Starting phenix.real_space_refine on Tue Jul 7 03:32:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hf1_34708/07_2026/8hf1_34708.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hf1_34708/07_2026/8hf1_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hf1_34708/07_2026/8hf1_34708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hf1_34708/07_2026/8hf1_34708.map" model { file = "/net/cci-nas-00/data/ceres_data/8hf1_34708/07_2026/8hf1_34708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hf1_34708/07_2026/8hf1_34708.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hf1_34708/07_2026/8hf1_34708.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hf1_34708/07_2026/8hf1_34708.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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-dev-6108/lib/python3.11/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: 8.41, 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: 3.59 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 5.51 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: 13.09 Time building geometry restraints manager: 4.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 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: 24070 19.96 - 39.92: 1851 39.92 - 59.88: 204 59.88 - 79.84: 66 79.84 - 99.80: 19 Dihedral angle restraints: 26210 sinusoidal: 11234 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 26207 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: 2.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.790 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 44.120 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.120 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 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 : 13.965 99.802 16492 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 are 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/Z covalent geometry : bond 0.00381 / 0.19 (43395) covalent geometry : angle 0.63534 / 0.36 (58957) hydrogen bonds : bond 0.16617 / 11.01 ( 2059) hydrogen bonds : angle 6.78481 / 4.93 ( 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 : 1.536 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: 0.2335 time to fit residues: 214.4596 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 : 1.571 ------------------------------------------------------------------------------- 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... 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 = 0.3895 r_free = 0.3895 target = 0.082372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.062329 restraints weight = 225942.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.063827 restraints weight = 125024.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.064901 restraints weight = 83634.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.065563 restraints weight = 62804.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.066051 restraints weight = 51656.639| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 43395 Z= 0.144 Angle : 0.653 9.326 58957 Z= 0.339 Chirality : 0.044 0.227 6663 Planarity : 0.004 0.043 7333 Dihedral : 6.510 93.623 6230 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.49 % Favored : 96.49 % Rotamer: Outliers : 0.81 % Allowed : 6.87 % Favored : 92.32 % 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 are not related in a simple way. whole: 0.09 (0.12), residues: 5049 helix: 0.68 (0.10), residues: 2463 sheet: -0.22 (0.22), residues: 524 loop : -0.49 (0.14), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 223 TYR 0.045 0.002 TYR G 519 PHE 0.042 0.002 PHE G1194 TRP 0.017 0.002 TRP G 986 HIS 0.009 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (43395) covalent geometry : angle 0.65322 / 0.34 (58957) hydrogen bonds : bond 0.04931 / 3.32 ( 2059) hydrogen bonds : angle 5.20526 / 3.74 ( 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 522 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 485 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9112 (tmm) cc_final: 0.8840 (tmm) REVERT: A 209 GLU cc_start: 0.9454 (pt0) cc_final: 0.9200 (pp20) REVERT: A 424 MET cc_start: 0.7693 (ppp) cc_final: 0.7161 (ppp) REVERT: A 601 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7540 (mt-10) REVERT: A 604 ARG cc_start: 0.8595 (tmm-80) cc_final: 0.8254 (ptt-90) REVERT: A 939 MET cc_start: 0.5791 (OUTLIER) cc_final: 0.5053 (tpp) REVERT: A 1261 ASP cc_start: 0.8171 (t0) cc_final: 0.7777 (t0) REVERT: C 218 MET cc_start: 0.7448 (mtm) cc_final: 0.7023 (ptm) REVERT: C 230 PHE cc_start: 0.8717 (t80) cc_final: 0.8172 (t80) REVERT: C 304 ASP cc_start: 0.8981 (OUTLIER) cc_final: 0.8525 (p0) REVERT: D 250 ASP cc_start: 0.8762 (m-30) cc_final: 0.8549 (m-30) REVERT: D 354 ASN cc_start: 0.7473 (t0) cc_final: 0.6800 (m-40) REVERT: D 429 ASN cc_start: 0.8067 (p0) cc_final: 0.7865 (t0) REVERT: D 487 MET cc_start: 0.8388 (tmm) cc_final: 0.8048 (tmm) REVERT: D 744 MET cc_start: 0.9050 (tpt) cc_final: 0.8781 (tpp) REVERT: D 805 MET cc_start: 0.8895 (ppp) cc_final: 0.8354 (ppp) REVERT: D 907 TYR cc_start: 0.8312 (m-80) cc_final: 0.7914 (m-80) REVERT: D 918 TYR cc_start: 0.7611 (m-10) cc_final: 0.7187 (m-80) REVERT: D 922 MET cc_start: 0.9104 (mpp) cc_final: 0.8895 (mmt) REVERT: D 935 LYS cc_start: 0.7657 (mmmt) cc_final: 0.7181 (mmmt) REVERT: D 985 LEU cc_start: 0.9415 (tp) cc_final: 0.9167 (tp) REVERT: D 1193 GLU cc_start: 0.9037 (tp30) cc_final: 0.8485 (tp30) REVERT: D 1237 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7699 (tm-30) REVERT: D 1389 MET cc_start: 0.8932 (mmm) cc_final: 0.8510 (mmm) REVERT: D 1689 MET cc_start: 0.8155 (mpp) cc_final: 0.7628 (mpp) REVERT: F 191 GLU cc_start: 0.8964 (tt0) cc_final: 0.8418 (mp0) REVERT: F 311 ILE cc_start: 0.7828 (mm) cc_final: 0.7468 (mt) REVERT: G 17 ASP cc_start: 0.9071 (m-30) cc_final: 0.8690 (p0) REVERT: G 75 MET cc_start: 0.8680 (mmm) cc_final: 0.8476 (mmm) REVERT: G 157 PHE cc_start: 0.7547 (m-80) cc_final: 0.7322 (m-10) REVERT: G 288 MET cc_start: 0.9206 (tmm) cc_final: 0.8803 (tmm) REVERT: G 322 MET cc_start: 0.9033 (tmm) cc_final: 0.8722 (tmm) REVERT: G 424 MET cc_start: 0.8381 (tmm) cc_final: 0.8097 (ptp) REVERT: G 458 MET cc_start: 0.8254 (tpp) cc_final: 0.8043 (tpp) REVERT: G 616 ILE cc_start: 0.7452 (mt) cc_final: 0.7096 (mt) REVERT: G 744 MET cc_start: -0.0149 (ttt) cc_final: -0.0737 (mmp) REVERT: G 893 MET cc_start: 0.0193 (mpp) cc_final: -0.0270 (mpp) REVERT: G 1379 LYS cc_start: 0.6903 (tptt) cc_final: 0.6627 (tppt) REVERT: G 1617 GLU cc_start: 0.9436 (tp30) cc_final: 0.8824 (tp30) REVERT: G 1707 LEU cc_start: 0.9284 (tt) cc_final: 0.9036 (pp) REVERT: I 206 GLU cc_start: 0.8171 (mp0) cc_final: 0.7942 (mp0) REVERT: I 226 TYR cc_start: 0.8774 (t80) cc_final: 0.8468 (t80) REVERT: I 252 ASP cc_start: 0.8059 (m-30) cc_final: 0.7850 (m-30) REVERT: I 304 ASP cc_start: 0.9287 (p0) cc_final: 0.9007 (p0) outliers start: 37 outliers final: 20 residues processed: 504 average time/residue: 0.2299 time to fit residues: 198.3945 Evaluate side-chains 404 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 382 time to evaluate : 1.648 ------------------------------------------------------------------------------- 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 304 ASP Chi-restraints excluded: chain D residue 42 LEU 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 1390 LEU 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: 10.0000 chunk 489 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 291 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 chunk 94 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 500 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 146 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 ASN A 339 GLN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS D 323 HIS D 454 ASN D 569 ASN ** D 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 948 GLN D 955 ASN ** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1286 HIS F 215 HIS G 72 GLN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 354 ASN G 801 GLN ** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.079881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.059641 restraints weight = 231383.