407 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 384 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1620 ILE Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 423 PHE Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 423 PHE Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 1443 THR Chi-restraints excluded: chain G residue 1474 ILE Chi-restraints excluded: chain G residue 1639 ASN Chi-restraints excluded: chain G residue 1654 ILE Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain I residue 290 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 401 optimal weight: 9.9990 chunk 489 optimal weight: 0.6980 chunk 157 optimal weight: 8.9990 chunk 291 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 500 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 339 GLN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 569 ASN ** D 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1286 HIS F 215 HIS ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 354 ASN G 801 GLN G1017 ASN ** G1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1631 GLN ** G1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.081687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.061311 restraints weight = 229057.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.062829 restraints weight = 125917.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.063900 restraints weight = 84055.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.064609 restraints weight = 63239.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.065043 restraints weight = 51968.417| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 43395 Z= 0.144 Angle : 0.611 12.151 58957 Z= 0.314 Chirality : 0.042 0.199 6663 Planarity : 0.004 0.057 7333 Dihedral : 10.205 92.565 6448 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.51 % Favored : 96.47 % Rotamer: Outliers : 1.23 % Allowed : 9.95 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.21 (0.12), residues: 5049 helix: 0.78 (0.10), residues: 2467 sheet: -0.08 (0.22), residues: 518 loop : -0.47 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 99 TYR 0.032 0.002 TYR G 519 PHE 0.034 0.001 PHE G1194 TRP 0.020 0.001 TRP G 102 HIS 0.007 0.001 HIS D 743 Details of bonding type rmsd covalent geometry : bond 0.00310 (43395) covalent geometry : angle 0.61130 (58957) hydrogen bonds : bond 0.04320 ( 2059) hydrogen bonds : angle 4.92493 ( 5864) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10098 Ramachandran restraints generated. 5049 Oldfield, 0 Emsley, 5049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10098 Ramachandran restraints generated. 5049 Oldfield, 0 Emsley, 5049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 429 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9168 (tmm) cc_final: 0.8845 (tmm) REVERT: A 424 MET cc_start: 0.7843 (ppp) cc_final: 0.7141 (ppp) REVERT: A 1261 ASP cc_start: 0.8094 (t0) cc_final: 0.7697 (t0) REVERT: A 1333 GLU cc_start: 0.7801 (tt0) cc_final: 0.7555 (tt0) REVERT: C 230 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8166 (t80) REVERT: C 262 LYS cc_start: 0.9269 (tppt) cc_final: 0.8905 (mmtt) REVERT: C 304 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8442 (p0) REVERT: D 208 MET cc_start: 0.8979 (tpp) cc_final: 0.8542 (mpp) REVERT: D 250 ASP cc_start: 0.8760 (m-30) cc_final: 0.8514 (m-30) REVERT: D 354 ASN cc_start: 0.7271 (t0) cc_final: 0.7061 (t0) REVERT: D 527 ASP cc_start: 0.8697 (m-30) cc_final: 0.8433 (m-30) REVERT: D 805 MET cc_start: 0.8939 (ppp) cc_final: 0.8401 (ppp) REVERT: D 907 TYR cc_start: 0.8508 (m-80) cc_final: 0.8128 (m-80) REVERT: D 918 TYR cc_start: 0.7643 (m-10) cc_final: 0.7343 (m-80) REVERT: D 922 MET cc_start: 0.9121 (mpp) cc_final: 0.8860 (mmt) REVERT: D 935 LYS cc_start: 0.7816 (mmmt) cc_final: 0.7246 (mmmt) REVERT: D 985 LEU cc_start: 0.9412 (tp) cc_final: 0.9167 (tp) REVERT: D 1237 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7554 (tm-30) REVERT: D 1368 ASP cc_start: 0.8763 (m-30) cc_final: 0.8525 (m-30) REVERT: D 1389 MET cc_start: 0.8962 (mmm) cc_final: 0.8564 (mmm) REVERT: D 1689 MET cc_start: 0.8187 (mpp) cc_final: 0.7663 (mpp) REVERT: F 186 MET cc_start: 0.7373 (ppp) cc_final: 0.7159 (tmm) REVERT: F 191 GLU cc_start: 0.9002 (tt0) cc_final: 0.8337 (mp0) REVERT: G 13 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9108 (mm) REVERT: G 17 ASP cc_start: 0.9090 (m-30) cc_final: 0.8665 (m-30) REVERT: G 66 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7400 (t) REVERT: G 243 GLU cc_start: 0.9473 (mm-30) cc_final: 0.9217 (mm-30) REVERT: G 288 MET cc_start: 0.9209 (tmm) cc_final: 0.8927 (tmm) REVERT: G 424 MET cc_start: 0.8411 (tmm) cc_final: 0.8025 (ptp) REVERT: G 458 MET cc_start: 0.8173 (tpp) cc_final: 0.7905 (tpp) REVERT: G 744 MET cc_start: -0.0190 (ttt) cc_final: -0.0656 (mmp) REVERT: G 893 MET cc_start: 0.0330 (mpp) cc_final: -0.0061 (mpp) REVERT: G 979 PHE cc_start: 0.4407 (OUTLIER) cc_final: 0.4190 (m-80) REVERT: G 1209 MET cc_start: 0.6193 (ppp) cc_final: 0.5538 (ptp) REVERT: G 1379 LYS cc_start: 0.6866 (tptt) cc_final: 0.6653 (tppt) REVERT: G 1388 LYS cc_start: 0.5911 (tttt) cc_final: 0.5538 (tmtt) REVERT: G 1391 GLU cc_start: 0.8803 (tp30) cc_final: 0.8480 (tp30) REVERT: G 1617 GLU cc_start: 0.9434 (tp30) cc_final: 0.8930 (tp30) REVERT: G 1647 GLU cc_start: 0.9246 (tp30) cc_final: 0.9021 (tp30) REVERT: G 1658 ARG cc_start: 0.7261 (mmm160) cc_final: 0.6395 (ptm160) REVERT: G 1665 HIS cc_start: 0.8436 (m-70) cc_final: 0.7991 (t70) REVERT: G 1689 MET cc_start: 0.1695 (mmt) cc_final: 0.1230 (mmt) REVERT: G 1707 LEU cc_start: 0.9317 (tt) cc_final: 0.9061 (pp) REVERT: I 199 LYS cc_start: 0.9004 (pttt) cc_final: 0.8696 (mtmm) REVERT: I 204 TYR cc_start: 0.8097 (m-80) cc_final: 0.7661 (m-80) REVERT: I 206 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7959 (mp0) REVERT: I 226 TYR cc_start: 0.8774 (t80) cc_final: 0.8455 (t80) REVERT: I 234 LEU cc_start: 0.9173 (tt) cc_final: 0.8685 (tt) outliers start: 56 outliers final: 23 residues processed: 460 average time/residue: 0.2469 time to fit residues: 195.2961 Evaluate side-chains 400 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 372 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 1620 ILE Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 625 MET Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 714 TYR Chi-restraints excluded: chain G residue 979 PHE Chi-restraints excluded: chain G residue 1282 ILE Chi-restraints excluded: chain G residue 1443 THR Chi-restraints excluded: chain G residue 1474 ILE Chi-restraints excluded: chain G residue 1481 PHE Chi-restraints excluded: chain G residue 1502 LEU Chi-restraints excluded: chain G residue 1600 PHE Chi-restraints excluded: chain G residue 1639 ASN Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain I residue 279 LEU Chi-restraints excluded: chain I residue 290 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 206 optimal weight: 0.9980 chunk 507 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 chunk 116 optimal weight: 0.0270 chunk 168 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 262 optimal weight: 0.2980 chunk 426 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 217 optimal weight: 0.9990 overall best weight: 0.