Starting phenix.real_space_refine on Tue Sep 15 18:26:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hf1_34708/09_2026/8hf1_34708.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hf1_34708/09_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_34708/09_2026/8hf1_34708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hf1_34708/09_2026/8hf1_34708.map" model { file = "/net/cci-nas-00/data/ceres_data/8hf1_34708/09_2026/8hf1_34708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hf1_34708/09_2026/8hf1_34708.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hf1_34708/09_2026/8hf1_34708.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hf1_34708/09_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 11} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 8} Link IDs: {'rna3p': 10} Time building chain proxies: 8.01, per 1000 atoms: 0.19 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: 3.77 Conformation dependent library (CDL) restraints added in 1.7 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: 5.15 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: 12.17 Time building geometry restraints manager: 4.95 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: 58589 3.14 - 6.27: 355 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 - 17.87: 23573 17.87 - 35.74: 2178 35.74 - 53.61: 328 53.61 - 71.49: 82 71.49 - 89.36: 49 Dihedral angle restraints: 26210 sinusoidal: 11234 harmonic: 14976 Sorted by residual: dihedral pdb=" O5' C M 43 " pdb=" C5' C M 43 " pdb=" C4' C M 43 " pdb=" C3' C M 43 " ideal model delta sinusoidal sigma weight residual 60.00 116.49 -56.49 3 6.40e+00 2.44e-02 5.16e+01 dihedral pdb=" O5' G J 1 " pdb=" C5' G J 1 " pdb=" C4' G J 1 " pdb=" C3' G J 1 " ideal model delta sinusoidal sigma weight residual 60.00 9.80 50.20 3 6.40e+00 2.44e-02 4.87e+01 dihedral pdb=" O5' G E 9 " pdb=" C5' G E 9 " pdb=" C4' G E 9 " pdb=" C3' G E 9 " ideal model delta sinusoidal sigma weight residual 60.00 109.99 -49.99 3 6.40e+00 2.44e-02 4.86e+01 ... (remaining 26207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 5583 0.054 - 0.108: 877 0.108 - 0.161: 136 0.161 - 0.215: 12 0.215 - 0.269: 55 Chirality restraints: 6663 Sorted by residual: chirality pdb=" P C K 43 " pdb=" OP1 C K 43 " pdb=" OP2 C K 43 " pdb=" O5' C K 43 " both_signs ideal model delta sigma weight residual True 2.17 -2.44 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" P A J 2 " pdb=" OP1 A J 2 " pdb=" OP2 A J 2 " pdb=" O5' A J 2 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" P C K 50 " pdb=" OP1 C K 50 " pdb=" OP2 C K 50 " pdb=" O5' C K 50 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (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: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.130 Process input model: 43.890 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.140 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.770 ------------------------------------------------------------------------------- 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 : 0.651 15.686 58957 Z= 0.359 Chirality : 0.046 0.269 6663 Planarity : 0.004 0.079 7333 Dihedral : 14.184 89.356 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 0.00382 / 0.19 (43395) covalent geometry : angle 0.65061 / 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 : 1.501 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: 0.2395 time to fit residues: 219.8672 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 : 1.651 ------------------------------------------------------------------------------- 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: 8.9990 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 = 0.082359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.062344 restraints weight = 225943.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.063824 restraints weight = 125578.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.064896 restraints weight = 83665.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.065620 restraints weight = 62798.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.066104 restraints weight = 51254.011| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 43395 Z= 0.145 Angle : 0.680 9.032 58957 Z= 0.345 Chirality : 0.046 0.264 6663 Planarity : 0.004 0.042 7333 Dihedral : 7.087 74.069 6230 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.45 % Favored : 96.53 % Rotamer: Outliers : 0.81 % Allowed : 6.89 % Favored : 92.30 % 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: 0.67 (0.10), residues: 2464 sheet: -0.22 (0.22), residues: 524 loop : -0.49 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1518 TYR 0.045 0.002 TYR G 519 PHE 0.043 0.002 PHE G1194 TRP 0.017 0.002 TRP G 986 HIS 0.009 0.001 HIS G 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (43395) covalent geometry : angle 0.68040 / 0.34 (58957) hydrogen bonds : bond 0.04908 / 3.30 ( 2059) hydrogen bonds : angle 5.20382 / 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 : 1.707 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: 0.9113 (tmm) cc_final: 0.8842 (tmm) REVERT: A 209 GLU cc_start: 0.9453 (pt0) cc_final: 0.9198 (pp20) REVERT: A 424 MET cc_start: 0.7693 (ppp) cc_final: 0.7157 (ppp) REVERT: A 601 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7541 (mt-10) REVERT: A 604 ARG cc_start: 0.8557 (tmm-80) cc_final: 0.8267 (ptt-90) REVERT: A 939 MET cc_start: 0.5871 (OUTLIER) cc_final: 0.5145 (tpp) REVERT: A 1261 ASP cc_start: 0.8169 (t0) cc_final: 0.7773 (t0) REVERT: C 226 TYR cc_start: 0.9475 (t80) cc_final: 0.9238 (t80) REVERT: C 230 PHE cc_start: 0.8717 (t80) cc_final: 0.8175 (t80) REVERT: C 304 ASP cc_start: 0.8981 (OUTLIER) cc_final: 0.8523 (p0) REVERT: D 