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.061077 restraints weight = 128179.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.062116 restraints weight = 86121.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.062760 restraints weight = 65162.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.063289 restraints weight = 53877.698| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 43395 Z= 0.189 Angle : 0.644 11.394 58957 Z= 0.332 Chirality : 0.043 0.240 6663 Planarity : 0.004 0.091 7333 Dihedral : 6.498 94.894 6226 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.94 % Favored : 96.04 % Rotamer: Outliers : 1.60 % Allowed : 10.41 % Favored : 87.99 % 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 are not related in a simple way. whole: 0.14 (0.12), residues: 5049 helix: 0.73 (0.10), residues: 2465 sheet: -0.13 (0.22), residues: 519 loop : -0.50 (0.14), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG C 198 TYR 0.042 0.002 TYR I 231 PHE 0.035 0.002 PHE G1194 TRP 0.025 0.002 TRP G 102 HIS 0.009 0.001 HIS D 743 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (43395) covalent geometry : angle 0.64415 / 0.33 (58957) hydrogen bonds : bond 0.04505 / 3.03 ( 2059) hydrogen bonds : angle 5.02108 / 3.62 ( 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 479 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 406 time to evaluate : 1.690 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 122 MET cc_start: 0.9198 (tmm) cc_final: 0.8877 (tmm) REVERT: A 424 MET cc_start: 0.7805 (ppp) cc_final: 0.7069 (ppp) REVERT: A 1261 ASP cc_start: 0.8169 (t0) cc_final: 0.7801 (t0) REVERT: A 1333 GLU cc_start: 0.7676 (tt0) cc_final: 0.7421 (tt0) REVERT: C 218 MET cc_start: 0.7471 (mtm) cc_final: 0.7004 (ptm) REVERT: C 230 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8219 (t80) REVERT: C 304 ASP cc_start: 0.8926 (OUTLIER) cc_final: 0.8504 (p0) REVERT: D 208 MET cc_start: 0.8791 (mmm) cc_final: 0.8472 (mmm) REVERT: D 250 ASP cc_start: 0.8844 (m-30) cc_final: 0.8593 (m-30) REVERT: D 527 ASP cc_start: 0.8726 (m-30) cc_final: 0.8517 (m-30) REVERT: D 805 MET cc_start: 0.9034 (ppp) cc_final: 0.8514 (ppp) REVERT: D 907 TYR cc_start: 0.8537 (m-80) cc_final: 0.8153 (m-80) REVERT: D 918 TYR cc_start: 0.7707 (m-10) cc_final: 0.7366 (m-80) REVERT: D 922 MET cc_start: 0.9141 (mpp) cc_final: 0.8874 (mmt) REVERT: D 935 LYS cc_start: 0.7833 (mmmt) cc_final: 0.7247 (mmmt) REVERT: D 1002 LEU cc_start: 0.9119 (mt) cc_final: 0.8892 (mt) REVERT: D 1237 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7576 (tm-30) REVERT: D 1368 ASP cc_start: 0.8794 (m-30) cc_final: 0.8516 (m-30) REVERT: D 1389 MET cc_start: 0.9023 (mmm) cc_final: 0.8658 (mmm) REVERT: D 1681 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7893 (tpp) REVERT: D 1689 MET cc_start: 0.8338 (mpp) cc_final: 0.7760 (mpp) REVERT: F 191 GLU cc_start: 0.9007 (tt0) cc_final: 0.8333 (mp0) REVERT: F 311 ILE cc_start: 0.7843 (mm) cc_final: 0.7613 (mt) REVERT: G 13 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.8945 (mm) REVERT: G 17 ASP cc_start: 0.9149 (m-30) cc_final: 0.8703 (p0) REVERT: G 66 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.7487 (t) REVERT: G 157 PHE cc_start: 0.7782 (m-80) cc_final: 0.7490 (m-10) REVERT: G 243 GLU cc_start: 0.9508 (mm-30) cc_final: 0.9282 (mm-30) REVERT: G 288 MET cc_start: 0.9249 (tmm) cc_final: 0.8912 (tmm) REVERT: G 744 MET cc_start: 0.0369 (ttt) cc_final: -0.0119 (mmp) REVERT: G 893 MET cc_start: 0.0397 (mpp) cc_final: -0.0017 (mpp) REVERT: G 979 PHE cc_start: 0.4541 (OUTLIER) cc_final: 0.4325 (m-80) REVERT: G 1209 MET cc_start: 0.5925 (ppp) cc_final: 0.5480 (ptp) REVERT: G 1379 LYS cc_start: 0.6942 (tptt) cc_final: 0.6705 (tppt) REVERT: G 1617 GLU cc_start: 0.9423 (tp30) cc_final: 0.8915 (tp30) REVERT: G 1647 GLU cc_start: 0.9292 (tp30) cc_final: 0.9090 (tp30) REVERT: G 1650 ARG cc_start: 0.7827 (ptm-80) cc_final: 0.7500 (ptm-80) REVERT: G 1658 ARG cc_start: 0.7288 (mmm160) cc_final: 0.6437 (ptm160) REVERT: G 1665 HIS cc_start: 0.8440 (m-70) cc_final: 0.7988 (t70) REVERT: G 1689 MET cc_start: 0.2017 (mmt) cc_final: 0.1529 (mmt) REVERT: G 1707 LEU cc_start: 0.9351 (tt) cc_final: 0.9078 (pp) REVERT: I 204 TYR cc_start: 0.8135 (m-80) cc_final: 0.7601 (m-80) REVERT: I 206 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7840 (mp0) outliers start: 73 outliers final: 36 residues processed: 449 average time/residue: 0.2416 time to fit residues: 187.7560 Evaluate side-chains 406 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 364 time to evaluate : 1.666 ------------------------------------------------------------------------------- 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 233 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 999 MET 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 305 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 424 MET Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 1681 MET 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 181 ILE 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 979 PHE Chi-restraints excluded: chain G residue 1282 ILE Chi-restraints excluded: chain G residue 1390 LEU 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 1500 THR 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: 0.8980 chunk 507 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 262 optimal weight: 10.0000 chunk 426 optimal weight: 6.9990 chunk 43 optimal weight: 0.0470 chunk 217 optimal weight: 0.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 ASN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1406 GLN ** D 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.080844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.060555 restraints weight = 226526.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.062015 restraints weight = 125128.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.063081 restraints weight = 83613.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.063777 restraints weight = 63187.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.064200 restraints weight = 52203.296| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 43395 Z= 0.125 Angle : 0.601 11.800 58957 Z= 0.307 Chirality : 0.041 0.207 6663 Planarity : 0.004 0.044 7333 Dihedral : 6.322 92.697 6226 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.31 % Favored : 96.67 % Rotamer: Outliers : 1.36 % Allowed : 12.62 % Favored : 86.02 % 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 are not related in a simple way. whole: 0.27 (0.12), residues: 5049 helix: 0.84 (0.10), residues: 2450 sheet: -0.02 (0.23), residues: 516 loop : -0.46 (0.14), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 604 TYR 0.042 0.002 TYR A1343 PHE 0.025 0.001 PHE G1194 TRP 0.018 0.001 TRP A 97 HIS 0.008 0.001 HIS G 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (43395) covalent geometry : angle 0.60073 / 0.31 (58957) hydrogen bonds : bond 0.04018 / 2.70 ( 2059) hydrogen bonds : angle 4.76594 / 3.43 ( 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 485 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 423 time to evaluate : 1.661 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 75 MET cc_start: 0.8548 (tpt) cc_final: 0.7242 (tpt) REVERT: A 122 MET cc_start: 0.9239 (tmm) cc_final: 0.8890 (tmm) REVERT: A 344 MET cc_start: 0.3652 (ttt) cc_final: 0.2953 (tmm) REVERT: A 360 MET cc_start: 0.8894 (mmm) cc_final: 0.8630 (mmm) REVERT: A 424 MET cc_start: 0.7967 (ppp) cc_final: 0.7196 (ppp) REVERT: A 747 ASN cc_start: 0.9039 (m110) cc_final: 0.8730 (t0) REVERT: A 893 MET cc_start: 0.6770 (ppp) cc_final: 0.6524 (ppp) REVERT: A 1261 ASP cc_start: 0.8189 (t0) cc_final: 0.7847 (t0) REVERT: A 1333 GLU cc_start: 0.7730 (tt0) cc_final: 0.7523 (tt0) REVERT: A 1602 MET cc_start: 0.8659 (mtt) cc_final: 0.8441 (mmm) REVERT: C 230 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8206 (t80) REVERT: C 267 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8726 (tp) REVERT: C 304 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8434 (p0) REVERT: D 122 MET cc_start: 0.9282 (tmm) cc_final: 0.9082 (tmm) REVERT: D 208 MET cc_start: 0.8864 (mmm) cc_final: 0.8438 (mmm) REVERT: D 250 ASP cc_start: 0.8798 (m-30) cc_final: 0.8512 (m-30) REVERT: D 360 MET cc_start: 0.8396 (tmm) cc_final: 0.7937 (tpp) REVERT: D 527 ASP cc_start: 0.8696 (m-30) cc_final: 0.8409 (m-30) REVERT: D 805 MET cc_start: 0.9008 (ppp) cc_final: 0.8504 (ppp) REVERT: D 907 TYR cc_start: 0.8502 (m-80) cc_final: 0.8128 (m-80) REVERT: D 922 MET cc_start: 0.9113 (mpp) cc_final: 0.8861 (mmt) REVERT: D 939 MET cc_start: 0.2625 (tpp) cc_final: 0.2331 (mpp) REVERT: D 1002 LEU cc_start: 0.9116 (mt) cc_final: 0.8778 (mt) REVERT: D 1237 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7476 (tm-30) REVERT: D 1681 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7898 (tpp) REVERT: D 1689 MET cc_start: 0.8245 (mpp) cc_final: 0.7742 (mpp) REVERT: F 191 GLU cc_start: 0.8975 (tt0) cc_final: 0.8356 (mp0) REVERT: F 247 TYR cc_start: 0.8053 (m-10) cc_final: 0.7848 (m-80) REVERT: F 311 ILE cc_start: 0.7962 (mm) cc_final: 0.7737 (mt) REVERT: G 13 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9183 (mm) REVERT: G 17 ASP cc_start: 0.9118 (m-30) cc_final: 0.8806 (m-30) REVERT: G 157 PHE cc_start: 0.7811 (m-80) cc_final: 0.7428 (m-80) REVERT: G 208 MET cc_start: 0.7667 (mmp) cc_final: 0.7088 (mmp) REVERT: G 243 GLU cc_start: 0.9502 (mm-30) cc_final: 0.9294 (mm-30) REVERT: G 288 MET cc_start: 0.9224 (tmm) cc_final: 0.8884 (tmm) REVERT: G 312 ARG cc_start: 0.9211 (mtm110) cc_final: 0.8900 (mtm110) REVERT: G 424 MET cc_start: 0.8488 (tmm) cc_final: 0.8013 (ptp) REVERT: G 744 MET cc_start: 0.0294 (ttt) cc_final: -0.0222 (mmp) REVERT: G 893 MET cc_start: 0.0312 (mpp) cc_final: -0.0090 (mpp) REVERT: G 1040 LYS cc_start: 0.7924 (pptt) cc_final: 0.7455 (mmtm) REVERT: G 1209 MET cc_start: 0.6045 (ppp) cc_final: 0.5678 (ppp) REVERT: G 1379 LYS cc_start: 0.6936 (tptt) cc_final: 0.6673 (tppt) REVERT: G 1447 ARG cc_start: 0.7609 (mmt180) cc_final: 0.7372 (mmt-90) REVERT: G 1617 GLU cc_start: 0.9428 (tp30) cc_final: 0.8942 (tp30) REVERT: G 1658 ARG cc_start: 0.7168 (mmm160) cc_final: 0.6372 (ptm160) REVERT: G 1665 HIS cc_start: 0.8445 (m-70) cc_final: 0.7980 (t70) REVERT: G 1689 MET cc_start: 0.2034 (mmt) cc_final: 0.1448 (mmt) REVERT: G 1707 LEU cc_start: 0.9309 (tt) cc_final: 0.9054 (pp) REVERT: I 199 LYS cc_start: 0.9074 (pttt) cc_final: 0.8858 (ptpt) REVERT: I 204 TYR cc_start: 0.7964 (m-80) cc_final: 0.7557 (m-80) REVERT: I 223 ARG cc_start: 0.8304 (ttt-90) cc_final: 0.7715 (ttt-90) REVERT: I 226 TYR cc_start: 0.8666 (t80) cc_final: 0.8363 (t80) outliers start: 62 outliers final: 30 residues processed: 463 average time/residue: 0.2386 time to fit residues: 190.0637 Evaluate side-chains 408 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 373 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1608 VAL Chi-restraints excluded: chain A residue 1620 ILE Chi-restraints excluded: chain A residue 1689 MET 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 354 ASN Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 1681 MET Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 625 MET Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 933 VAL Chi-restraints excluded: chain G residue 1282 ILE Chi-restraints excluded: chain G residue 1390 LEU 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: 10.0000 chunk 108 optimal weight: 5.9990 chunk 225 optimal weight: 5.9990 chunk 154 optimal weight: 8.9990 chunk 207 optimal weight: 0.8980 chunk 416 optimal weight: 5.9990 chunk 310 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 chunk 361 optimal weight: 10.0000 chunk 453 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 517 GLN A 550 HIS ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN A1353 ASN D 72 GLN D 429 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 D1685 GLN ** D1712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 749 GLN G 955 ASN ** G1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1495 ASN G1541 ASN ** G1646 GLN ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.077423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.057559 restraints weight = 233195.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.058791 restraints weight = 127436.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.059824 restraints weight = 85458.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.060520 restraints weight = 64670.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.060917 restraints weight = 53198.973| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 43395 Z= 0.213 Angle : 0.666 12.124 58957 Z= 0.342 Chirality : 0.042 0.177 6663 Planarity : 0.005 0.049 7333 Dihedral : 6.399 97.693 6226 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.24 % Favored : 95.74 % Rotamer: Outliers : 2.34 % Allowed : 13.94 % Favored : 83.72 % 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 are not related in a simple way. whole: 0.23 (0.12), residues: 5049 helix: 0.82 (0.10), residues: 2446 sheet: -0.02 (0.24), residues: 456 loop : -0.48 (0.14), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 99 TYR 0.036 0.002 TYR G 519 PHE 0.032 0.002 PHE G 818 TRP 0.019 0.002 TRP G 102 HIS 0.007 0.001 HIS D1522 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (43395) covalent geometry : angle 0.66638 / 0.34 (58957) hydrogen bonds : bond 0.04266 / 2.86 ( 2059) hydrogen bonds : angle 4.84907 / 3.50 ( 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 480 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 373 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9298 (tmm) cc_final: 0.8949 (tmm) REVERT: A 360 MET cc_start: 0.8972 (mmm) cc_final: 0.8731 (mmm) REVERT: A 424 MET cc_start: 0.7931 (ppp) cc_final: 0.7027 (ppp) REVERT: A 635 MET cc_start: 0.7719 (mmm) cc_final: 0.7462 (mmm) REVERT: A 882 VAL cc_start: 0.9081 (OUTLIER) cc_final: 0.7838 (p) REVERT: A 893 MET cc_start: 0.7086 (ppp) cc_final: 0.6676 (ppp) REVERT: A 939 MET cc_start: 0.6546 (OUTLIER) cc_final: 0.6112 (tpp) REVERT: A 1240 LEU cc_start: 0.8873 (mt) cc_final: 0.8659 (mt) REVERT: A 1261 ASP cc_start: 0.8402 (t0) cc_final: 0.8137 (t70) REVERT: A 1602 MET cc_start: 0.8699 (mtt) cc_final: 0.8365 (mmm) REVERT: A 1681 MET cc_start: 0.8545 (tmm) cc_final: 0.7690 (tmm) REVERT: C 230 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8330 (t80) REVERT: C 285 CYS cc_start: 0.8542 (m) cc_final: 0.8089 (p) REVERT: C 304 ASP cc_start: 0.8947 (OUTLIER) cc_final: 0.8534 (p0) REVERT: D 208 MET cc_start: 0.8740 (mmm) cc_final: 0.8355 (mmm) REVERT: D 250 ASP cc_start: 0.8925 (m-30) cc_final: 0.8693 (m-30) REVERT: D 360 MET cc_start: 0.8523 (tmm) cc_final: 0.8130 (tpp) REVERT: D 458 MET cc_start: 0.9256 (tpp) cc_final: 0.8851 (tpp) REVERT: D 894 LEU cc_start: 0.8509 (tt) cc_final: 0.8252 (tp) REVERT: D 907 TYR cc_start: 0.8589 (m-80) cc_final: 0.8200 (m-80) REVERT: D 922 MET cc_start: 0.9177 (mpp) cc_final: 0.8723 (mtt) REVERT: D 1002 LEU cc_start: 0.9227 (mt) cc_final: 0.8994 (mt) REVERT: D 1237 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7602 (tm-30) REVERT: G 13 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9239 (mm) REVERT: G 17 ASP cc_start: 0.9175 (m-30) cc_final: 0.8876 (m-30) REVERT: G 63 MET cc_start: 0.6685 (tpp) cc_final: 0.6401 (mmm) REVERT: G 156 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8859 (mm) REVERT: G 243 GLU cc_start: 0.9537 (mm-30) cc_final: 0.9328 (mm-30) REVERT: G 288 MET cc_start: 0.9277 (tmm) cc_final: 0.8883 (tmm) REVERT: G 312 ARG cc_start: 0.9257 (mtm110) cc_final: 0.8991 (mtm110) REVERT: G 744 MET cc_start: 0.0907 (ttt) cc_final: 0.0345 (mmp) REVERT: G 1040 LYS cc_start: 0.7830 (pptt) cc_final: 0.7372 (mptt) REVERT: G 1209 MET cc_start: 0.6092 (ppp) cc_final: 0.5779 (ptp) REVERT: G 1617 GLU cc_start: 0.9420 (tp30) cc_final: 0.8837 (tp30) REVERT: G 1658 ARG cc_start: 0.7060 (mmm160) cc_final: 0.6339 (ptm160) REVERT: G 1665 HIS cc_start: 0.8440 (m-70) cc_final: 0.8114 (t70) REVERT: G 1689 MET cc_start: 0.2231 (mmt) cc_final: 0.1554 (mmt) REVERT: I 199 LYS cc_start: 0.9112 (pttt) cc_final: 0.8897 (mttt) REVERT: I 309 MET cc_start: 