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN D 429 ASN ** D 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1495 ASN ** G1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.082210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.061952 restraints weight = 224883.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.063533 restraints weight = 123422.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.064604 restraints weight = 81932.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.065275 restraints weight = 61663.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.065789 restraints weight = 50874.822| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 43395 Z= 0.120 Angle : 0.591 10.541 58957 Z= 0.302 Chirality : 0.041 0.210 6663 Planarity : 0.004 0.042 7333 Dihedral : 10.101 91.582 6448 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.31 % Favored : 96.67 % Rotamer: Outliers : 1.38 % Allowed : 11.99 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.27 (0.12), residues: 5049 helix: 0.80 (0.10), residues: 2472 sheet: 0.03 (0.23), residues: 507 loop : -0.43 (0.14), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 261 TYR 0.030 0.001 TYR G1000 PHE 0.022 0.001 PHE G1194 TRP 0.017 0.001 TRP A 97 HIS 0.007 0.001 HIS G 803 Details of bonding type rmsd covalent geometry : bond 0.00264 (43395) covalent geometry : angle 0.59131 (58957) hydrogen bonds : bond 0.03989 ( 2059) hydrogen bonds : angle 4.75014 ( 5864) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10098 Ramachandran restraints generated. 5049 Oldfield, 0 Emsley, 5049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10098 Ramachandran restraints generated. 5049 Oldfield, 0 Emsley, 5049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 424 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9167 (tmm) cc_final: 0.8817 (tmm) REVERT: A 360 MET cc_start: 0.8787 (mmm) cc_final: 0.8529 (mmm) REVERT: A 424 MET cc_start: 0.7959 (ppp) cc_final: 0.7259 (ppp) REVERT: A 747 ASN cc_start: 0.9023 (m110) cc_final: 0.8689 (t0) REVERT: A 893 MET cc_start: 0.6688 (ppp) cc_final: 0.6377 (ppp) REVERT: A 1261 ASP cc_start: 0.8113 (t0) cc_final: 0.7732 (t70) REVERT: C 218 MET cc_start: 0.7434 (mtm) cc_final: 0.6907 (ptm) REVERT: C 230 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8165 (t80) REVERT: C 267 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8682 (tp) REVERT: C 304 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.8485 (p0) REVERT: D 63 MET cc_start: 0.7908 (ttp) cc_final: 0.7662 (ttp) REVERT: D 75 MET cc_start: 0.9153 (ttt) cc_final: 0.8578 (tmm) REVERT: D 122 MET cc_start: 0.9265 (tmm) cc_final: 0.9026 (tmm) REVERT: D 208 MET cc_start: 0.9054 (tpp) cc_final: 0.8445 (mmm) REVERT: D 250 ASP cc_start: 0.8750 (m-30) cc_final: 0.8478 (m-30) REVERT: D 360 MET cc_start: 0.8367 (tmm) cc_final: 0.7912 (tpp) REVERT: D 527 ASP cc_start: 0.8691 (m-30) cc_final: 0.8401 (m-30) REVERT: D 805 MET cc_start: 0.8931 (ppp) cc_final: 0.8413 (ppp) REVERT: D 907 TYR cc_start: 0.8464 (m-80) cc_final: 0.8069 (m-80) REVERT: D 922 MET cc_start: 0.9088 (mpp) cc_final: 0.8833 (mmt) REVERT: D 999 MET cc_start: 0.9203 (mmm) cc_final: 0.8899 (mpp) REVERT: D 1237 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7571 (tm-30) REVERT: D 1389 MET cc_start: 0.8956 (mmm) cc_final: 0.8579 (mmm) REVERT: D 1689 MET cc_start: 0.8252 (mpp) cc_final: 0.7760 (mpp) REVERT: F 191 GLU cc_start: 0.8933 (tt0) cc_final: 0.8319 (mp0) REVERT: G 13 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9150 (mm) REVERT: G 17 ASP cc_start: 0.9066 (m-30) cc_final: 0.8738 (m-30) REVERT: G 156 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8727 (mm) REVERT: G 243 GLU cc_start: 0.9480 (mm-30) cc_final: 0.9237 (mm-30) REVERT: G 288 MET cc_start: 0.9202 (tmm) cc_final: 0.8891 (tmm) REVERT: G 322 MET cc_start: 0.9409 (ttp) cc_final: 0.8752 (tmm) REVERT: G 424 MET cc_start: 0.8425 (tmm) cc_final: 0.7968 (ptp) REVERT: G 458 MET cc_start: 0.8337 (tpp) cc_final: 0.7954 (tpp) REVERT: G 744 MET cc_start: 0.0086 (ttt) cc_final: -0.0386 (mmp) REVERT: G 893 MET cc_start: 0.0464 (mpp) cc_final: 0.0121 (mpp) REVERT: G 1040 LYS cc_start: 0.6861 (pptt) cc_final: 0.6513 (mmtm) REVERT: G 1209 MET cc_start: 0.6206 (ppp) cc_final: 0.5692 (mtm) REVERT: G 1379 LYS cc_start: 0.6925 (tptt) cc_final: 0.6710 (tppt) REVERT: G 1617 GLU cc_start: 0.9449 (tp30) cc_final: 0.8945 (tp30) REVERT: G 1658 ARG cc_start: 0.7200 (mmm160) cc_final: 0.6394 (ptm160) REVERT: G 1664 LYS cc_start: 0.8776 (mtmm) cc_final: 0.8501 (pttm) REVERT: G 1689 MET cc_start: 0.1700 (mmt) cc_final: 0.1141 (mmt) REVERT: G 1707 LEU cc_start: 0.9277 (tt) cc_final: 0.8895 (pp) REVERT: I 199 LYS cc_start: 0.9084 (pttt) cc_final: 0.8858 (ptpt) REVERT: I 204 TYR cc_start: 0.7975 (m-80) cc_final: 0.7550 (m-80) REVERT: I 223 ARG cc_start: 0.8175 (ttt-90) cc_final: 0.7705 (ttt-90) REVERT: I 226 TYR cc_start: 0.8726 (t80) cc_final: 0.8404 (t80) outliers start: 63 outliers final: 30 residues processed: 460 average time/residue: 0.2439 time to fit residues: 192.3149 Evaluate side-chains 407 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 372 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 1608 VAL Chi-restraints excluded: chain A residue 1620 ILE Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 423 PHE Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 479 LEU Chi-restraints excluded: chain G residue 625 MET Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 714 TYR Chi-restraints excluded: chain G residue 1282 ILE Chi-restraints excluded: chain G residue 1474 ILE Chi-restraints excluded: chain G residue 1481 PHE Chi-restraints excluded: chain G residue 1502 LEU Chi-restraints excluded: chain G residue 1521 LEU Chi-restraints excluded: chain G residue 1522 HIS Chi-restraints excluded: chain G residue 1639 ASN Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 279 LEU Chi-restraints excluded: chain I residue 290 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 470 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 225 optimal weight: 8.9990 chunk 154 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 416 optimal weight: 8.9990 chunk 310 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 170 optimal weight: 7.9990 chunk 361 optimal weight: 6.9990 chunk 453 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN A 449 GLN A 517 GLN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1406 GLN C 301 HIS D 323 HIS D 454 ASN ** D 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 ASN ** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1439 ASN ** D1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN ** G 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 749 GLN G 955 ASN ** G1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1541 ASN ** G1646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.078281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.058139 restraints weight = 232676.