250 ASP cc_start: 0.8754 (m-30) cc_final: 0.8545 (m-30) REVERT: D 354 ASN cc_start: 0.7471 (t0) cc_final: 0.6800 (m-40) REVERT: D 429 ASN cc_start: 0.8067 (p0) cc_final: 0.7863 (t0) REVERT: D 487 MET cc_start: 0.8381 (tmm) cc_final: 0.8040 (tmm) REVERT: D 744 MET cc_start: 0.9035 (tpt) cc_final: 0.8761 (tpp) REVERT: D 779 VAL cc_start: 0.9207 (t) cc_final: 0.8984 (t) REVERT: D 805 MET cc_start: 0.8887 (ppp) cc_final: 0.8349 (ppp) REVERT: D 907 TYR cc_start: 0.8310 (m-80) cc_final: 0.7933 (m-80) REVERT: D 918 TYR cc_start: 0.7608 (m-10) cc_final: 0.7182 (m-80) REVERT: D 922 MET cc_start: 0.9104 (mpp) cc_final: 0.8893 (mmt) REVERT: D 935 LYS cc_start: 0.7643 (mmmt) cc_final: 0.7167 (mmmt) REVERT: D 939 MET cc_start: 0.3017 (tpp) cc_final: 0.2597 (tpp) REVERT: D 985 LEU cc_start: 0.9413 (tp) cc_final: 0.9162 (tp) REVERT: D 1193 GLU cc_start: 0.9037 (tp30) cc_final: 0.8486 (tp30) REVERT: D 1237 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7697 (tm-30) REVERT: D 1269 ILE cc_start: 0.9179 (mm) cc_final: 0.8975 (pt) REVERT: D 1389 MET cc_start: 0.8934 (mmm) cc_final: 0.8516 (mmm) REVERT: D 1689 MET cc_start: 0.8153 (mpp) cc_final: 0.7626 (mpp) REVERT: F 191 GLU cc_start: 0.8977 (tt0) cc_final: 0.8438 (mp0) REVERT: F 311 ILE cc_start: 0.7825 (mm) cc_final: 0.7466 (mt) REVERT: G 17 ASP cc_start: 0.9084 (m-30) cc_final: 0.8707 (p0) REVERT: G 75 MET cc_start: 0.8680 (mmm) cc_final: 0.8475 (mmm) REVERT: G 157 PHE cc_start: 0.7528 (m-80) cc_final: 0.7298 (m-10) REVERT: G 288 MET cc_start: 0.9207 (tmm) cc_final: 0.8804 (tmm) REVERT: G 322 MET cc_start: 0.9032 (tmm) cc_final: 0.8720 (tmm) REVERT: G 424 MET cc_start: 0.8386 (tmm) cc_final: 0.8088 (ptp) REVERT: G 458 MET cc_start: 0.8158 (tpp) cc_final: 0.7904 (tpp) REVERT: G 616 ILE cc_start: 0.7452 (mt) cc_final: 0.7032 (mt) REVERT: G 744 MET cc_start: -0.0098 (ttt) cc_final: -0.0704 (mmp) REVERT: G 893 MET cc_start: 0.0237 (mpp) cc_final: -0.0238 (mpp) REVERT: G 1379 LYS cc_start: 0.6905 (tptt) cc_final: 0.6627 (tppt) REVERT: G 1388 LYS cc_start: 0.6486 (tttt) cc_final: 0.6237 (tmtt) REVERT: G 1617 GLU cc_start: 0.9449 (tp30) cc_final: 0.8823 (tp30) REVERT: G 1650 ARG cc_start: 0.7689 (ptm-80) cc_final: 0.7229 (ptm-80) REVERT: G 1707 LEU cc_start: 0.9285 (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: 0.8773 (t80) cc_final: 0.8468 (t80) REVERT: I 252 ASP cc_start: 0.8057 (m-30) cc_final: 0.7849 (m-30) REVERT: I 304 ASP cc_start: 0.9286 (p0) cc_final: 0.9008 (p0) outliers start: 37 outliers final: 20 residues processed: 505 average time/residue: 0.2452 time to fit residues: 213.1315 Evaluate side-chains 408 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 386 time to evaluate : 1.653 ------------------------------------------------------------------------------- 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: 7.9990 chunk 157 optimal weight: 8.9990 chunk 291 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 500 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 HIS A 339 GLN A 517 GLN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS D 142 HIS D 323 HIS D 454 ASN D 569 ASN D 791 GLN ** D1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1286 HIS ** D1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 HIS G 72 GLN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 354 ASN G 749 GLN 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.077461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.057541 restraints weight = 234193.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.058810 restraints weight = 128235.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.059822 restraints weight = 85964.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.060441 restraints weight = 65100.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.060906 restraints weight = 53977.831| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 43395 Z= 0.258 Angle : 0.763 12.011 58957 Z= 0.384 Chirality : 0.047 0.373 6663 Planarity : 0.006 0.181 7333 Dihedral : 7.090 62.335 6226 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.56 % Favored : 95.42 % Rotamer: Outliers : 1.84 % Allowed : 11.35 % Favored : 86.81 % 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: -0.13 (0.12), residues: 5049 helix: 0.52 (0.10), residues: 2466 sheet: -0.37 (0.22), residues: 533 loop : -0.61 (0.14), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.044 0.001 ARG C 198 TYR 0.046 0.002 TYR I 231 PHE 0.034 0.002 PHE G1194 TRP 0.028 0.002 TRP G 102 HIS 0.012 0.002 HIS D 743 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.26 (43395) covalent geometry : angle 0.76344 / 0.38 (58957) hydrogen bonds : bond 0.04930 / 3.31 ( 2059) hydrogen bonds : angle 5.22378 / 3.77 ( 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: 84 poor density : 395 time to evaluate : 2.030 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: 0.9250 (tmm) cc_final: 0.8919 (tmm) REVERT: A 322 MET cc_start: 0.9187 (tmm) cc_final: 0.8963 (tmm) REVERT: A 424 MET cc_start: 0.7853 (ppp) cc_final: 0.7048 (ppp) REVERT: A 635 MET cc_start: 0.8046 (mmm) cc_final: 0.7573 (mmm) REVERT: A 891 LYS cc_start: 0.8977 (tttt) cc_final: 0.8573 (tmtt) REVERT: A 1240 LEU cc_start: 0.8856 (mt) cc_final: 0.8591 (mt) REVERT: A 1261 ASP cc_start: 0.8345 (t0) cc_final: 0.8062 (t70) REVERT: A 1333 GLU cc_start: 0.7576 (tt0) cc_final: 0.7278 (tt0) REVERT: C 218 MET cc_start: 0.7468 (mtm) cc_final: 0.7068 (ptm) REVERT: C 230 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8335 (t80) REVERT: C 304 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8535 (p0) REVERT: D 208 MET cc_start: 0.9068 (tpp) cc_final: 0.8645 (mmm) REVERT: D 360 MET cc_start: 0.8540 (tmm) cc_final: 0.8111 (tpp) REVERT: D 458 