0.9353 (tpp) cc_final: 0.8908 (tpt) outliers start: 107 outliers final: 63 residues processed: 450 average time/residue: 0.2325 time to fit residues: 181.5232 Evaluate side-chains 418 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 349 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 198 ASN 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 907 TYR 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 1620 ILE Chi-restraints excluded: chain A residue 1689 MET 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 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 305 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 400 CYS Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 1225 THR 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 13 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 123 VAL 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 457 LEU Chi-restraints excluded: chain G residue 541 GLU 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 933 VAL Chi-restraints excluded: chain G residue 1390 LEU Chi-restraints excluded: chain G residue 1430 LEU Chi-restraints excluded: chain G residue 1474 ILE Chi-restraints excluded: chain G residue 1521 LEU Chi-restraints excluded: chain G residue 1522 HIS Chi-restraints excluded: chain G residue 1532 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 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: 3.9990 chunk 186 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 446 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 335 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 416 optimal weight: 10.0000 chunk 336 optimal weight: 2.9990 chunk 492 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 HIS ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 HIS ** 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** ** G1656 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.077935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.057765 restraints weight = 231267.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.059254 restraints weight = 126734.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.060259 restraints weight = 84476.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.060888 restraints weight = 64135.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.061360 restraints weight = 53274.573| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 43395 Z= 0.150 Angle : 0.617 14.018 58957 Z= 0.314 Chirality : 0.042 0.181 6663 Planarity : 0.004 0.048 7333 Dihedral : 6.244 94.691 6226 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.37 % Favored : 96.61 % Rotamer: Outliers : 1.97 % Allowed : 15.51 % Favored : 82.52 % 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 are not related in a simple way. whole: 0.33 (0.12), residues: 5049 helix: 0.92 (0.10), residues: 2461 sheet: -0.03 (0.24), residues: 468 loop : -0.46 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 79 TYR 0.030 0.002 TYR G 519 PHE 0.043 0.001 PHE G1393 TRP 0.015 0.001 TRP G 986 HIS 0.007 0.001 HIS G 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (43395) covalent geometry : angle 0.61703 / 0.31 (58957) hydrogen bonds : bond 0.03849 / 2.58 ( 2059) hydrogen bonds : angle 4.69836 / 3.38 ( 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 464 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 374 time to evaluate : 1.778 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: 0.8558 (ttm) cc_final: 0.8346 (ttm) REVERT: A 122 MET cc_start: 0.9330 (tmm) cc_final: 0.8988 (tmm) REVERT: A 360 MET cc_start: 0.9029 (mmm) cc_final: 0.8809 (mmm) REVERT: A 424 MET cc_start: 0.7999 (ppp) cc_final: 0.7077 (ppp) REVERT: A 635 MET cc_start: 0.7786 (mmm) cc_final: 0.7515 (mmm) REVERT: A 747 ASN cc_start: 0.8986 (m110) cc_final: 0.8650 (t0) REVERT: A 908 MET cc_start: 0.1965 (mmt) cc_final: 0.1250 (mmm) REVERT: A 939 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.6213 (tpp) REVERT: A 1261 ASP cc_start: 0.8412 (t0) cc_final: 0.8182 (t70) REVERT: A 1602 MET cc_start: 0.8726 (mtt) cc_final: 0.8423 (mmm) REVERT: A 1681 MET cc_start: 0.8512 (tmm) cc_final: 0.7673 (tmm) REVERT: C 230 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8332 (t80) REVERT: C 285 CYS cc_start: 0.8500 (m) cc_final: 0.7945 (p) REVERT: C 304 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8440 (p0) REVERT: D 208 MET cc_start: 0.8751 (mmm) cc_final: 0.8395 (mmm) REVERT: D 250 ASP cc_start: 0.8925 (m-30) cc_final: 0.8651 (m-30) REVERT: D 360 MET cc_start: 0.8520 (tmm) cc_final: 0.8137 (tpp) REVERT: D 458 MET cc_start: 0.9241 (tpp) cc_final: 0.8999 (tpp) REVERT: D 805 MET cc_start: 0.9216 (ppp) cc_final: 0.8870 (ppp) REVERT: D 893 MET cc_start: 0.6406 (ttt) cc_final: 0.6052 (ttm) REVERT: D 894 LEU cc_start: 0.8411 (tt) cc_final: 0.8147 (tt) REVERT: D 907 TYR cc_start: 0.8545 (m-80) cc_final: 0.8168 (m-80) REVERT: D 922 MET cc_start: 0.9176 (mpp) cc_final: 0.8789 (mtt) REVERT: D 939 MET cc_start: 0.3553 (tpp) cc_final: 0.3319 (tpp) REVERT: D 999 MET cc_start: 0.9246 (mmm) cc_final: 0.8948 (mtm) REVERT: D 1002 LEU cc_start: 0.9257 (mt) cc_final: 0.9023 (mt) REVERT: D 1193 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8760 (tt0) REVERT: D 1237 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7545 (tm-30) REVERT: D 1333 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8711 (pt0) REVERT: D 1389 MET cc_start: 0.9059 (mmm) cc_final: 0.8787 (mmm) REVERT: D 1602 MET cc_start: 0.8780 (mmm) cc_final: 0.8386 (mmm) REVERT: D 1689 MET cc_start: 0.7968 (mpp) cc_final: 0.7543 (mpp) REVERT: G 17 ASP cc_start: 0.9119 (m-30) cc_final: 0.8705 (m-30) REVERT: G 156 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8913 (mm) REVERT: G 243 GLU cc_start: 0.9531 (mm-30) cc_final: 0.9324 (mm-30) REVERT: G 312 ARG cc_start: 0.9250 (mtm110) cc_final: 0.9010 (mtm110) REVERT: G 424 MET cc_start: 0.8421 (tmm) cc_final: 0.7911 (ptp) REVERT: G 484 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8820 (p) REVERT: G 744 MET cc_start: 0.1017 (ttt) cc_final: 0.0487 (mmp) REVERT: G 818 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7613 (t80) REVERT: G 1040 LYS cc_start: 0.7952 (pptt) cc_final: 0.7486 (mptt) REVERT: G 1209 MET cc_start: 0.5946 (ppp) cc_final: 0.5501 (mtm) REVERT: G 1215 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8574 (mp) REVERT: G 1617 GLU cc_start: 0.9430 (tp30) cc_final: 0.8996 (tp30) REVERT: G 1658 ARG cc_start: 0.7068 (mmm160) cc_final: 0.6353 (ptm160) REVERT: G 1665 HIS cc_start: 0.8445 (m-70) cc_final: 0.8015 (t70) REVERT: G 1689 MET cc_start: 0.2280 (mmt) cc_final: 0.1518 (mmt) REVERT: G 1707 LEU cc_start: 0.9400 (tt) cc_final: 0.9103 (pp) REVERT: I 226 TYR cc_start: 0.8601 (t80) cc_final: 0.8258 (t80) outliers start: 90 outliers final: 56 residues processed: 433 average time/residue: 0.2394 time to fit residues: 180.1516 Evaluate side-chains 413 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 348 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 233 THR 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 1608 VAL Chi-restraints excluded: chain A residue 1620 ILE Chi-restraints excluded: chain A residue 1689 MET 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 296 THR Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 354 ASN 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 849 MET Chi-restraints excluded: chain D residue 971 LEU Chi-restraints excluded: chain D residue 1193 GLU Chi-restraints excluded: chain D residue 1333 GLU Chi-restraints excluded: chain D residue 1554 VAL Chi-restraints excluded: chain D residue 1669 VAL Chi-restraints excluded: chain D residue 1681 MET Chi-restraints excluded: chain F residue 239 ILE 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 72 GLN Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 237 LEU 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 933 VAL Chi-restraints excluded: chain G residue 1215 LEU Chi-restraints excluded: chain G residue 1282 ILE Chi-restraints excluded: chain G residue 1390 LEU Chi-restraints excluded: chain G residue 1430 LEU Chi-restraints excluded: chain G residue 1444 PHE Chi-restraints excluded: chain G residue 1500 THR Chi-restraints excluded: chain G residue 1522 HIS Chi-restraints excluded: chain G residue 1532 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 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: 2.9990 chunk 479 optimal weight: 10.0000 chunk 429 optimal weight: 40.0000 chunk 236 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 434 optimal weight: 20.0000 chunk 492 optimal weight: 3.9990 chunk 386 optimal weight: 0.0270 chunk 143 optimal weight: 0.0060 chunk 58 optimal weight: 0.9990 chunk 309 optimal weight: 4.9990 overall best weight: 1.