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.059651 restraints weight = 128856.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.060591 restraints weight = 87035.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.061252 restraints weight = 65907.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.061703 restraints weight = 54598.298| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 43395 Z= 0.219 Angle : 0.669 11.295 58957 Z= 0.344 Chirality : 0.043 0.180 6663 Planarity : 0.005 0.046 7333 Dihedral : 10.074 97.459 6448 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.20 % Favored : 95.78 % Rotamer: Outliers : 2.06 % Allowed : 13.50 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.23 (0.12), residues: 5049 helix: 0.80 (0.10), residues: 2449 sheet: 0.01 (0.24), residues: 487 loop : -0.46 (0.14), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 866 TYR 0.034 0.002 TYR G 519 PHE 0.027 0.002 PHE G 818 TRP 0.020 0.002 TRP G 102 HIS 0.012 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00480 (43395) covalent geometry : angle 0.66884 (58957) hydrogen bonds : bond 0.04246 ( 2059) hydrogen bonds : angle 4.85525 ( 5864) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10098 Ramachandran restraints generated. 5049 Oldfield, 0 Emsley, 5049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10098 Ramachandran restraints generated. 5049 Oldfield, 0 Emsley, 5049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 379 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9233 (tmm) cc_final: 0.8862 (tmm) REVERT: A 344 MET cc_start: 0.5132 (ptm) cc_final: 0.4249 (ppp) REVERT: A 360 MET cc_start: 0.8920 (mmm) cc_final: 0.8692 (mmm) REVERT: A 424 MET cc_start: 0.7904 (ppp) cc_final: 0.7061 (ppp) REVERT: A 635 MET cc_start: 0.7779 (mmm) cc_final: 0.7518 (mmm) REVERT: A 893 MET cc_start: 0.7097 (ppp) cc_final: 0.6654 (ppp) REVERT: A 939 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.6255 (tpp) REVERT: A 1261 ASP cc_start: 0.8338 (t0) cc_final: 0.8009 (t0) REVERT: A 1602 MET cc_start: 0.8681 (mmm) cc_final: 0.7822 (mmm) REVERT: C 230 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8260 (t80) REVERT: C 304 ASP cc_start: 0.8931 (OUTLIER) cc_final: 0.8522 (p0) REVERT: D 122 MET cc_start: 0.9402 (tmm) cc_final: 0.9024 (tmm) REVERT: D 208 MET cc_start: 0.8807 (tpp) cc_final: 0.8246 (mmm) REVERT: D 250 ASP cc_start: 0.8907 (m-30) cc_final: 0.8615 (m-30) REVERT: D 354 ASN cc_start: 0.6994 (t0) cc_final: 0.6371 (m-40) REVERT: D 360 MET cc_start: 0.8482 (tmm) cc_final: 0.8081 (tpp) REVERT: D 907 TYR cc_start: 0.8545 (m-80) cc_final: 0.8169 (m-80) REVERT: D 922 MET cc_start: 0.9124 (mpp) cc_final: 0.8703 (mtt) REVERT: D 1002 LEU cc_start: 0.9156 (mt) cc_final: 0.8930 (mt) REVERT: D 1237 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7615 (tm-30) REVERT: D 1333 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8721 (pt0) REVERT: D 1689 MET cc_start: 0.8365 (mpp) cc_final: 0.7763 (mpp) REVERT: F 186 MET cc_start: 0.7731 (ppp) cc_final: 0.7374 (tmm) REVERT: G 17 ASP cc_start: 0.9161 (m-30) cc_final: 0.8851 (m-30) REVERT: G 72 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8673 (pp30) REVERT: G 156 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8802 (mm) REVERT: G 243 GLU cc_start: 0.9533 (mm-30) cc_final: 0.9309 (mm-30) REVERT: G 252 MET cc_start: 0.9058 (tpp) cc_final: 0.8808 (mmm) REVERT: G 273 LYS cc_start: 0.8504 (mttp) cc_final: 0.8069 (mmmt) REVERT: G 288 MET cc_start: 0.9294 (tmm) cc_final: 0.8908 (tmm) REVERT: G 312 ARG cc_start: 0.9249 (mtm110) cc_final: 0.8967 (mtm110) REVERT: G 744 MET cc_start: 0.0505 (ttt) cc_final: -0.0029 (mmp) REVERT: G 805 MET cc_start: 0.2773 (ptp) cc_final: 0.2564 (ttt) REVERT: G 1040 LYS cc_start: 0.6843 (pptt) cc_final: 0.6462 (mptt) REVERT: G 1209 MET cc_start: 0.6018 (ppp) cc_final: 0.5603 (ptp) REVERT: G 1617 GLU cc_start: 0.9411 (tp30) cc_final: 0.8816 (tp30) REVERT: G 1658 ARG cc_start: 0.7159 (mmm160) cc_final: 0.6430 (ptm160) REVERT: G 1707 LEU cc_start: 0.9280 (tt) cc_final: 0.8947 (pp) REVERT: I 199 LYS cc_start: 0.9092 (pttt) cc_final: 0.8879 (ptpt) REVERT: I 204 TYR cc_start: 0.8049 (m-80) cc_final: 0.7612 (m-80) outliers start: 94 outliers final: 51 residues processed: 444 average time/residue: 0.2427 time to fit residues: 185.8743 Evaluate side-chains 416 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 359 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 907 TYR Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1480 ASP Chi-restraints excluded: chain A residue 1620 ILE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 400 CYS Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 1333 GLU Chi-restraints excluded: chain D residue 1669 VAL Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 457 LEU Chi-restraints excluded: chain G residue 479 LEU Chi-restraints excluded: chain G residue 625 MET Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 714 TYR Chi-restraints excluded: chain G residue 1474 ILE Chi-restraints excluded: chain G residue 1521 LEU Chi-restraints excluded: chain G residue 1600 PHE Chi-restraints excluded: chain G residue 1639 ASN Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 279 LEU Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 311 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 56 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 446 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 335 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 416 optimal weight: 8.9990 chunk 336 optimal weight: 0.9990 chunk 492 optimal weight: 5.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1353 ASN D 72 GLN D 864 GLN ** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1685 GLN ** D1712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.079797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.059645 restraints weight = 227471.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.061232 restraints weight = 124656.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.062230 restraints weight = 83410.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.062938 restraints weight = 62663.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.063419 restraints weight = 51454.050| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 43395 Z= 0.121 Angle : 0.602 12.972 58957 Z= 0.304 Chirality : 0.041 0.194 6663 Planarity : 0.004 0.046 7333 Dihedral : 9.961 93.040 6448 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.25 % Favored : 96.73 % Rotamer: Outliers : 1.62 % Allowed : 14.96 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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 aren not related in a simple way. whole: 0.34 (0.12), residues: 5049 helix: 0.87 (0.10), residues: 2467 sheet: 0.10 (0.24), residues: 483 loop : -0.40 (0.14), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 99 TYR 0.031 0.001 TYR G1000 PHE 0.032 0.001 PHE G1393 TRP 0.019 0.001 TRP A 442 HIS 0.007 0.001 HIS G 800 Details of bonding type rmsd covalent geometry : bond 0.00266 (43395) covalent geometry : angle 0.60163 (58957) hydrogen bonds : bond 0.03766 ( 2059) hydrogen bonds : angle 4.64563 ( 5864) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10098 Ramachandran restraints generated. 