MET cc_start: 0.9240 (tpp) cc_final: 0.8742 (tpp) REVERT: D 527 ASP cc_start: 0.8765 (m-30) cc_final: 0.8536 (m-30) REVERT: D 907 TYR cc_start: 0.8577 (m-80) cc_final: 0.8204 (m-80) REVERT: D 918 TYR cc_start: 0.7869 (m-10) cc_final: 0.7453 (m-80) REVERT: D 922 MET cc_start: 0.9170 (mpp) cc_final: 0.8876 (mmt) REVERT: D 935 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7665 (mmmt) REVERT: D 1002 LEU cc_start: 0.9232 (mt) cc_final: 0.9019 (mt) REVERT: D 1368 ASP cc_start: 0.8941 (m-30) cc_final: 0.8679 (m-30) REVERT: D 1389 MET cc_start: 0.9099 (mmm) cc_final: 0.8834 (mmm) REVERT: D 1681 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7997 (tpp) REVERT: D 1689 MET cc_start: 0.8431 (mpp) cc_final: 0.7798 (mpp) REVERT: G 13 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9184 (mm) REVERT: G 17 ASP cc_start: 0.9160 (m-30) cc_final: 0.8731 (m-30) REVERT: G 66 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.7704 (t) REVERT: G 75 MET cc_start: 0.8773 (mmm) cc_final: 0.8562 (mmm) REVERT: G 208 MET cc_start: 0.7804 (mmp) cc_final: 0.7136 (mmp) REVERT: G 252 MET cc_start: 0.9055 (tpp) cc_final: 0.8828 (mmm) REVERT: G 273 LYS cc_start: 0.8480 (mttp) cc_final: 0.8001 (mmmt) REVERT: G 288 MET cc_start: 0.9311 (tmm) cc_final: 0.8953 (tmm) REVERT: G 744 MET cc_start: 0.0793 (ttt) cc_final: 0.0170 (mmp) REVERT: G 893 MET cc_start: 0.0624 (mpp) cc_final: 0.0164 (mpp) REVERT: G 1040 LYS cc_start: 0.8180 (pptt) cc_final: 0.7966 (mptt) REVERT: G 1209 MET cc_start: 0.6493 (ppp) cc_final: 0.5875 (ptp) REVERT: G 1379 LYS cc_start: 0.6908 (tptt) cc_final: 0.6608 (tppt) REVERT: G 1388 LYS cc_start: 0.6921 (tttt) cc_final: 0.6686 (tttt) REVERT: G 1617 GLU cc_start: 0.9396 (tp30) cc_final: 0.8892 (tp30) REVERT: G 1658 ARG cc_start: 0.7141 (mmm160) cc_final: 0.6357 (ptm160) REVERT: G 1665 HIS cc_start: 0.8478 (m-70) cc_final: 0.8028 (t70) REVERT: G 1689 MET cc_start: 0.2095 (mmt) cc_final: 0.1522 (mmt) REVERT: G 1707 LEU cc_start: 0.9389 (tt) cc_final: 0.9095 (pp) REVERT: I 204 TYR cc_start: 0.8220 (m-80) cc_final: 0.7646 (m-80) outliers start: 84 outliers final: 47 residues processed: 445 average time/residue: 0.2448 time to fit residues: 188.0864 Evaluate side-chains 401 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 349 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASN 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 895 VAL Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1620 ILE Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain 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 482 VAL Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 1225 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 66 THR Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 479 LEU Chi-restraints excluded: chain G residue 625 MET Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 758 LEU Chi-restraints excluded: chain G residue 922 MET Chi-restraints excluded: chain G residue 933 VAL Chi-restraints excluded: chain G residue 1282 ILE Chi-restraints excluded: chain G residue 1443 THR Chi-restraints excluded: chain G residue 1474 ILE Chi-restraints excluded: chain G residue 1481 PHE Chi-restraints excluded: chain G residue 1500 THR Chi-restraints excluded: chain G residue 1502 LEU Chi-restraints excluded: chain G residue 1521 LEU Chi-restraints excluded: chain G residue 1600 PHE Chi-restraints excluded: chain G residue 1636 VAL Chi-restraints excluded: chain G residue 1639 ASN Chi-restraints excluded: chain G residue 1654 ILE Chi-restraints excluded: chain I residue 202 THR 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: 3.9990 chunk 507 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 168 optimal weight: 0.0970 chunk 83 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 262 optimal weight: 0.0270 chunk 426 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 217 optimal weight: 0.9990 overall best weight: 1.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 ASN A 550 HIS A1406 GLN ** D 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 948 GLN D 955 ASN ** D1191 GLN ** 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 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.079233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.059014 restraints weight = 227584.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.060569 restraints weight = 124854.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.061558 restraints weight = 83135.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.062230 restraints weight = 63175.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.062656 restraints weight = 52318.474| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 43395 Z= 0.132 Angle : 0.632 11.669 58957 Z= 0.317 Chirality : 0.044 0.259 6663 Planarity : 0.004 0.046 7333 Dihedral : 6.775 61.414 6226 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.33 % Favored : 96.65 % Rotamer: Outliers : 1.73 % Allowed : 13.63 % Favored : 84.64 % 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: 0.17 (0.12), residues: 5049 helix: 0.77 (0.10), residues: 2464 sheet: -0.14 (0.23), residues: 506 loop : -0.51 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G1009 TYR 0.049 0.002 TYR A1343 PHE 0.031 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 0.00292 / 0.13 (43395) covalent geometry : angle 0.63243 / 0.32 (58957) hydrogen bonds : bond 0.04088 / 2.74 ( 2059) hydrogen bonds : angle 4.82778 / 3.47 ( 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 483 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 404 time to evaluate : 1.577 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 75 MET cc_start: 0.8500 (tpt) cc_final: 0.7034 (tpt) REVERT: A 122 MET cc_start: 