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 ASN D 864 GLN D1439 ASN ** D1712 HIS ** 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 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** ** G1656 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.078277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.058318 restraints weight = 228360.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.059767 restraints weight = 125397.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.060777 restraints weight = 84022.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.061464 restraints weight = 63820.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.061876 restraints weight = 52880.656| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 43395 Z= 0.126 Angle : 0.614 14.446 58957 Z= 0.308 Chirality : 0.041 0.174 6663 Planarity : 0.004 0.051 7333 Dihedral : 6.107 94.026 6226 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.80 % Favored : 96.18 % Rotamer: Outliers : 2.10 % Allowed : 16.32 % Favored : 81.58 % 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 are not related in a simple way. whole: 0.41 (0.12), residues: 5049 helix: 0.97 (0.10), residues: 2447 sheet: 0.02 (0.24), residues: 476 loop : -0.39 (0.14), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 223 TYR 0.035 0.001 TYR I 231 PHE 0.047 0.001 PHE G1393 TRP 0.015 0.001 TRP G 986 HIS 0.006 0.001 HIS G 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (43395) covalent geometry : angle 0.61385 / 0.31 (58957) hydrogen bonds : bond 0.03733 / 2.50 ( 2059) hydrogen bonds : angle 4.59764 / 3.30 ( 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 477 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 381 time to evaluate : 1.695 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: 0.9334 (tmm) cc_final: 0.8987 (tmm) REVERT: A 222 MET cc_start: 0.7700 (tpt) cc_final: 0.6861 (tmm) REVERT: A 372 MET cc_start: 0.7080 (ttt) cc_final: 0.6759 (ttt) REVERT: A 424 MET cc_start: 0.8000 (ppp) cc_final: 0.7090 (ppp) REVERT: A 635 MET cc_start: 0.7854 (mmm) cc_final: 0.7586 (mmm) REVERT: A 747 ASN cc_start: 0.8997 (m110) cc_final: 0.8676 (t0) REVERT: A 908 MET cc_start: 0.2241 (mmt) cc_final: 0.1510 (mmm) REVERT: A 939 MET cc_start: 0.6499 (OUTLIER) cc_final: 0.6153 (tpp) REVERT: A 1261 ASP cc_start: 0.8444 (t0) cc_final: 0.8203 (t70) REVERT: A 1681 MET cc_start: 0.8498 (tmm) cc_final: 0.7693 (tmm) REVERT: C 218 MET cc_start: 0.7577 (mtm) cc_final: 0.6855 (ptm) REVERT: C 230 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8309 (t80) REVERT: C 285 CYS cc_start: 0.8625 (m) cc_final: 0.8350 (p) REVERT: C 304 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.8538 (p0) REVERT: D 121 ASP cc_start: 0.8957 (m-30) cc_final: 0.8676 (m-30) REVERT: D 208 MET cc_start: 0.8867 (mmm) cc_final: 0.8544 (mmm) REVERT: D 250 ASP cc_start: 0.8981 (m-30) cc_final: 0.8645 (m-30) REVERT: D 360 MET cc_start: 0.8485 (tmm) cc_final: 0.8106 (tpp) REVERT: D 458 MET cc_start: 0.9202 (tpp) cc_final: 0.8988 (tpp) REVERT: D 487 MET cc_start: 0.8604 (tmm) cc_final: 0.8038 (tmm) REVERT: D 864 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8425 (pm20) REVERT: D 894 LEU cc_start: 0.8492 (tt) cc_final: 0.8197 (tt) REVERT: D 922 MET cc_start: 0.9184 (mpp) cc_final: 0.8794 (mtt) REVERT: D 939 MET cc_start: 0.2994 (tpp) cc_final: 0.2639 (tpp) REVERT: D 1002 LEU cc_start: 0.9291 (mt) cc_final: 0.9025 (mt) REVERT: D 1237 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7539 (tm-30) REVERT: D 1333 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8711 (pt0) REVERT: D 1389 MET cc_start: 0.9086 (mmm) cc_final: 0.8796 (mmm) REVERT: D 1602 MET cc_start: 0.8834 (mmm) cc_final: 0.8625 (mmm) REVERT: D 1689 MET cc_start: 0.7739 (mpp) cc_final: 0.7339 (mpp) REVERT: F 191 GLU cc_start: 0.8948 (tt0) cc_final: 0.8253 (mp0) REVERT: G 17 ASP cc_start: 0.9098 (m-30) cc_final: 0.8685 (m-30) REVERT: G 156 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8996 (mm) REVERT: G 243 GLU cc_start: 0.9542 (mm-30) cc_final: 0.9332 (mm-30) REVERT: G 270 ASP cc_start: 0.6752 (OUTLIER) cc_final: 0.6231 (p0) REVERT: G 288 MET cc_start: 0.9386 (ttp) cc_final: 0.9134 (tmm) REVERT: G 312 ARG cc_start: 0.9219 (mtm110) cc_final: 0.9003 (mtm110) REVERT: G 424 MET cc_start: 0.8502 (tmm) cc_final: 0.7893 (ptp) REVERT: G 484 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8840 (p) REVERT: G 682 HIS cc_start: 0.6979 (p90) cc_final: 0.6483 (p90) REVERT: G 744 MET cc_start: 0.0969 (ttt) cc_final: 0.0409 (mmp) REVERT: G 818 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7649 (t80) REVERT: G 1040 LYS cc_start: 0.7962 (pptt) cc_final: 0.7471 (mptt) REVERT: G 1209 MET cc_start: 0.5540 (ppp) cc_final: 0.5204 (ptp) REVERT: G 1215 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8663 (mp) REVERT: G 1617 GLU cc_start: 0.9394 (tp30) cc_final: 0.8922 (tp30) REVERT: G 1658 ARG cc_start: 0.7149 (mmm160) cc_final: 0.6460 (ptm160) REVERT: G 1665 HIS cc_start: 0.8436 (m-70) cc_final: 0.8010 (t70) REVERT: G 1689 MET cc_start: 0.2189 (mmt) cc_final: 0.1403 (mmt) REVERT: G 1707 LEU cc_start: 0.9417 (tt) cc_final: 0.9118 (pp) REVERT: I 204 TYR cc_start: 0.7730 (m-80) cc_final: 0.7457 (m-80) REVERT: I 214 ASP cc_start: 0.8772 (t0) cc_final: 0.8472 (t0) REVERT: I 226 TYR cc_start: 0.8611 (t80) cc_final: 0.8233 (t80) REVERT: I 258 MET cc_start: 0.8788 (mmm) cc_final: 0.8392 (mmm) REVERT: I 263 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.6762 (mm) REVERT: I 309 MET cc_start: 0.9368 (tpp) cc_final: 0.8903 (tpt) outliers start: 96 outliers final: 61 residues processed: 449 average time/residue: 0.2432 time to fit residues: 188.0186 Evaluate side-chains 424 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 352 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 509 LYS Chi-restraints excluded: chain A residue 758 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 999 MET Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1422 ASN Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1608 VAL Chi-restraints excluded: chain A residue 1620 ILE Chi-restraints excluded: chain A residue 1689 MET 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 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 303 LEU Chi-restraints excluded: chain D residue 354 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 596 VAL Chi-restraints excluded: chain D residue 849 MET Chi-restraints excluded: chain D residue 864 GLN Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 992 LEU Chi-restraints excluded: chain D residue 1248 VAL Chi-restraints excluded: chain D residue 1333 GLU 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 72 GLN Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain G residue 457 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 933 VAL Chi-restraints excluded: chain G residue 1199 THR Chi-restraints excluded: chain G residue 1215 LEU Chi-restraints excluded: chain G residue 1282 ILE Chi-restraints excluded: chain G residue 1390 LEU Chi-restraints excluded: chain G residue 1430 LEU Chi-restraints excluded: chain G residue 1443 THR Chi-restraints excluded: chain G residue 1454 LEU Chi-restraints excluded: chain G residue 1474 ILE Chi-restraints excluded: chain G residue 1522 HIS Chi-restraints excluded: chain G residue 1532 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 I residue 233 THR Chi-restraints excluded: chain I residue 263 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 69 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 225 optimal weight: 0.7980 chunk 483 optimal weight: 9.9990 chunk 354 optimal weight: 10.0000 chunk 383 optimal weight: 8.9990 chunk 141 optimal weight: 0.9980 chunk 301 optimal weight: 0.9980 chunk 319 optimal weight: 0.0040 chunk 54 optimal weight: 0.8980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 ASN C 301 HIS D1306 ASN D1338 ASN D1439 ASN ** D1712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 475 HIS ** 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** ** G1656 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.078940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.058967 restraints weight = 227451.