5049 Oldfield, 0 Emsley, 5049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10098 Ramachandran restraints generated. 5049 Oldfield, 0 Emsley, 5049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 399 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8593 (ttm) cc_final: 0.8146 (ttm) REVERT: A 122 MET cc_start: 0.9303 (tmm) cc_final: 0.8950 (tmm) REVERT: A 344 MET cc_start: 0.5009 (ptm) cc_final: 0.4210 (ppp) REVERT: A 424 MET cc_start: 0.8016 (ppp) cc_final: 0.7127 (ppp) REVERT: A 534 ASP cc_start: 0.8454 (p0) cc_final: 0.8170 (p0) REVERT: A 601 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7441 (pt0) REVERT: A 635 MET cc_start: 0.7753 (mmm) cc_final: 0.7526 (mmm) REVERT: A 747 ASN cc_start: 0.9056 (m110) cc_final: 0.8702 (t0) REVERT: A 893 MET cc_start: 0.6979 (ppp) cc_final: 0.6768 (ppp) REVERT: A 939 MET cc_start: 0.6579 (OUTLIER) cc_final: 0.6240 (tpp) REVERT: A 1261 ASP cc_start: 0.8342 (t0) cc_final: 0.8092 (t70) REVERT: A 1602 MET cc_start: 0.8672 (mmm) cc_final: 0.7856 (mmm) REVERT: A 1681 MET cc_start: 0.8310 (tmm) cc_final: 0.7458 (tmm) REVERT: C 218 MET cc_start: 0.7505 (mtm) cc_final: 0.6842 (ptm) REVERT: C 230 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8233 (t80) REVERT: C 304 ASP cc_start: 0.8908 (OUTLIER) cc_final: 0.8440 (p0) REVERT: D 122 MET cc_start: 0.9372 (tmm) cc_final: 0.8976 (tmm) REVERT: D 208 MET cc_start: 0.8850 (tpp) cc_final: 0.8378 (mmm) REVERT: D 250 ASP cc_start: 0.8880 (m-30) cc_final: 0.8550 (m-30) REVERT: D 354 ASN cc_start: 0.6941 (t0) cc_final: 0.6330 (m-40) REVERT: D 360 MET cc_start: 0.8453 (tmm) cc_final: 0.8042 (tpp) REVERT: D 805 MET cc_start: 0.9109 (ppp) cc_final: 0.8788 (ppp) REVERT: D 864 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8416 (pm20) REVERT: D 907 TYR cc_start: 0.8518 (m-80) cc_final: 0.8135 (m-80) REVERT: D 922 MET cc_start: 0.9125 (mpp) cc_final: 0.8666 (mtt) REVERT: D 1002 LEU cc_start: 0.9172 (mt) cc_final: 0.8921 (mt) REVERT: D 1237 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7545 (tm-30) REVERT: F 191 GLU cc_start: 0.8958 (tt0) cc_final: 0.8319 (mp0) REVERT: G 17 ASP cc_start: 0.9115 (m-30) cc_final: 0.8717 (m-30) REVERT: G 156 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8830 (mm) REVERT: G 208 MET cc_start: 0.7975 (mmp) cc_final: 0.7109 (mmt) REVERT: G 243 GLU cc_start: 0.9527 (mm-30) cc_final: 0.9316 (mm-30) REVERT: G 270 ASP cc_start: 0.5643 (t0) cc_final: 0.5151 (p0) REVERT: G 273 LYS cc_start: 0.8380 (mttp) cc_final: 0.7976 (mmmt) REVERT: G 288 MET cc_start: 0.9243 (tmm) cc_final: 0.8883 (tmm) REVERT: G 312 ARG cc_start: 0.9225 (mtm110) cc_final: 0.8918 (mtm110) REVERT: G 424 MET cc_start: 0.8470 (tmm) cc_final: 0.8014 (ptp) REVERT: G 484 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8752 (p) REVERT: G 744 MET cc_start: 0.0566 (ttt) cc_final: 0.0040 (mmp) REVERT: G 818 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.7585 (t80) REVERT: G 1040 LYS cc_start: 0.6867 (pptt) cc_final: 0.6490 (mptt) REVERT: G 1209 MET cc_start: 0.6047 (ppp) cc_final: 0.5609 (mtm) REVERT: G 1617 GLU cc_start: 0.9453 (tp30) cc_final: 0.9030 (tp30) REVERT: G 1658 ARG cc_start: 0.7013 (mmm160) cc_final: 0.6336 (ptm160) REVERT: G 1707 LEU cc_start: 0.9255 (tt) cc_final: 0.8961 (pp) REVERT: I 199 LYS cc_start: 0.9117 (pttt) cc_final: 0.8906 (mttt) REVERT: I 204 TYR cc_start: 0.7903 (m-80) cc_final: 0.7566 (m-80) REVERT: I 226 TYR cc_start: 0.8670 (t80) cc_final: 0.8384 (t80) outliers start: 74 outliers final: 42 residues processed: 449 average time/residue: 0.2481 time to fit residues: 192.6336 Evaluate side-chains 420 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 371 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1480 ASP Chi-restraints excluded: chain A residue 1608 VAL Chi-restraints excluded: chain A residue 1620 ILE Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 400 CYS Chi-restraints excluded: chain D residue 864 GLN Chi-restraints excluded: chain D residue 989 LEU Chi-restraints excluded: chain D residue 1248 VAL Chi-restraints excluded: chain D residue 1333 GLU Chi-restraints excluded: chain D residue 1506 LEU Chi-restraints excluded: chain D residue 1554 VAL Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 457 LEU Chi-restraints excluded: chain G residue 479 LEU Chi-restraints excluded: chain G residue 484 THR Chi-restraints excluded: chain G residue 625 MET Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 713 PHE Chi-restraints excluded: chain G residue 758 LEU Chi-restraints excluded: chain G residue 818 PHE Chi-restraints excluded: chain G residue 1282 ILE Chi-restraints excluded: chain G residue 1430 LEU Chi-restraints excluded: chain G residue 1474 ILE Chi-restraints excluded: chain G residue 1500 THR Chi-restraints excluded: chain G residue 1522 HIS Chi-restraints excluded: chain G residue 1600 PHE Chi-restraints excluded: chain G residue 1639 ASN Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 279 LEU Chi-restraints excluded: chain I residue 290 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 398 optimal weight: 9.9990 chunk 479 optimal weight: 8.9990 chunk 429 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 434 optimal weight: 5.9990 chunk 492 optimal weight: 7.9990 chunk 386 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 309 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 550 HIS ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS ** D 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.076825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.056756 restraints weight = 232381.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.058125 restraints weight = 128159.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.059104 restraints weight = 86012.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.059713 restraints weight = 65597.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.060184 restraints weight = 54711.679| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 43395 Z= 0.215 Angle : 0.664 13.956 58957 Z= 0.340 Chirality : 0.043 0.195 6663 Planarity : 0.004 0.047 7333 Dihedral : 9.945 98.258 6448 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.00 % Favored : 95.98 % Rotamer: Outliers : 1.90 % Allowed : 15.84 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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 aren not related in a simple way. whole: 0.27 (0.12), residues: 5049 helix: 0.88 (0.10), residues: 2444 sheet: -0.09 (0.24), residues: 485 loop : -0.48 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 307 TYR 0.034 0.002 TYR G 519 PHE 0.053 0.002 PHE G1393 TRP 0.018 0.002 TRP A 442 HIS 0.007 0.001 HIS G 803 Details of bonding type rmsd covalent geometry : bond 0.00470 (43395) covalent geometry : angle 0.66366 (58957) hydrogen bonds : bond 0.04124 ( 2059) hydrogen bonds : angle 4.83003 ( 5864) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10098 Ramachandran restraints generated. 5049 Oldfield, 0 Emsley, 5049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10098 Ramachandran restraints generated. 