0.9284 (tmm) cc_final: 0.8931 (tmm) REVERT: A 344 MET cc_start: 0.3832 (ttt) cc_final: 0.3172 (tmm) REVERT: A 360 MET cc_start: 0.8941 (mmm) cc_final: 0.8689 (mmm) REVERT: A 424 MET cc_start: 0.7965 (ppp) cc_final: 0.7094 (ppp) REVERT: A 635 MET cc_start: 0.8003 (mmm) cc_final: 0.7642 (mmm) REVERT: A 747 ASN cc_start: 0.9092 (m110) cc_final: 0.8683 (t0) REVERT: A 891 LYS cc_start: 0.8948 (tttt) cc_final: 0.8679 (tttp) REVERT: A 1261 ASP cc_start: 0.8402 (t0) cc_final: 0.8101 (t70) REVERT: A 1333 GLU cc_start: 0.7792 (tt0) cc_final: 0.7391 (tt0) REVERT: A 1602 MET cc_start: 0.8668 (mmm) cc_final: 0.8350 (mmm) REVERT: C 230 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8268 (t80) REVERT: C 304 ASP cc_start: 0.8948 (OUTLIER) cc_final: 0.8526 (p0) REVERT: D 75 MET cc_start: 0.9118 (ttt) cc_final: 0.8597 (tmm) REVERT: D 122 MET cc_start: 0.9281 (tmm) cc_final: 0.9071 (tmm) REVERT: D 208 MET cc_start: 0.9003 (tpp) cc_final: 0.8499 (mmm) REVERT: D 250 ASP cc_start: 0.8931 (m-30) cc_final: 0.8669 (m-30) REVERT: D 360 MET cc_start: 0.8488 (tmm) cc_final: 0.8063 (tpp) REVERT: D 458 MET cc_start: 0.9190 (tpp) cc_final: 0.8853 (tpp) REVERT: D 527 ASP cc_start: 0.8753 (m-30) cc_final: 0.8519 (m-30) REVERT: D 805 MET cc_start: 0.9212 (ppp) cc_final: 0.8719 (ppp) REVERT: D 893 MET cc_start: 0.6957 (ttt) cc_final: 0.6711 (ttm) REVERT: D 907 TYR cc_start: 0.8529 (m-80) cc_final: 0.8146 (m-80) REVERT: D 922 MET cc_start: 0.9167 (mpp) cc_final: 0.8788 (mtt) REVERT: D 939 MET cc_start: 0.3542 (tpp) cc_final: 0.3113 (tpp) REVERT: D 989 LEU cc_start: 0.9595 (mp) cc_final: 0.9356 (mm) REVERT: D 1002 LEU cc_start: 0.9186 (mt) cc_final: 0.8969 (mt) REVERT: D 1237 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7591 (tm-30) REVERT: D 1389 MET cc_start: 0.9057 (mmm) cc_final: 0.8766 (mmm) REVERT: D 1523 PHE cc_start: 0.8287 (p90) cc_final: 0.6583 (p90) REVERT: D 1681 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7947 (tpp) REVERT: D 1689 MET cc_start: 0.8345 (mpp) cc_final: 0.7814 (mpp) REVERT: G 17 ASP cc_start: 0.9117 (m-30) cc_final: 0.8684 (m-30) REVERT: G 75 MET cc_start: 0.8688 (mmm) cc_final: 0.8477 (mmm) REVERT: G 252 MET cc_start: 0.9049 (tpp) cc_final: 0.8830 (mmm) REVERT: G 273 LYS cc_start: 0.8303 (mttp) cc_final: 0.7933 (mmmt) REVERT: G 288 MET cc_start: 0.9253 (tmm) cc_final: 0.8859 (tmm) REVERT: G 312 ARG cc_start: 0.9243 (mtm110) cc_final: 0.8801 (mtm110) REVERT: G 744 MET cc_start: 0.0609 (ttt) cc_final: 0.0102 (mmp) REVERT: G 893 MET cc_start: 0.0187 (mpp) cc_final: -0.0198 (mpp) REVERT: G 979 PHE cc_start: 0.4793 (OUTLIER) cc_final: 0.4587 (m-80) REVERT: G 1040 LYS cc_start: 0.7958 (pptt) cc_final: 0.7672 (mptt) REVERT: G 1209 MET cc_start: 0.6204 (ppp) cc_final: 0.5554 (ptp) REVERT: G 1379 LYS cc_start: 0.6842 (tptt) cc_final: 0.6584 (tppt) REVERT: G 1388 LYS cc_start: 0.6799 (tttt) cc_final: 0.6378 (tmtt) REVERT: G 1389 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6845 (ttm) REVERT: G 1447 ARG cc_start: 0.7557 (mmt180) cc_final: 0.7287 (mmt-90) REVERT: G 1480 ASP cc_start: 0.9117 (t0) cc_final: 0.8886 (t0) REVERT: G 1617 GLU cc_start: 0.9418 (tp30) cc_final: 0.8892 (tp30) REVERT: G 1658 ARG cc_start: 0.7171 (mmm160) cc_final: 0.6365 (ptm160) REVERT: G 1665 HIS cc_start: 0.8467 (m-70) cc_final: 0.7993 (t70) REVERT: G 1689 MET cc_start: 0.2363 (mmt) cc_final: 0.1723 (mmt) REVERT: G 1707 LEU cc_start: 0.9352 (tt) cc_final: 0.9094 (pp) REVERT: I 204 TYR cc_start: 0.7988 (m-80) cc_final: 0.7577 (m-80) REVERT: I 283 LEU cc_start: 0.9156 (mp) cc_final: 0.8569 (tt) outliers start: 79 outliers final: 42 residues processed: 461 average time/residue: 0.2388 time to fit residues: 190.6381 Evaluate side-chains 405 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 358 time to evaluate : 1.663 ------------------------------------------------------------------------------- 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 404 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1427 ASP 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 207 LEU Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 400 CYS Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 1669 VAL Chi-restraints excluded: chain D residue 1681 MET 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 457 LEU Chi-restraints excluded: chain G residue 625 MET Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 713 PHE Chi-restraints excluded: chain G residue 922 MET Chi-restraints excluded: chain G residue 979 PHE Chi-restraints excluded: chain G residue 1282 ILE Chi-restraints excluded: chain G residue 1389 MET Chi-restraints excluded: chain G residue 1430 LEU Chi-restraints excluded: chain G residue 1474 ILE Chi-restraints excluded: chain G residue 1500 THR Chi-restraints excluded: chain G residue 1502 LEU Chi-restraints excluded: chain G residue 1522 HIS 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 279 LEU Chi-restraints excluded: chain I residue 290 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 470 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 225 optimal weight: 0.7980 chunk 154 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 416 optimal weight: 8.9990 chunk 310 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 361 optimal weight: 9.9990 chunk 453 optimal weight: 5.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 ASN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** D1522 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** G 955 ASN ** G1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1495 ASN ** 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 = 0.3741 r_free = 0.3741 target = 0.075478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.055523 restraints weight = 236176.