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.060555 restraints weight = 124835.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.061517 restraints weight = 83245.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.062174 restraints weight = 62720.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.062653 restraints weight = 51698.781| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 43395 Z= 0.115 Angle : 0.626 14.537 58957 Z= 0.309 Chirality : 0.041 0.258 6663 Planarity : 0.004 0.054 7333 Dihedral : 6.020 92.845 6226 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.33 % Favored : 96.65 % Rotamer: Outliers : 1.71 % Allowed : 16.93 % Favored : 81.36 % 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 are not related in a simple way. whole: 0.43 (0.12), residues: 5049 helix: 0.96 (0.10), residues: 2452 sheet: 0.05 (0.24), residues: 476 loop : -0.35 (0.14), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 866 TYR 0.023 0.001 TYR G 519 PHE 0.040 0.001 PHE G1393 TRP 0.014 0.001 TRP G 986 HIS 0.006 0.001 HIS A1522 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (43395) covalent geometry : angle 0.62629 / 0.31 (58957) hydrogen bonds : bond 0.03634 / 2.43 ( 2059) hydrogen bonds : angle 4.55215 / 3.25 ( 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 456 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 378 time to evaluate : 1.690 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: 0.9324 (tmm) cc_final: 0.8957 (tmm) REVERT: A 372 MET cc_start: 0.7058 (ttt) cc_final: 0.6603 (ttm) REVERT: A 424 MET cc_start: 0.8028 (ppp) cc_final: 0.7085 (ppp) REVERT: A 744 MET cc_start: 0.8689 (tpp) cc_final: 0.8451 (tpp) REVERT: A 747 ASN cc_start: 0.8950 (m110) cc_final: 0.8695 (t0) REVERT: A 748 LEU cc_start: 0.9061 (mt) cc_final: 0.8810 (mt) REVERT: A 939 MET cc_start: 0.6543 (OUTLIER) cc_final: 0.6206 (tpp) REVERT: A 1261 ASP cc_start: 0.8433 (t0) cc_final: 0.8195 (t70) REVERT: A 1602 MET cc_start: 0.8805 (mmt) cc_final: 0.8309 (mmm) REVERT: A 1681 MET cc_start: 0.8486 (tmm) cc_final: 0.7758 (tmm) REVERT: C 230 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8290 (t80) REVERT: C 285 CYS cc_start: 0.8630 (m) cc_final: 0.7949 (p) REVERT: C 304 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.8459 (p0) REVERT: D 208 MET cc_start: 0.8851 (mmm) cc_final: 0.8528 (mmm) REVERT: D 250 ASP cc_start: 0.8966 (m-30) cc_final: 0.8726 (m-30) REVERT: D 360 MET cc_start: 0.8466 (tmm) cc_final: 0.8071 (tpp) REVERT: D 458 MET cc_start: 0.9229 (tpp) cc_final: 0.9018 (tpp) REVERT: D 487 MET cc_start: 0.8594 (tmm) cc_final: 0.8034 (tmm) REVERT: D 744 MET cc_start: 0.9395 (tpp) cc_final: 0.9158 (tpp) REVERT: D 893 MET cc_start: 0.6421 (ttt) cc_final: 0.6047 (ttm) REVERT: D 894 LEU cc_start: 0.8498 (tt) cc_final: 0.8183 (tt) REVERT: D 922 MET cc_start: 0.9165 (mpp) cc_final: 0.8777 (mtt) REVERT: D 939 MET cc_start: 0.3456 (tpp) cc_final: 0.2986 (tpp) REVERT: D 967 MET cc_start: 0.6814 (tmm) cc_final: 0.5125 (ptp) REVERT: D 1002 LEU cc_start: 0.9328 (mt) cc_final: 0.9053 (mt) REVERT: D 1237 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7558 (tm-30) REVERT: D 1371 GLU cc_start: 0.8846 (pm20) cc_final: 0.8524 (pm20) REVERT: D 1681 MET cc_start: 0.8404 (tmm) cc_final: 0.8105 (tpp) REVERT: D 1689 MET cc_start: 0.7733 (mpp) cc_final: 0.7334 (mpp) REVERT: F 191 GLU cc_start: 0.8888 (tt0) cc_final: 0.8183 (mp0) REVERT: F 309 MET cc_start: 0.8961 (mmm) cc_final: 0.8585 (mmm) REVERT: G 17 ASP cc_start: 0.9091 (m-30) cc_final: 0.8684 (m-30) REVERT: G 156 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.9009 (mm) REVERT: G 180 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8563 (mp0) REVERT: G 243 GLU cc_start: 0.9544 (mm-30) cc_final: 0.9342 (mm-30) REVERT: G 270 ASP cc_start: 0.6721 (p0) cc_final: 0.6272 (p0) REVERT: G 288 MET cc_start: 0.9364 (ttp) cc_final: 0.9090 (tmm) REVERT: G 308 ASP cc_start: 0.8904 (t0) cc_final: 0.8442 (t0) REVERT: G 312 ARG cc_start: 0.9198 (mtm110) cc_final: 0.8935 (mtm-85) REVERT: G 424 MET cc_start: 0.8509 (tmm) cc_final: 0.7871 (ptp) REVERT: G 484 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8834 (p) REVERT: G 566 LEU cc_start: 0.9278 (tt) cc_final: 0.9052 (pp) REVERT: G 633 ASP cc_start: 0.8739 (t70) cc_final: 0.8538 (p0) REVERT: G 682 HIS cc_start: 0.6871 (p90) cc_final: 0.6365 (p90) REVERT: G 744 MET cc_start: 0.0980 (ttt) cc_final: 0.0419 (mmp) REVERT: G 818 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7597 (t80) REVERT: G 1040 LYS cc_start: 0.7907 (pptt) cc_final: 0.7424 (mptt) REVERT: G 1209 MET cc_start: 0.5521 (ppp) cc_final: 0.5186 (ptp) REVERT: G 1215 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8675 (mp) REVERT: G 1617 GLU cc_start: 0.9332 (tp30) cc_final: 0.8914 (tp30) REVERT: G 1658 ARG cc_start: 0.7113 (mmm160) cc_final: 0.6480 (ptm160) REVERT: G 1665 HIS cc_start: 0.8424 (m-70) cc_final: 0.7998 (t70) REVERT: G 1689 MET cc_start: 0.2286 (mmt) cc_final: 0.1450 (mmt) REVERT: G 1707 LEU cc_start: 0.9415 (tt) cc_final: 0.9078 (pp) REVERT: I 226 TYR cc_start: 0.8611 (t80) cc_final: 0.8246 (t80) REVERT: I 258 MET cc_start: 0.8732 (mmm) cc_final: 0.8419 (mmm) REVERT: I 263 ILE cc_start: 0.6925 (OUTLIER) cc_final: 0.6719 (mm) outliers start: 78 outliers final: 56 residues processed: 430 average time/residue: 0.2344 time to fit residues: 174.5081 Evaluate side-chains 427 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 363 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 758 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 999 MET Chi-restraints excluded: chain A residue 1422 ASN Chi-restraints excluded: chain A residue 1423 THR 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 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 253 ASN Chi-restraints excluded: chain D residue 354 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 596 VAL Chi-restraints excluded: chain D residue 745 TYR Chi-restraints excluded: chain D residue 849 MET Chi-restraints excluded: chain D residue 918 TYR Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 992 LEU 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 D residue 1669 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 457 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 818 PHE Chi-restraints excluded: chain G residue 916 THR Chi-restraints excluded: chain G residue 933 VAL Chi-restraints excluded: chain G residue 1215 LEU Chi-restraints excluded: chain G residue 1282 ILE Chi-restraints excluded: chain G residue 1390 LEU Chi-restraints excluded: chain G residue 1430 LEU Chi-restraints excluded: chain G residue 1443 THR Chi-restraints excluded: chain G residue 1454 LEU Chi-restraints excluded: chain G residue 1522 HIS Chi-restraints excluded: chain G residue 1532 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 I residue 233 THR Chi-restraints excluded: chain I residue 263 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 23 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 419 optimal weight: 0.5980 chunk 378 optimal weight: 10.0000 chunk 385 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 296 optimal weight: 0.5980 chunk 118 optimal weight: 0.0070 chunk 138 optimal weight: 5.9990 chunk 313 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1013 ASN D 864 GLN D1439 ASN ** D1712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 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** ** G1656 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.079382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.059259 restraints weight = 226560.