5049 Oldfield, 0 Emsley, 5049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 367 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9311 (tmm) cc_final: 0.8949 (tmm) REVERT: A 222 MET cc_start: 0.7562 (tpt) cc_final: 0.6758 (tmm) REVERT: A 360 MET cc_start: 0.8946 (mmm) cc_final: 0.8713 (mmm) REVERT: A 424 MET cc_start: 0.7978 (ppp) cc_final: 0.7028 (ppp) REVERT: A 534 ASP cc_start: 0.8391 (p0) cc_final: 0.8105 (p0) REVERT: A 601 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7406 (pt0) REVERT: A 635 MET cc_start: 0.7858 (mmm) cc_final: 0.7561 (mmm) REVERT: A 908 MET cc_start: 0.2041 (mmt) cc_final: 0.1280 (mmm) REVERT: A 939 MET cc_start: 0.6577 (OUTLIER) cc_final: 0.6214 (tpp) REVERT: A 1261 ASP cc_start: 0.8454 (t0) cc_final: 0.8238 (t70) REVERT: A 1602 MET cc_start: 0.8692 (mmm) cc_final: 0.8071 (mmm) REVERT: A 1681 MET cc_start: 0.8483 (tmm) cc_final: 0.7612 (tmm) REVERT: C 230 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8301 (t80) REVERT: C 304 ASP cc_start: 0.8951 (OUTLIER) cc_final: 0.8531 (p0) REVERT: D 208 MET cc_start: 0.8902 (tpp) cc_final: 0.8264 (mmm) REVERT: D 250 ASP cc_start: 0.8957 (m-30) cc_final: 0.8675 (m-30) REVERT: D 354 ASN cc_start: 0.6982 (t0) cc_final: 0.6343 (m-40) REVERT: D 360 MET cc_start: 0.8540 (tmm) cc_final: 0.8169 (tpp) REVERT: D 458 MET cc_start: 0.9170 (tpp) cc_final: 0.8880 (tpp) REVERT: D 805 MET cc_start: 0.9169 (ppp) cc_final: 0.8753 (ppp) REVERT: D 855 LEU cc_start: 0.9028 (mt) cc_final: 0.8767 (tt) REVERT: D 893 MET cc_start: 0.6887 (ttt) cc_final: 0.6567 (ttm) REVERT: D 907 TYR cc_start: 0.8595 (m-80) cc_final: 0.8194 (m-80) REVERT: D 922 MET cc_start: 0.9175 (mpp) cc_final: 0.8730 (mtt) REVERT: D 1002 LEU cc_start: 0.9231 (mt) cc_final: 0.9001 (mt) REVERT: D 1237 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7605 (tm-30) REVERT: D 1297 GLU cc_start: 0.8399 (pm20) cc_final: 0.8113 (pm20) REVERT: D 1389 MET cc_start: 0.9108 (mmm) cc_final: 0.8847 (mmm) REVERT: D 1602 MET cc_start: 0.8900 (mpp) cc_final: 0.8255 (mmm) REVERT: D 1689 MET cc_start: 0.7742 (mpp) cc_final: 0.7281 (mpp) REVERT: F 186 MET cc_start: 0.7815 (ppp) cc_final: 0.7401 (tmm) REVERT: G 17 ASP cc_start: 0.9136 (m-30) cc_final: 0.8740 (m-30) REVERT: G 63 MET cc_start: 0.7017 (tpp) cc_final: 0.6772 (mmm) REVERT: G 154 MET cc_start: 0.9254 (mmm) cc_final: 0.8969 (mmm) REVERT: G 156 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8854 (mm) REVERT: G 243 GLU cc_start: 0.9553 (mm-30) cc_final: 0.9343 (mm-30) REVERT: G 312 ARG cc_start: 0.9254 (mtm110) cc_final: 0.9014 (mtm110) REVERT: G 424 MET cc_start: 0.8503 (tmm) cc_final: 0.7956 (ptp) REVERT: G 484 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8901 (p) REVERT: G 744 MET cc_start: 0.0853 (ttt) cc_final: 0.0326 (mmp) REVERT: G 818 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.7643 (t80) REVERT: G 1209 MET cc_start: 0.5920 (ppp) cc_final: 0.5492 (ptp) REVERT: G 1480 ASP cc_start: 0.9106 (t0) cc_final: 0.8893 (t0) REVERT: G 1617 GLU cc_start: 0.9426 (tp30) cc_final: 0.8908 (tp30) REVERT: G 1658 ARG cc_start: 0.7035 (mmm160) cc_final: 0.6374 (ptm160) REVERT: I 223 ARG cc_start: 0.8163 (ttt-90) cc_final: 0.7501 (ttt-90) REVERT: I 258 MET cc_start: 0.8897 (mmm) cc_final: 0.8550 (mmm) REVERT: I 309 MET cc_start: 0.9353 (tpp) cc_final: 0.8857 (tpt) outliers start: 87 outliers final: 53 residues processed: 431 average time/residue: 0.2393 time to fit residues: 179.8289 Evaluate side-chains 400 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 341 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1480 ASP Chi-restraints excluded: chain A residue 1608 VAL Chi-restraints excluded: chain A residue 1620 ILE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain D residue 400 CYS Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 1248 VAL Chi-restraints excluded: chain D residue 1554 VAL Chi-restraints excluded: chain D residue 1669 VAL Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 457 LEU Chi-restraints excluded: chain G residue 484 THR Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain G residue 625 MET Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 713 PHE Chi-restraints excluded: chain G residue 758 LEU Chi-restraints excluded: chain G residue 818 PHE Chi-restraints excluded: chain G residue 1282 ILE Chi-restraints excluded: chain G residue 1389 MET Chi-restraints excluded: chain G residue 1405 THR Chi-restraints excluded: chain G residue 1430 LEU Chi-restraints excluded: chain G residue 1474 ILE Chi-restraints excluded: chain G residue 1500 THR Chi-restraints excluded: chain G residue 1600 PHE Chi-restraints excluded: chain G residue 1639 ASN Chi-restraints excluded: chain G residue 1654 ILE Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 279 LEU Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 311 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 69 optimal weight: 0.0470 chunk 123 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 225 optimal weight: 4.9990 chunk 483 optimal weight: 10.0000 chunk 354 optimal weight: 0.8980 chunk 383 optimal weight: 10.0000 chunk 141 optimal weight: 0.2980 chunk 301 optimal weight: 0.9980 chunk 319 optimal weight: 0.6980 chunk 54 optimal weight: 0.4980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1306 ASN D1338 ASN D1439 ASN ** D1712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 HIS ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 475 HIS ** G 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.079066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.058947 restraints weight = 227042.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.060492 restraints weight = 123033.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.061521 restraints weight = 81741.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.062166 restraints weight = 61737.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.062669 restraints weight = 51155.099| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 43395 Z= 0.119 Angle : 0.617 14.776 58957 Z= 0.309 Chirality : 0.041 0.254 6663 Planarity : 0.004 0.047 7333 Dihedral : 9.830 92.818 6448 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.23 % Favored : 96.75 % Rotamer: Outliers : 1.42 % Allowed : 16.89 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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 aren not related in a simple way. whole: 0.40 (0.12), residues: 5049 helix: 0.96 (0.10), residues: 2443 sheet: 0.04 (0.24), residues: 473 loop : -0.39 (0.14), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 198 TYR 0.025 0.001 TYR G 519 PHE 0.041 0.001 PHE G1393 TRP 0.027 0.001 TRP A 442 HIS 0.005 0.001 HIS A1522 Details of bonding type rmsd covalent geometry : bond 0.00258 (43395) covalent geometry : angle 0.61681 (58957) hydrogen bonds : bond 0.03706 ( 2059) hydrogen bonds : angle 4.60148 ( 5864) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10098 Ramachandran restraints generated. 5049 Oldfield, 0 Emsley, 5049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10098 Ramachandran restraints generated. 