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.056909 restraints weight = 129724.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.057889 restraints weight = 86927.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.058539 restraints weight = 66021.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.058990 restraints weight = 54774.638| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 43395 Z= 0.270 Angle : 0.742 10.176 58957 Z= 0.373 Chirality : 0.046 0.337 6663 Planarity : 0.005 0.049 7333 Dihedral : 6.964 60.777 6226 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.54 % Favored : 95.44 % Rotamer: Outliers : 2.49 % Allowed : 15.23 % Favored : 82.28 % 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: -0.01 (0.12), residues: 5049 helix: 0.68 (0.10), residues: 2438 sheet: -0.41 (0.23), residues: 495 loop : -0.61 (0.14), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 99 TYR 0.035 0.002 TYR G 519 PHE 0.045 0.002 PHE G 818 TRP 0.016 0.002 TRP G 986 HIS 0.009 0.002 HIS D1522 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.27 (43395) covalent geometry : angle 0.74185 / 0.37 (58957) hydrogen bonds : bond 0.04540 / 3.04 ( 2059) hydrogen bonds : angle 5.06368 / 3.65 ( 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 478 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 364 time to evaluate : 1.603 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: 0.9307 (tmm) cc_final: 0.8958 (tmm) REVERT: A 360 MET cc_start: 0.9016 (mmm) cc_final: 0.8757 (mmm) REVERT: A 424 MET cc_start: 0.7947 (ppp) cc_final: 0.7029 (ppp) REVERT: A 635 MET cc_start: 0.8053 (mmm) cc_final: 0.7759 (mmm) REVERT: A 891 LYS cc_start: 0.9023 (tttt) cc_final: 0.8742 (tttp) REVERT: A 908 MET cc_start: 0.2060 (mmt) cc_final: 0.1339 (mmm) REVERT: A 939 MET cc_start: 0.6371 (mmm) cc_final: 0.5829 (tpt) REVERT: A 1240 LEU cc_start: 0.8954 (mt) cc_final: 0.8703 (mt) REVERT: A 1343 TYR cc_start: 0.6358 (m-80) cc_final: 0.6083 (m-80) REVERT: C 230 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8474 (t80) REVERT: C 285 CYS cc_start: 0.8515 (m) cc_final: 0.8177 (p) REVERT: C 304 ASP cc_start: 0.8983 (OUTLIER) cc_final: 0.8539 (p0) REVERT: D 208 MET cc_start: 0.9051 (tpp) cc_final: 0.8396 (mmm) REVERT: D 360 MET cc_start: 0.8530 (tmm) cc_final: 0.8131 (tpp) REVERT: D 589 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.6858 (t80) REVERT: D 922 MET cc_start: 0.9254 (mpp) cc_final: 0.8835 (mtt) REVERT: D 971 LEU cc_start: 0.9268 (mt) cc_final: 0.9034 (mt) REVERT: D 1002 LEU cc_start: 0.9318 (mt) cc_final: 0.9078 (mt) REVERT: D 1237 GLU cc_start: 0.8465 (tm-30) cc_final: 0.7813 (tm-30) REVERT: D 1389 MET cc_start: 0.9179 (mmm) cc_final: 0.8949 (mmm) REVERT: D 1681 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7963 (tmm) REVERT: G 17 ASP cc_start: 0.9146 (m-30) cc_final: 0.8819 (m-30) REVERT: G 63 MET cc_start: 0.6641 (tpp) cc_final: 0.6386 (mmm) REVERT: G 75 MET cc_start: 0.8747 (mmm) cc_final: 0.8522 (mmm) REVERT: G 252 MET cc_start: 0.9131 (tpp) cc_final: 0.8925 (mmm) REVERT: G 484 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.8963 (p) REVERT: G 744 MET cc_start: 0.1487 (ttt) cc_final: 0.0907 (mmp) REVERT: G 893 MET cc_start: 0.0284 (mpp) cc_final: 0.0070 (mpp) REVERT: G 1040 LYS cc_start: 0.7986 (pptt) cc_final: 0.7570 (mptt) REVERT: G 1209 MET cc_start: 0.6165 (ppp) cc_final: 0.5627 (ptp) REVERT: G 1388 LYS cc_start: 0.7096 (tttt) cc_final: 0.6782 (tttt) REVERT: G 1389 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7475 (ttm) REVERT: G 1617 GLU cc_start: 0.9421 (tp30) cc_final: 0.8836 (tp30) REVERT: G 1658 ARG cc_start: 0.7157 (mmm160) cc_final: 0.6419 (ptm-80) REVERT: G 1665 HIS cc_start: 0.8465 (m-70) cc_final: 0.8064 (t70) REVERT: G 1689 MET cc_start: 0.2330 (mmt) cc_final: 0.1597 (mmt) REVERT: I 214 ASP cc_start: 0.8714 (t0) cc_final: 0.8505 (t0) REVERT: I 309 MET cc_start: 0.9300 (tpp) cc_final: 0.8779 (tpt) outliers start: 114 outliers final: 71 residues processed: 444 average time/residue: 0.2390 time to fit residues: 185.4416 Evaluate side-chains 415 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 338 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 190 GLU 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 464 LEU Chi-restraints excluded: chain A residue 895 VAL 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 1554 VAL 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 B residue 359 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 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 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 468 ILE Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 589 PHE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 1248 VAL Chi-restraints excluded: chain D residue 1439 ASN Chi-restraints excluded: chain D residue 1451 LEU 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 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 123 VAL 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 479 LEU Chi-restraints excluded: chain G residue 484 THR 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 922 MET Chi-restraints excluded: chain G residue 933 VAL Chi-restraints excluded: chain G residue 1282 ILE Chi-restraints excluded: chain G residue 1389 MET Chi-restraints excluded: chain G residue 1430 LEU Chi-restraints excluded: chain G residue 1443 THR Chi-restraints excluded: chain G residue 1500 THR 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 1695 VAL Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 279 LEU Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 311 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 56 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 446 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 335 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 416 optimal weight: 8.9990 chunk 336 optimal weight: 2.9990 chunk 492 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 72 GLN ** D 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 428 ASN ** G 800 HIS ** 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 = 0.3757 r_free = 0.3757 target = 0.076134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.056358 restraints weight = 232789.