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.060722 restraints weight = 122700.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.061772 restraints weight = 81316.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.062475 restraints weight = 61368.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.062947 restraints weight = 50521.302| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 43395 Z= 0.112 Angle : 0.630 14.401 58957 Z= 0.311 Chirality : 0.041 0.241 6663 Planarity : 0.004 0.052 7333 Dihedral : 5.899 92.204 6226 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.43 % Favored : 96.55 % Rotamer: Outliers : 1.88 % Allowed : 17.11 % Favored : 81.01 % 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 are not related in a simple way. whole: 0.44 (0.12), residues: 5049 helix: 0.94 (0.10), residues: 2461 sheet: 0.14 (0.24), residues: 473 loop : -0.34 (0.14), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 223 TYR 0.033 0.001 TYR I 231 PHE 0.037 0.001 PHE G1393 TRP 0.015 0.001 TRP G 986 HIS 0.007 0.001 HIS D1286 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (43395) covalent geometry : angle 0.63012 / 0.31 (58957) hydrogen bonds : bond 0.03559 / 2.38 ( 2059) hydrogen bonds : angle 4.51428 / 3.23 ( 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 474 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 388 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9302 (tmm) cc_final: 0.8910 (tmm) REVERT: A 222 MET cc_start: 0.8251 (tmm) cc_final: 0.7963 (tmm) REVERT: A 372 MET cc_start: 0.7212 (ttt) cc_final: 0.6798 (ttm) REVERT: A 424 MET cc_start: 0.8073 (ppp) cc_final: 0.7108 (ppp) REVERT: A 534 ASP cc_start: 0.8590 (p0) cc_final: 0.8207 (p0) REVERT: A 744 MET cc_start: 0.8697 (tpp) cc_final: 0.8427 (tpp) REVERT: A 747 ASN cc_start: 0.8928 (m110) cc_final: 0.8697 (t0) REVERT: A 748 LEU cc_start: 0.8998 (mt) cc_final: 0.8715 (mt) REVERT: A 939 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6287 (tpp) REVERT: A 1261 ASP cc_start: 0.8410 (t0) cc_final: 0.8183 (t70) REVERT: A 1472 GLU cc_start: 0.8862 (pp20) cc_final: 0.8404 (tm-30) REVERT: A 1602 MET cc_start: 0.8553 (mmt) cc_final: 0.8237 (mmm) REVERT: A 1681 MET cc_start: 0.8486 (tmm) cc_final: 0.7755 (tmm) REVERT: C 230 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8256 (t80) REVERT: C 267 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8766 (tp) REVERT: C 285 CYS cc_start: 0.8607 (m) cc_final: 0.7961 (p) REVERT: C 304 ASP cc_start: 0.8929 (OUTLIER) cc_final: 0.8466 (p0) REVERT: D 208 MET cc_start: 0.8833 (mmm) cc_final: 0.8517 (mmm) REVERT: D 222 MET cc_start: 0.8476 (ttt) cc_final: 0.8272 (ttt) REVERT: D 250 ASP cc_start: 0.9078 (m-30) cc_final: 0.8682 (m-30) REVERT: D 360 MET cc_start: 0.8485 (tmm) cc_final: 0.8080 (tpp) REVERT: D 487 MET cc_start: 0.8574 (tmm) cc_final: 0.8029 (tmm) REVERT: D 805 MET cc_start: 0.9126 (ppp) cc_final: 0.8578 (ppp) REVERT: D 864 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8338 (pm20) REVERT: D 893 MET cc_start: 0.6398 (ttt) cc_final: 0.6110 (ttm) REVERT: D 894 LEU cc_start: 0.8534 (tt) cc_final: 0.8184 (tt) REVERT: D 922 MET cc_start: 0.9181 (mpp) cc_final: 0.8803 (mtt) REVERT: D 939 MET cc_start: 0.2188 (tpp) cc_final: 0.1870 (tpp) REVERT: D 1002 LEU cc_start: 0.9316 (mt) cc_final: 0.9005 (mt) REVERT: D 1237 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7543 (tm-30) REVERT: D 1371 GLU cc_start: 0.8773 (pm20) cc_final: 0.8383 (pm20) REVERT: D 1681 MET cc_start: 0.8531 (tmm) cc_final: 0.8210 (tpp) REVERT: D 1689 MET cc_start: 0.7660 (mpp) cc_final: 0.7297 (mpp) REVERT: F 191 GLU cc_start: 0.8890 (tt0) cc_final: 0.8191 (mp0) REVERT: F 309 MET cc_start: 0.8926 (mmm) cc_final: 0.8499 (mmm) REVERT: G 17 ASP cc_start: 0.9121 (m-30) cc_final: 0.8698 (m-30) REVERT: G 156 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.9012 (mm) REVERT: G 180 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8573 (mp0) REVERT: G 270 ASP cc_start: 0.6585 (p0) cc_final: 0.6143 (p0) REVERT: G 288 MET cc_start: 0.9352 (ttp) cc_final: 0.9142 (ttt) REVERT: G 308 ASP cc_start: 0.8880 (t0) cc_final: 0.8671 (t0) REVERT: G 424 MET cc_start: 0.8553 (tmm) cc_final: 0.7900 (ptp) REVERT: G 484 THR cc_start: 0.9079 (OUTLIER) cc_final: 0.8795 (p) REVERT: G 620 MET cc_start: 0.8088 (mtp) cc_final: 0.7596 (ttp) REVERT: G 682 HIS cc_start: 0.6834 (p90) cc_final: 0.6323 (p90) REVERT: G 744 MET cc_start: 0.0915 (ttt) cc_final: 0.0367 (mmp) REVERT: G 818 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7685 (t80) REVERT: G 1040 LYS cc_start: 0.7904 (pptt) cc_final: 0.7417 (mmtm) REVERT: G 1209 MET cc_start: 0.5693 (ppp) cc_final: 0.5395 (ppp) REVERT: G 1215 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8613 (mp) REVERT: G 1528 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8226 (tm-30) REVERT: G 1617 GLU cc_start: 0.9335 (tp30) cc_final: 0.8923 (tp30) REVERT: G 1658 ARG cc_start: 0.7152 (mmm160) cc_final: 0.6539 (ptm160) REVERT: G 1665 HIS cc_start: 0.8467 (m-70) cc_final: 0.8004 (t70) REVERT: G 1689 MET cc_start: 0.2304 (mmt) cc_final: 0.1414 (mmt) REVERT: G 1696 TYR cc_start: 0.7281 (m-80) cc_final: 0.6929 (m-10) REVERT: G 1707 LEU cc_start: 0.9411 (tt) cc_final: 0.9071 (pp) REVERT: I 223 ARG cc_start: 0.8540 (ttt90) cc_final: 0.8118 (tpt-90) REVERT: I 226 TYR cc_start: 0.8598 (t80) cc_final: 0.8222 (t80) REVERT: I 258 MET cc_start: 0.8689 (mmm) cc_final: 0.8275 (mmm) REVERT: I 263 ILE cc_start: 0.6904 (OUTLIER) cc_final: 0.6633 (mm) outliers start: 86 outliers final: 59 residues processed: 449 average time/residue: 0.2385 time to fit residues: 184.6820 Evaluate side-chains 440 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 371 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 758 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 1422 ASN Chi-restraints excluded: chain A residue 1423 THR 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 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 354 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 596 VAL Chi-restraints excluded: chain D residue 849 MET Chi-restraints excluded: chain D residue 864 GLN Chi-restraints excluded: chain D residue 918 TYR Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 992 LEU 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 66 THR Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 156 LEU 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 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 809 ASP Chi-restraints excluded: chain G residue 818 PHE Chi-restraints excluded: chain G residue 933 VAL Chi-restraints excluded: chain G residue 1003 LEU Chi-restraints excluded: chain G residue 1215 LEU Chi-restraints excluded: chain G residue 1282 ILE Chi-restraints excluded: chain G residue 1390 LEU Chi-restraints excluded: chain G residue 1430 LEU Chi-restraints excluded: chain G residue 1443 THR Chi-restraints excluded: chain G residue 1454 LEU Chi-restraints excluded: chain G residue 1474 ILE Chi-restraints excluded: chain G residue 1522 HIS Chi-restraints excluded: chain G residue 1532 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 263 ILE Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 190 optimal weight: 4.9990 chunk 423 optimal weight: 20.0000 chunk 292 optimal weight: 7.9990 chunk 413 optimal weight: 7.9990 chunk 404 optimal weight: 7.9990 chunk 96 optimal weight: 30.0000 chunk 158 optimal weight: 2.9990 chunk 489 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 497 optimal weight: 6.9990 chunk 234 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 ASN A 747 ASN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 679 HIS ** D 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1306 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 323 HIS G 428 ASN ** G 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1363 ASN G1519 HIS G1656 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.076213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.056282 restraints weight = 232836.