5049 Oldfield, 0 Emsley, 5049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 388 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9295 (tmm) cc_final: 0.8935 (tmm) REVERT: A 344 MET cc_start: 0.4011 (ppp) cc_final: 0.3349 (ppp) REVERT: A 360 MET cc_start: 0.9086 (mmm) cc_final: 0.8858 (mmm) REVERT: A 372 MET cc_start: 0.7175 (ttt) cc_final: 0.6906 (ptm) REVERT: A 424 MET cc_start: 0.8111 (ppp) cc_final: 0.7189 (ppp) REVERT: A 534 ASP cc_start: 0.8314 (p0) cc_final: 0.8090 (p0) REVERT: A 601 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7521 (pt0) REVERT: A 635 MET cc_start: 0.7793 (mmm) cc_final: 0.7546 (mmm) REVERT: A 744 MET cc_start: 0.8650 (tpp) cc_final: 0.8445 (tpp) REVERT: A 747 ASN cc_start: 0.8974 (m110) cc_final: 0.8681 (t0) REVERT: A 748 LEU cc_start: 0.9022 (mt) cc_final: 0.8819 (mt) REVERT: A 893 MET cc_start: 0.7051 (ppp) cc_final: 0.6825 (ppp) REVERT: A 908 MET cc_start: 0.1800 (mmt) cc_final: 0.1140 (mmm) REVERT: A 939 MET cc_start: 0.6630 (OUTLIER) cc_final: 0.6271 (tpp) REVERT: A 1261 ASP cc_start: 0.8403 (t0) cc_final: 0.8164 (t70) REVERT: A 1602 MET cc_start: 0.8756 (mmm) cc_final: 0.8011 (mmm) REVERT: A 1681 MET cc_start: 0.8436 (tmm) cc_final: 0.7652 (tmm) REVERT: C 230 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8291 (t80) REVERT: C 304 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8415 (p0) REVERT: D 154 MET cc_start: 0.9225 (mmp) cc_final: 0.8833 (mmm) REVERT: D 208 MET cc_start: 0.8951 (tpp) cc_final: 0.8345 (mmm) REVERT: D 250 ASP cc_start: 0.8936 (m-30) cc_final: 0.8609 (m-30) REVERT: D 354 ASN cc_start: 0.6809 (t0) cc_final: 0.6227 (m-40) REVERT: D 360 MET cc_start: 0.8448 (tmm) cc_final: 0.8063 (tpp) REVERT: D 458 MET cc_start: 0.9224 (tpp) cc_final: 0.8905 (tpp) REVERT: D 487 MET cc_start: 0.8554 (tmm) cc_final: 0.8020 (tmm) REVERT: D 620 MET cc_start: 0.8324 (mmm) cc_final: 0.8082 (mmm) REVERT: D 744 MET cc_start: 0.9397 (tpp) cc_final: 0.9170 (tpp) REVERT: D 805 MET cc_start: 0.9138 (ppp) cc_final: 0.8732 (ppp) REVERT: D 894 LEU cc_start: 0.8409 (tp) cc_final: 0.8207 (tp) REVERT: D 922 MET cc_start: 0.9149 (mpp) cc_final: 0.8778 (mtt) REVERT: D 1002 LEU cc_start: 0.9307 (mt) cc_final: 0.9046 (mt) REVERT: D 1237 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7520 (tm-30) REVERT: D 1297 GLU cc_start: 0.8314 (pm20) cc_final: 0.8036 (pm20) REVERT: D 1371 GLU cc_start: 0.8759 (pm20) cc_final: 0.8366 (pm20) REVERT: D 1389 MET cc_start: 0.9030 (mmm) cc_final: 0.8717 (mmm) REVERT: D 1602 MET cc_start: 0.9055 (mpp) cc_final: 0.8758 (mmp) REVERT: D 1689 MET cc_start: 0.7660 (mpp) cc_final: 0.7324 (mpp) REVERT: F 191 GLU cc_start: 0.8900 (tt0) cc_final: 0.8214 (mp0) REVERT: G 17 ASP cc_start: 0.9099 (m-30) cc_final: 0.8685 (m-30) REVERT: G 63 MET cc_start: 0.7073 (tpp) cc_final: 0.6765 (mmm) REVERT: G 180 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8560 (mp0) REVERT: G 243 GLU cc_start: 0.9522 (mm-30) cc_final: 0.9305 (mm-30) REVERT: G 273 LYS cc_start: 0.8400 (mttp) cc_final: 0.8060 (mmmt) REVERT: G 288 MET cc_start: 0.9372 (ttp) cc_final: 0.9110 (tmm) REVERT: G 312 ARG cc_start: 0.9215 (mtm110) cc_final: 0.8969 (mtm110) REVERT: G 484 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8820 (p) REVERT: G 682 HIS cc_start: 0.6780 (p90) cc_final: 0.6272 (p90) REVERT: G 744 MET cc_start: 0.0803 (ttt) cc_final: 0.0294 (mmp) REVERT: G 818 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.7649 (t80) REVERT: G 1209 MET cc_start: 0.5737 (ppp) cc_final: 0.5262 (ptp) REVERT: G 1528 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8322 (tm-30) REVERT: G 1617 GLU cc_start: 0.9438 (tp30) cc_final: 0.8945 (tp30) REVERT: G 1658 ARG cc_start: 0.7092 (mmm160) cc_final: 0.6504 (ptm160) REVERT: G 1707 LEU cc_start: 0.9266 (tt) cc_final: 0.9006 (pp) REVERT: I 206 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7567 (mm-30) REVERT: I 226 TYR cc_start: 0.8708 (t80) cc_final: 0.8389 (t80) REVERT: I 309 MET cc_start: 0.9339 (tpp) cc_final: 0.8886 (tpt) outliers start: 65 outliers final: 48 residues processed: 434 average time/residue: 0.2513 time to fit residues: 188.4302 Evaluate side-chains 414 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 361 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1480 ASP Chi-restraints excluded: chain A residue 1608 VAL Chi-restraints excluded: chain A residue 1620 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain D residue 400 CYS Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 1194 PHE Chi-restraints excluded: chain D residue 1248 VAL Chi-restraints excluded: chain D residue 1554 VAL Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 457 LEU Chi-restraints excluded: chain G residue 479 LEU Chi-restraints excluded: chain G residue 484 THR Chi-restraints excluded: chain G residue 625 MET Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 713 PHE Chi-restraints excluded: chain G residue 758 LEU Chi-restraints excluded: chain G residue 818 PHE Chi-restraints excluded: chain G residue 1282 ILE Chi-restraints excluded: chain G residue 1430 LEU Chi-restraints excluded: chain G residue 1522 HIS Chi-restraints excluded: chain G residue 1600 PHE Chi-restraints excluded: chain G residue 1639 ASN Chi-restraints excluded: chain G residue 1654 ILE Chi-restraints excluded: chain G residue 1675 VAL Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 279 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 23 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 419 optimal weight: 1.9990 chunk 378 optimal weight: 8.9990 chunk 385 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 296 optimal weight: 1.9990 chunk 118 optimal weight: 0.0770 chunk 138 optimal weight: 7.9990 chunk 313 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.078806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.058844 restraints weight = 226587.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.060388 restraints weight = 124870.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.061392 restraints weight = 83571.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.062064 restraints weight = 63581.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.062500 restraints weight = 52621.812| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 43395 Z= 0.120 Angle : 0.625 15.515 58957 Z= 0.312 Chirality : 0.041 0.277 6663 Planarity : 0.004 0.048 7333 Dihedral : 9.748 93.787 6448 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.53 % Favored : 96.45 % Rotamer: Outliers : 1.44 % Allowed : 17.22 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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 aren not related in a simple way. whole: 0.43 (0.12), residues: 5049 helix: 0.97 (0.10), residues: 2446 sheet: 0.13 (0.24), residues: 467 loop : -0.39 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 223 TYR 0.034 0.001 TYR A1343 PHE 0.048 0.001 PHE G1393 TRP 0.029 0.001 TRP A 442 HIS 0.005 0.001 HIS I 224 Details of bonding type rmsd covalent geometry : bond 0.00268 (43395) covalent geometry : angle 0.62533 (58957) hydrogen bonds : bond 0.03633 ( 2059) hydrogen bonds : angle 4.58216 ( 5864) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10098 Ramachandran restraints generated. 