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.057720 restraints weight = 126452.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.058734 restraints weight = 83926.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.059347 restraints weight = 63422.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.059845 restraints weight = 52656.559| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 43395 Z= 0.176 Angle : 0.662 12.532 58957 Z= 0.330 Chirality : 0.044 0.305 6663 Planarity : 0.004 0.051 7333 Dihedral : 6.822 61.610 6226 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.78 % Favored : 96.20 % Rotamer: Outliers : 2.23 % Allowed : 16.74 % Favored : 81.03 % 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: 0.15 (0.12), residues: 5049 helix: 0.82 (0.10), residues: 2438 sheet: -0.32 (0.23), residues: 490 loop : -0.55 (0.14), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 99 TYR 0.028 0.002 TYR G 519 PHE 0.040 0.002 PHE G1393 TRP 0.014 0.001 TRP G 986 HIS 0.006 0.001 HIS G 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (43395) covalent geometry : angle 0.66183 / 0.33 (58957) hydrogen bonds : bond 0.04081 / 2.73 ( 2059) hydrogen bonds : angle 4.84119 / 3.48 ( 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 469 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 367 time to evaluate : 1.704 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: A 122 MET cc_start: 0.9371 (tmm) cc_final: 0.9026 (tmm) REVERT: A 222 MET cc_start: 0.7424 (tpt) cc_final: 0.6942 (tmm) REVERT: A 360 MET cc_start: 0.9090 (mmm) cc_final: 0.8864 (mmm) REVERT: A 424 MET cc_start: 0.8012 (ppp) cc_final: 0.7103 (ppp) REVERT: A 635 MET cc_start: 0.7971 (mmm) cc_final: 0.7658 (mmm) REVERT: A 747 ASN cc_start: 0.8957 (m110) cc_final: 0.8569 (t0) REVERT: A 891 LYS cc_start: 0.9092 (tttt) cc_final: 0.8779 (tttp) REVERT: A 908 MET cc_start: 0.2563 (mmt) cc_final: 0.1937 (mmm) REVERT: A 1333 GLU cc_start: 0.7691 (tt0) cc_final: 0.7466 (tt0) REVERT: A 1343 TYR cc_start: 0.6383 (m-80) cc_final: 0.6097 (m-80) REVERT: A 1602 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.7951 (mmm) REVERT: C 190 MET cc_start: 0.8066 (tpp) cc_final: 0.7860 (tpp) REVERT: C 230 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8354 (t80) REVERT: C 285 CYS cc_start: 0.8613 (m) cc_final: 0.8244 (p) REVERT: C 304 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8537 (p0) REVERT: D 208 MET cc_start: 0.8833 (tpp) cc_final: 0.8366 (mmm) REVERT: D 360 MET cc_start: 0.8513 (tmm) cc_final: 0.8120 (tpp) REVERT: D 424 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8678 (ppp) REVERT: D 527 ASP cc_start: 0.8763 (m-30) cc_final: 0.8538 (m-30) REVERT: D 893 MET cc_start: 0.7092 (ttt) cc_final: 0.6682 (ttt) REVERT: D 922 MET cc_start: 0.9218 (mpp) cc_final: 0.8795 (mtt) REVERT: D 939 MET cc_start: 0.4019 (tpp) cc_final: 0.3787 (tpp) REVERT: D 1002 LEU cc_start: 0.9359 (mt) cc_final: 0.9112 (mt) REVERT: D 1237 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7602 (tm-30) REVERT: D 1297 GLU cc_start: 0.8404 (pm20) cc_final: 0.8175 (pm20) REVERT: D 1681 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8098 (tmm) REVERT: F 255 MET cc_start: 0.9320 (mmt) cc_final: 0.9098 (mmp) REVERT: G 17 ASP cc_start: 0.9135 (m-30) cc_final: 0.8711 (m-30) REVERT: G 63 MET cc_start: 0.6901 (tpp) cc_final: 0.6682 (mmm) REVERT: G 75 MET cc_start: 0.8717 (mmm) cc_final: 0.8469 (mmm) REVERT: G 288 MET cc_start: 0.9252 (ttt) cc_final: 0.8733 (tmm) REVERT: G 424 MET cc_start: 0.8427 (tmm) cc_final: 0.7694 (ptp) REVERT: G 744 MET cc_start: 0.1739 (ttt) cc_final: 0.1104 (mmp) REVERT: G 818 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7793 (t80) REVERT: G 1040 LYS cc_start: 0.7975 (pptt) cc_final: 0.7549 (mptt) REVERT: G 1209 MET cc_start: 0.5934 (ppp) cc_final: 0.5579 (ptp) REVERT: G 1388 LYS cc_start: 0.6936 (tttt) cc_final: 0.6619 (tttt) REVERT: G 1389 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7362 (ttm) REVERT: G 1528 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8300 (tm-30) REVERT: G 1617 GLU cc_start: 0.9419 (tp30) cc_final: 0.8924 (tp30) REVERT: G 1658 ARG cc_start: 0.7247 (mmm160) cc_final: 0.6622 (ptm160) REVERT: G 1665 HIS cc_start: 0.8283 (m-70) cc_final: 0.7964 (t70) REVERT: G 1689 MET cc_start: 0.2615 (mmt) cc_final: 0.1877 (mmt) REVERT: G 1707 LEU cc_start: 0.9474 (tt) cc_final: 0.9169 (pp) REVERT: I 204 TYR cc_start: 0.8000 (m-80) cc_final: 0.7502 (m-80) REVERT: I 223 ARG cc_start: 0.8237 (ttt-90) cc_final: 0.7700 (ttt-90) REVERT: I 258 MET cc_start: 0.8801 (mmm) cc_final: 0.8451 (mmm) REVERT: I 263 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.6937 (mm) outliers start: 102 outliers final: 68 residues processed: 438 average time/residue: 0.2337 time to fit residues: 179.4305 Evaluate side-chains 418 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 342 time to evaluate : 1.660 ------------------------------------------------------------------------------- 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 404 LEU Chi-restraints excluded: chain A residue 882 VAL 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 1602 MET Chi-restraints excluded: chain A residue 1608 VAL