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.057745 restraints weight = 126995.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.058827 restraints weight = 84806.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.059502 restraints weight = 64193.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.059899 restraints weight = 53172.632| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 43395 Z= 0.214 Angle : 0.709 16.389 58957 Z= 0.356 Chirality : 0.043 0.282 6663 Planarity : 0.004 0.052 7333 Dihedral : 6.069 98.373 6226 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.18 % Favored : 95.80 % Rotamer: Outliers : 1.71 % Allowed : 17.50 % Favored : 80.79 % 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 are not related in a simple way. whole: 0.39 (0.12), residues: 5049 helix: 0.96 (0.11), residues: 2449 sheet: -0.07 (0.24), residues: 483 loop : -0.37 (0.14), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG D1330 TYR 0.025 0.002 TYR G 519 PHE 0.031 0.002 PHE G1393 TRP 0.017 0.002 TRP A 97 HIS 0.009 0.001 HIS D1522 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (43395) covalent geometry : angle 0.70936 / 0.36 (58957) hydrogen bonds : bond 0.03990 / 2.68 ( 2059) hydrogen bonds : angle 4.71732 / 3.38 ( 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 441 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 363 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8571 (mmm) cc_final: 0.8286 (tpt) REVERT: A 372 MET cc_start: 0.7461 (ttt) cc_final: 0.7123 (ttm) REVERT: A 424 MET cc_start: 0.7930 (ppp) cc_final: 0.6886 (ppp) REVERT: A 534 ASP cc_start: 0.8515 (p0) cc_final: 0.8081 (p0) REVERT: A 747 ASN cc_start: 0.8999 (m-40) cc_final: 0.8701 (t0) REVERT: A 939 MET cc_start: 0.6564 (OUTLIER) cc_final: 0.6226 (tpp) REVERT: A 1602 MET cc_start: 0.8784 (mmt) cc_final: 0.8295 (mmm) REVERT: A 1681 MET cc_start: 0.8561 (tmm) cc_final: 0.7755 (tmm) REVERT: C 230 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8341 (t80) REVERT: C 267 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8766 (tp) REVERT: C 285 CYS cc_start: 0.8651 (m) cc_final: 0.8141 (p) REVERT: C 304 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8538 (p0) REVERT: D 208 MET cc_start: 0.8883 (mmm) cc_final: 0.8553 (mmm) REVERT: D 250 ASP cc_start: 0.9154 (m-30) cc_final: 0.8742 (m-30) REVERT: D 360 MET cc_start: 0.8498 (tmm) cc_final: 0.8176 (tpp) REVERT: D 589 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.6826 (t80) REVERT: D 922 MET cc_start: 0.9220 (mpp) cc_final: 0.8837 (mtt) REVERT: D 939 MET cc_start: 0.3816 (tpp) cc_final: 0.3301 (tpp) REVERT: D 967 MET cc_start: 0.6321 (tmm) cc_final: 0.5522 (mmt) REVERT: D 1237 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7567 (tm-30) REVERT: D 1689 MET cc_start: 0.7759 (mpp) cc_final: 0.7332 (mpp) REVERT: G 17 ASP cc_start: 0.9193 (m-30) cc_final: 0.8823 (m-30) REVERT: G 156 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9063 (mm) REVERT: G 180 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8611 (mp0) REVERT: G 270 ASP cc_start: 0.6825 (p0) cc_final: 0.6329 (p0) REVERT: G 288 MET cc_start: 0.9392 (ttp) cc_final: 0.9157 (ttt) REVERT: G 424 MET cc_start: 0.8516 (tmm) cc_final: 0.7892 (ptp) REVERT: G 484 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8905 (p) REVERT: G 620 MET cc_start: 0.8106 (mtp) cc_final: 0.7825 (ttp) REVERT: G 682 HIS cc_start: 0.6720 (p90) cc_final: 0.6114 (p90) REVERT: G 744 MET cc_start: 0.1383 (ttt) cc_final: 0.0800 (mmp) REVERT: G 818 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7694 (t80) REVERT: G 1040 LYS cc_start: 0.7868 (pptt) cc_final: 0.7380 (mptt) REVERT: G 1209 MET cc_start: 0.5949 (ppp) cc_final: 0.5690 (ppp) REVERT: G 1617 GLU cc_start: 0.9389 (tp30) cc_final: 0.8921 (tp30) REVERT: G 1658 ARG cc_start: 0.7262 (mmm160) cc_final: 0.6646 (ptm160) REVERT: G 1665 HIS cc_start: 0.8416 (m-70) cc_final: 0.8061 (t70) REVERT: G 1689 MET cc_start: 0.2842 (mmt) cc_final: 0.2164 (mmt) REVERT: G 1696 TYR cc_start: 0.7291 (m-80) cc_final: 0.7006 (m-10) REVERT: G 1707 LEU cc_start: 0.9493 (tt) cc_final: 0.9101 (pp) REVERT: I 258 MET cc_start: 0.8889 (mmm) cc_final: 0.8276 (mmm) REVERT: I 263 ILE cc_start: 0.7292 (OUTLIER) cc_final: 0.6887 (mm) REVERT: I 309 MET cc_start: 0.8737 (mmm) cc_final: 0.8435 (mmm) outliers start: 78 outliers final: 61 residues processed: 415 average time/residue: 0.2347 time to fit residues: 168.9814 Evaluate side-chains 412 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 342 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 758 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 999 MET Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1422 ASN Chi-restraints excluded: chain A residue 1423 THR 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 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 354 ASN Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain D residue 400 CYS Chi-restraints excluded: chain D residue 424 MET Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 589 PHE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 849 MET Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 992 LEU 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 66 THR Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 156 LEU 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 809 ASP Chi-restraints excluded: chain G residue 818 PHE Chi-restraints excluded: chain G residue 933 VAL Chi-restraints excluded: chain G residue 1003 LEU Chi-restraints excluded: chain G residue 1183 LYS Chi-restraints excluded: chain G residue 1282 ILE Chi-restraints excluded: chain G residue 1430 LEU Chi-restraints excluded: chain G residue 1443 THR Chi-restraints excluded: chain G residue 1454 LEU Chi-restraints excluded: chain G residue 1521 LEU Chi-restraints excluded: chain G residue 1532 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 I residue 233 THR Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 311 ILE 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: 0.9980 chunk 491 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 480 optimal weight: 3.9990 chunk 203 optimal weight: 0.0060 chunk 507 optimal weight: 10.0000 chunk 454 optimal weight: 0.3980 chunk 17 optimal weight: 5.9990 chunk 400 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 ASN A 429 ASN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1191 GLN ** 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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 428 ASN ** G 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1363 ASN ** 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 = 0.3762 r_free = 0.3762 target = 0.076324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.056358 restraints weight = 232738.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.057844 restraints weight = 127253.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.058880 restraints weight = 85349.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.059496 restraints weight = 64342.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.059969 restraints weight = 53426.684| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.148 43395 Z= 0.217 Angle : 0.775 59.117 58957 Z= 0.408 Chirality : 0.042 0.433 6663 Planarity : 0.004 0.071 7333 Dihedral : 6.074 98.412 6226 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.24 % Favored : 95.72 % Rotamer: Outliers : 1.66 % Allowed : 17.68 % Favored : 80.66 % 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 are not related in a simple way. whole: 0.39 (0.12), residues: 5049 helix: 0.95 (0.11), residues: 2447 sheet: -0.09 (0.24), residues: 483 loop : -0.37 (0.14), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D1330 TYR 0.024 0.002 TYR G 519 PHE 0.030 0.002 PHE G1393 TRP 0.020 0.002 TRP A 442 HIS 0.008 0.001 HIS D1522 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (43395) covalent geometry : angle 0.77499 / 0.41 (58957) hydrogen bonds : bond 0.03976 / 2.67 ( 2059) hydrogen bonds : angle 4.71293 / 3.37 ( 5864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10119.88 seconds wall clock time: 175 minutes 19.30 seconds (10519.30 seconds total)