5049 Oldfield, 0 Emsley, 5049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10098 Ramachandran restraints generated. 5049 Oldfield, 0 Emsley, 5049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 372 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9264 (tmm) cc_final: 0.8866 (tmm) REVERT: A 222 MET cc_start: 0.8178 (tmm) cc_final: 0.7932 (tmm) REVERT: A 344 MET cc_start: 0.4206 (ppp) cc_final: 0.3433 (ppp) REVERT: A 360 MET cc_start: 0.9025 (mmm) cc_final: 0.8779 (mmm) REVERT: A 372 MET cc_start: 0.7232 (ttt) cc_final: 0.6928 (ptm) REVERT: A 424 MET cc_start: 0.8235 (ppp) cc_final: 0.7217 (ppp) REVERT: A 534 ASP cc_start: 0.8226 (p0) cc_final: 0.7993 (p0) REVERT: A 601 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7545 (pt0) REVERT: A 635 MET cc_start: 0.7846 (mmm) cc_final: 0.7645 (mmm) REVERT: A 744 MET cc_start: 0.8731 (tpp) cc_final: 0.8488 (tpp) REVERT: A 747 ASN cc_start: 0.8953 (m110) cc_final: 0.8699 (t0) REVERT: A 748 LEU cc_start: 0.9045 (mt) cc_final: 0.8788 (mt) REVERT: A 893 MET cc_start: 0.7060 (ppp) cc_final: 0.6843 (ppp) REVERT: A 908 MET cc_start: 0.2215 (mmt) cc_final: 0.1434 (mmm) REVERT: A 939 MET cc_start: 0.6636 (OUTLIER) cc_final: 0.6290 (tpp) REVERT: A 1261 ASP cc_start: 0.8424 (t0) cc_final: 0.8189 (t70) REVERT: A 1602 MET cc_start: 0.8760 (mmm) cc_final: 0.8192 (mmm) REVERT: A 1681 MET cc_start: 0.8431 (tmm) cc_final: 0.7645 (tmm) REVERT: C 230 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8311 (t80) REVERT: C 304 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8483 (p0) REVERT: D 154 MET cc_start: 0.9246 (mmp) cc_final: 0.8917 (mmm) REVERT: D 208 MET cc_start: 0.8987 (tpp) cc_final: 0.8371 (mmm) REVERT: D 222 MET cc_start: 0.8467 (ttt) cc_final: 0.8262 (ttt) REVERT: D 250 ASP cc_start: 0.8941 (m-30) cc_final: 0.8602 (m-30) REVERT: D 354 ASN cc_start: 0.6782 (t0) cc_final: 0.6217 (m-40) REVERT: D 360 MET cc_start: 0.8444 (tmm) cc_final: 0.8066 (tpp) REVERT: D 458 MET cc_start: 0.9211 (tpp) cc_final: 0.8952 (tpp) REVERT: D 487 MET cc_start: 0.8586 (tmm) cc_final: 0.8035 (tmm) REVERT: D 620 MET cc_start: 0.8310 (mmm) cc_final: 0.8036 (mmm) REVERT: D 908 MET cc_start: 0.4532 (mpp) cc_final: 0.4263 (mpp) REVERT: D 922 MET cc_start: 0.9190 (mpp) cc_final: 0.8748 (mtt) REVERT: D 1002 LEU cc_start: 0.9333 (mt) cc_final: 0.9025 (mt) REVERT: D 1237 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7562 (tm-30) REVERT: D 1371 GLU cc_start: 0.8850 (pm20) cc_final: 0.8473 (pm20) REVERT: D 1389 MET cc_start: 0.9058 (mmm) cc_final: 0.8748 (mmm) REVERT: D 1602 MET cc_start: 0.9082 (mpp) cc_final: 0.8837 (mmt) REVERT: D 1689 MET cc_start: 0.7697 (mpp) cc_final: 0.7357 (mpp) REVERT: F 191 GLU cc_start: 0.8892 (tt0) cc_final: 0.8177 (mp0) REVERT: F 309 MET cc_start: 0.8861 (mmm) cc_final: 0.8354 (mmm) REVERT: G 17 ASP cc_start: 0.9092 (m-30) cc_final: 0.8722 (m-30) REVERT: G 180 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8582 (mp0) REVERT: G 243 GLU cc_start: 0.9537 (mm-30) cc_final: 0.9333 (mm-30) REVERT: G 288 MET cc_start: 0.9364 (ttp) cc_final: 0.9115 (tmm) REVERT: G 424 MET cc_start: 0.8607 (tmm) cc_final: 0.7892 (ptp) REVERT: G 484 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8834 (p) REVERT: G 620 MET cc_start: 0.8025 (mtp) cc_final: 0.7766 (mtp) REVERT: G 744 MET cc_start: 0.0924 (ttt) cc_final: 0.0391 (mmp) REVERT: G 818 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7691 (t80) REVERT: G 1209 MET cc_start: 0.5707 (ppp) cc_final: 0.5341 (ptp) REVERT: G 1528 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8295 (tm-30) REVERT: G 1617 GLU cc_start: 0.9399 (tp30) cc_final: 0.8945 (tp30) REVERT: G 1658 ARG cc_start: 0.7063 (mmm160) cc_final: 0.6515 (ptm160) REVERT: G 1696 TYR cc_start: 0.7437 (m-80) cc_final: 0.7107 (m-10) REVERT: G 1707 LEU cc_start: 0.9271 (tt) cc_final: 0.9006 (pp) REVERT: I 309 MET cc_start: 0.9314 (tpp) cc_final: 0.8836 (tpt) outliers start: 66 outliers final: 47 residues processed: 421 average time/residue: 0.2450 time to fit residues: 178.6541 Evaluate side-chains 409 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 357 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1480 ASP Chi-restraints excluded: chain A residue 1608 VAL Chi-restraints excluded: chain A residue 1620 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain D residue 400 CYS Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 1194 PHE Chi-restraints excluded: chain D residue 1248 VAL Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 457 LEU Chi-restraints excluded: chain G residue 484 THR Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain G residue 625 MET Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 713 PHE Chi-restraints excluded: chain G residue 758 LEU Chi-restraints excluded: chain G residue 818 PHE Chi-restraints excluded: chain G residue 1282 ILE Chi-restraints excluded: chain G residue 1430 LEU Chi-restraints excluded: chain G residue 1522 HIS Chi-restraints excluded: chain G residue 1600 PHE Chi-restraints excluded: chain G residue 1639 ASN Chi-restraints excluded: chain G residue 1654 ILE Chi-restraints excluded: chain G residue 1675 VAL Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 190 optimal weight: 0.7980 chunk 423 optimal weight: 20.0000 chunk 292 optimal weight: 3.9990 chunk 413 optimal weight: 4.9990 chunk 404 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 489 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 497 optimal weight: 6.9990 chunk 234 optimal weight: 0.9980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN A 747 ASN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 948 GLN D 955 ASN D1439 ASN ** D1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 428 ASN G 570 ASN ** G 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1519 HIS ** G1715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.076901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.057084 restraints weight = 230021.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.058585 restraints weight = 126961.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.059542 restraints weight = 85438.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.060302 restraints weight = 65362.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.060710 restraints weight = 53765.823| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 43395 Z= 0.167 Angle : 0.665 15.110 58957 Z= 0.333 Chirality : 0.042 0.242 6663 Planarity : 0.004 0.048 7333 Dihedral : 9.760 96.913 6448 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.94 % Favored : 96.04 % Rotamer: Outliers : 1.33 % Allowed : 17.37 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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 aren not related in a simple way. whole: 0.37 (0.12), residues: 5049 helix: 0.98 (0.11), residues: 2443 sheet: -0.12 (0.24), residues: 471 loop : -0.43 (0.14), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 312 TYR 0.030 0.002 TYR G 346 PHE 0.038 0.002 PHE G1393 TRP 0.028 0.001 TRP A 442 HIS 0.005 0.001 HIS D1519 Details of bonding type rmsd covalent geometry : bond 0.00372 (43395) covalent geometry : angle 0.66470 (58957) hydrogen bonds : bond 0.03833 ( 2059) hydrogen bonds : angle 4.70103 ( 5864) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10098 Ramachandran restraints generated. 5049 Oldfield, 0 Emsley, 5049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10098 Ramachandran restraints generated. 5049 Oldfield, 0 Emsley, 5049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 351 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8712 (mmm) cc_final: 0.8380 (tpt) REVERT: A 122 MET cc_start: 0.9314 (tmm) cc_final: 0.8928 (tmm) REVERT: A 222 MET cc_start: 0.8210 (tmm) cc_final: 0.7179 (tmm) REVERT: A 360 MET cc_start: 0.9047 (mmm) cc_final: 0.8793 (mmm) REVERT: A 372 MET cc_start: 0.7322 (ttt) cc_final: 0.7001 (ptm) REVERT: A 424 MET cc_start: 0.8120 (ppp) cc_final: 0.7070 (ppp) REVERT: A 534 ASP cc_start: 0.8164 (p0) cc_final: 0.7905 (p0) REVERT: A 635 MET cc_start: 0.7888 (mmm) cc_final: 0.7665 (mmm) REVERT: A 747 ASN cc_start: 0.8977 (m-40) cc_final: 0.8697 (t0) REVERT: A 908 MET cc_start: 0.2278 (mmt) cc_final: 0.1548 (mmm) REVERT: A 939 MET cc_start: 0.6569 (OUTLIER) cc_final: 0.6237 (tpp) REVERT: A 1261 ASP cc_start: 0.8501 (t0) cc_final: 0.8283 (t70) REVERT: A 1602 MET cc_start: 0.8741 (mmm) cc_final: 0.7781 (mmm) REVERT: A 1681 MET cc_start: 0.8480 (tmm) cc_final: 0.7625 (tmm) REVERT: C 218 MET cc_start: 0.7523 (mtm) cc_final: 0.6752 (ptm) REVERT: C 230 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8323 (t80) REVERT: C 304 ASP cc_start: 0.8979 (OUTLIER) cc_final: 0.8543 (p0) REVERT: D 154 MET cc_start: 0.9206 (mmp) cc_final: 0.8909 (mmm) REVERT: D 208 MET cc_start: 0.8974 (tpp) cc_final: 0.8372 (mmm) REVERT: D 250 ASP cc_start: 0.8971 (m-30) cc_final: 0.8704 (m-30) REVERT: D 354 ASN cc_start: 0.6800 (t0) cc_final: 0.6194 (m-40) REVERT: D 360 MET cc_start: 0.8480 (tmm) cc_final: 0.8137 (tpp) REVERT: D 620 MET cc_start: 0.8360 (mmm) cc_final: 0.8104 (mmm) REVERT: D 922 MET cc_start: 0.9195 (mpp) cc_final: 0.8784 (mtt) REVERT: D 1237 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7625 (tm-30) REVERT: D 1297 GLU cc_start: 0.8527 (pm20) cc_final: 0.8278 (pm20) REVERT: D 1389 MET cc_start: 0.9177 (mmm) cc_final: 0.8900 (mmm) REVERT: D 1602 MET cc_start: 0.9081 (mpp) cc_final: 0.8450 (mmm) REVERT: D 1689 MET cc_start: 0.7698 (mpp) cc_final: 0.7400 (mpp) REVERT: F 218 MET cc_start: 0.8034 (pmm) cc_final: 0.7526 (ptt) REVERT: G 17 ASP cc_start: 0.9177 (m-30) cc_final: 0.8802 (m-30) REVERT: G 180 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8606 (mp0) REVERT: G 243 GLU cc_start: 0.9545 (mm-30) cc_final: 0.9342 (mm-30) REVERT: G 288 MET cc_start: 0.9409 (ttp) cc_final: 0.9193 (ttt) REVERT: G 424 MET cc_start: 0.8578 (tmm) cc_final: 0.7810 (ptp) REVERT: G 484 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8915 (p) REVERT: G 620 MET cc_start: 0.8183 (mtp) cc_final: 0.7931 (mtp) REVERT: G 633 ASP cc_start: 0.8735 (t0) cc_final: 0.8439 (p0) REVERT: G 744 MET cc_start: 0.1148 (ttt) cc_final: 0.0648 (mmp) REVERT: G 818 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.7495 (t80) REVERT: G 1213 GLU cc_start: 0.5937 (OUTLIER) cc_final: 0.5674 (tt0) REVERT: G 1528 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8318 (tm-30) REVERT: G 1617 GLU cc_start: 0.9413 (tp30) cc_final: 0.8930 (tp30) REVERT: G 1658 ARG cc_start: 0.7118 (mmm160) cc_final: 0.6596 (ptm160) REVERT: G 1707 LEU cc_start: 0.9345 (tt) cc_final: 0.9065 (pp) outliers start: 61 outliers final: 49 residues processed: 399 average time/residue: 0.2460 time to fit residues: 169.7508 Evaluate side-chains 397 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 342 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1480 ASP Chi-restraints excluded: chain A residue 1535 ILE Chi-restraints excluded: chain A residue 1608 VAL Chi-restraints excluded: chain A residue 1620 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain D residue 400 CYS Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 1194 PHE Chi-restraints excluded: chain D residue 1248 VAL Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 457 LEU Chi-restraints excluded: chain G residue 484 THR Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain G residue 625 MET Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 713 PHE Chi-restraints excluded: chain G residue 758 LEU Chi-restraints excluded: chain G residue 818 PHE Chi-restraints excluded: chain G residue 1213 GLU Chi-restraints excluded: chain G residue 1282 ILE Chi-restraints excluded: chain G residue 1430 LEU Chi-restraints excluded: chain G residue 1600 PHE Chi-restraints excluded: chain G residue 1639 ASN Chi-restraints excluded: chain G residue 1654 ILE Chi-restraints excluded: chain G residue 1675 VAL Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 497 optimal weight: 5.9990 chunk 377 optimal weight: 0.9990 chunk 491 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 480 optimal weight: 10.0000 chunk 203 optimal weight: 0.0070 chunk 507 optimal weight: 10.0000 chunk 454 optimal weight: 0.3980 chunk 17 optimal weight: 7.9990 chunk 400 optimal weight: 0.0870 chunk 122 optimal weight: 0.2980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 ASN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 773 ASN D 948 GLN D 955 ASN ** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 428 ASN ** G 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1519 HIS ** G1715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.077086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.057181 restraints weight = 230209.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.058646 restraints weight = 125777.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.059548 restraints weight = 84751.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.060198 restraints weight = 64301.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.060647 restraints weight = 53322.576| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 43395 Z= 0.180 Angle : 0.736 59.185 58957 Z= 0.389 Chirality : 0.042 0.490 6663 Planarity : 0.004 0.066 7333 Dihedral : 9.762 96.938 6448 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.98 % Favored : 95.98 % Rotamer: Outliers : 1.36 % Allowed : 17.57 % Favored : 81.08 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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 aren not related in a simple way. whole: 0.38 (0.12), residues: 5049 helix: 0.99 (0.11), residues: 2441 sheet: -0.13 (0.24), residues: 471 loop : -0.42 (0.14), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 369 TYR 0.026 0.002 TYR G 519 PHE 0.037 0.001 PHE G1393 TRP 0.023 0.001 TRP A 442 HIS 0.004 0.001 HIS D1519 Details of bonding type rmsd covalent geometry : bond 0.00394 (43395) covalent geometry : angle 0.73637 (58957) hydrogen bonds : bond 0.03827 ( 2059) hydrogen bonds : angle 4.69913 ( 5864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10773.33 seconds wall clock time: 186 minutes 15.86 seconds (11175.86 seconds total)