Chi-restraints excluded: chain A residue 1620 ILE Chi-restraints excluded: chain A residue 1654 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 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 42 LEU 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 596 VAL Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 989 LEU Chi-restraints excluded: chain D residue 1194 PHE Chi-restraints excluded: chain D residue 1248 VAL Chi-restraints excluded: chain D residue 1506 LEU 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 276 VAL Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 72 GLN 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 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 818 PHE Chi-restraints excluded: chain G residue 916 THR Chi-restraints excluded: chain G residue 922 MET Chi-restraints excluded: chain G residue 933 VAL Chi-restraints excluded: chain G residue 1183 LYS Chi-restraints excluded: chain G residue 1282 ILE Chi-restraints excluded: chain G residue 1389 MET 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 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 G residue 1667 LYS Chi-restraints excluded: chain G residue 1671 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 398 optimal weight: 20.0000 chunk 479 optimal weight: 20.0000 chunk 429 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 434 optimal weight: 20.0000 chunk 492 optimal weight: 5.9990 chunk 386 optimal weight: 0.2980 chunk 143 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 309 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 ASN D 279 GLN D 791 GLN ** D 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1439 ASN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 570 ASN ** G1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1541 ASN ** G1656 HIS ** 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 = 0.3772 r_free = 0.3772 target = 0.076812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.056905 restraints weight = 231118.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.058247 restraints weight = 125323.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.059290 restraints weight = 83414.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.059911 restraints weight = 63009.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.060367 restraints weight = 52414.370| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 43395 Z= 0.137 Angle : 0.650 14.029 58957 Z= 0.321 Chirality : 0.044 0.286 6663 Planarity : 0.004 0.057 7333 Dihedral : 6.695 61.509 6226 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.92 % Favored : 96.06 % Rotamer: Outliers : 2.43 % Allowed : 16.98 % Favored : 80.60 % 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: 0.26 (0.12), residues: 5049 helix: 0.91 (0.10), residues: 2442 sheet: -0.32 (0.24), residues: 470 loop : -0.46 (0.14), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 99 TYR 0.038 0.001 TYR I 231 PHE 0.038 0.001 PHE G1393 TRP 0.014 0.001 TRP G 986 HIS 0.005 0.001 HIS G 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (43395) covalent geometry : angle 0.64967 / 0.32 (58957) hydrogen bonds : bond 0.03862 / 2.60 ( 2059) hydrogen bonds : angle 4.67427 / 3.36 ( 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 484 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 373 time to evaluate : 1.782 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 63 MET cc_start: 0.8515 (mmm) cc_final: 0.8182 (tpt) REVERT: A 122 MET cc_start: 0.9400 (tmm) cc_final: 0.9079 (tmm) REVERT: A 222 MET cc_start: 0.7405 (tpt) cc_final: 0.6851 (tmm) REVERT: A 360 MET cc_start: 0.9083 (mmm) cc_final: 0.8866 (mmm) REVERT: A 424 MET cc_start: 0.8085 (ppp) cc_final: 0.7246 (ppp) REVERT: A 635 MET cc_start: 0.7930 (mmm) cc_final: 0.7507 (mmm) REVERT: A 747 ASN cc_start: 0.8952 (m110) cc_final: 0.8580 (t0) REVERT: A 891 LYS cc_start: 0.9075 (tttt) cc_final: 0.8719 (tttp) REVERT: A 908 MET cc_start: 0.2691 (mmt) cc_final: 0.2033 (mmm) REVERT: A 939 MET cc_start: 0.6272 (mmm) cc_final: 0.5760 (tpt) REVERT: A 1333 GLU cc_start: 0.7621 (tt0) cc_final: 0.7390 (tt0) REVERT: A 1472 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8437 (tm-30) REVERT: A 1494 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8214 (pmm) REVERT: A 1602 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8003 (mmm) REVERT: A 1681 MET cc_start: 0.8279 (tmm) cc_final: 0.7533 (tmm) REVERT: C 230 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8341 (t80) REVERT: C 285 CYS cc_start: 0.8656 (m) cc_final: 0.8066 (p) REVERT: C 304 ASP cc_start: 0.9015 (OUTLIER) cc_final: 0.8566 (p0) REVERT: D 154 MET cc_start: 0.9195 (mmm) cc_final: 0.8951 (mmp) REVERT: D 208 MET cc_start: 0.8837 (tpp) cc_final: 0.8403 (mmm) REVERT: D 250 ASP cc_start: 0.9043 (m-30) cc_final: 0.8731 (m-30) REVERT: D 360 MET cc_start: 0.8534 (tmm) cc_final: 0.8194 (tpp) REVERT: D 487 MET cc_start: 0.8618 (tmm) cc_final: 0.8075 (tmm) REVERT: D 527 ASP cc_start: 0.8724 (m-30) cc_final: 0.8486 (m-30) REVERT: D 589 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.6907 (t80) REVERT: D 893 MET cc_start: 0.7023 (ttt) cc_final: 0.6701 (ttt) REVERT: D 922 MET cc_start: 0.9211 (mpp) cc_final: 0.8808 (mtt) REVERT: D 939 MET cc_start: 0.4004 (tpp) cc_final: 0.3660 (tpp) REVERT: D 1237 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7556 (tm-30) REVERT: D 1333 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8695 (pt0) REVERT: D 1681 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8176 (mmm) REVERT: G 17 ASP cc_start: 0.9172 (m-30) cc_final: 0.8750 (m-30) REVERT: G 75 MET cc_start: 0.8729 (mmm) cc_final: 0.8474 (mmm) REVERT: G 270 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6690 (p0) REVERT: G 288 MET cc_start: 0.9246 (ttt) cc_final: 0.8765 (tmm) REVERT: G 484 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8920 (p) REVERT: G 682 HIS cc_start: 0.6962 (p90) cc_final: 0.6542 (p90) REVERT: G 744 MET cc_start: 0.1726 (ttt) cc_final: 0.1117 (mmp) REVERT: G 818 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7864 (t80) REVERT: G 849 MET cc_start: 0.4226 (mtp) cc_final: 0.2327 (tmm) REVERT: G 1040 LYS cc_start: 0.7964 (pptt) cc_final: 0.7503 (mptt) REVERT: G 1215 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8752 (mp) REVERT: G 1388 LYS cc_start: 0.6849 (tttt) cc_final: 0.6588 (tttt) REVERT: G 1389 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7451 (ttm) REVERT: G 1455 THR cc_start: 0.9072 (m) cc_final: 0.8560 (p) REVERT: G 1617 GLU cc_start: 0.9409 (tp30) cc_final: 0.8924 (tp30) REVERT: G 1658 ARG cc_start: 0.7239 (mmm160) cc_final: 0.6602 (ptm160) REVERT: G 1665 HIS cc_start: 0.8336 (m-70) cc_final: 0.8046 (t70) REVERT: G 1689 MET cc_start: 0.2748 (mmt) cc_final: 0.2002 (mmt) REVERT: G 1707 LEU cc_start: 0.9489 (tt) cc_final: 0.9112 (pp) REVERT: I 204 TYR cc_start: 0.7751 (m-80) cc_final: 0.7479 (m-80) REVERT: I 223 ARG cc_start: 0.8319 (ttt-90) cc_final: 0.7684 (ttt-90) REVERT: I 263 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.7106 (mm) REVERT: I 270 VAL cc_start: 0.9182 (OUTLIER) cc_final: 0.8971 (m) REVERT: I 309 MET cc_start: 0.9336 (tpp) cc_final: 0.8801 (tpt) outliers start: 111 outliers final: 70 residues processed: 454 average time/residue: 0.2344 time to fit residues: 185.5373 Evaluate side-chains 432 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 348 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 895 VAL 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 1494 MET Chi-restraints excluded: chain A residue 1535 ILE Chi-restraints excluded: chain A residue 1602 MET 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 207 LEU Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 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 536 VAL Chi-restraints excluded: chain D residue 589 PHE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 779 VAL 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 D residue 1681 MET 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 37 VAL Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain G residue 484 THR Chi-restraints excluded: chain G residue 541 GLU Chi-restraints excluded: chain G residue 584 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 916 THR Chi-restraints excluded: chain G residue 922 MET 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 1215 LEU Chi-restraints excluded: chain G residue 1275 TYR Chi-restraints excluded: chain G residue 1282 ILE Chi-restraints excluded: chain G residue 1389 MET Chi-restraints excluded: chain G residue 1430 LEU Chi-restraints excluded: chain G residue 1443 THR 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 G residue 1671 SER 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 Chi-restraints excluded: chain I residue 311 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 69 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 94 optimal weight: 20.0000 chunk 225 optimal weight: 0.9980 chunk 483 optimal weight: 10.0000 chunk 354 optimal weight: 5.9990 chunk 383 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 301 optimal weight: 0.7980 chunk 319 optimal weight: 0.2980 chunk 54 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 ASN ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS D 864 GLN ** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1338 ASN D1439 ASN D1509 ASN ** D1712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 475 HIS ** 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** ** I 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.077994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.058071 restraints weight = 228054.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.059616 restraints weight = 123206.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.060683 restraints weight = 82168.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.061326 restraints weight = 61634.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.061785 restraints weight = 50755.707| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43395 Z= 0.117 Angle : 0.643 14.620 58957 Z= 0.315 Chirality : 0.043 0.268 6663 Planarity : 0.004 0.055 7333 Dihedral : 6.568 60.571 6226 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.31 % Favored : 96.67 % Rotamer: Outliers : 1.90 % Allowed : 17.83 % Favored : 80.27 % 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: 0.34 (0.12), residues: 5049 helix: 0.93 (0.10), residues: 2447 sheet: -0.11 (0.24), residues: 469 loop : -0.42 (0.14), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 99 TYR 0.037 0.001 TYR A1343 PHE 0.029 0.001 PHE G1393 TRP 0.014 0.001 TRP G 986 HIS 0.006 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (43395) covalent geometry : angle 0.64284 / 0.32 (58957) hydrogen bonds : bond 0.03690 / 2.47 ( 2059) hydrogen bonds : angle 4.59425 / 3.29 ( 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 484 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 397 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8514 (mmm) cc_final: 0.8187 (tpt) REVERT: A 122 MET cc_start: 0.9417 (tmm) cc_final: 0.9090 (tmm) REVERT: A 222 MET cc_start: 0.7412 (tpt) cc_final: 0.6892 (tmm) REVERT: A 424 MET cc_start: 0.8258 (ppp) cc_final: 0.7269 (ppp) REVERT: A 635 MET cc_start: 0.7824 (mmm) cc_final: 0.7401 (mmm) REVERT: A 747 ASN cc_start: 0.8908 (m110) cc_final: 0.8610 (t0) REVERT: A 891 LYS cc_start: 0.9002 (tttt) cc_final: 0.8656 (tttp) REVERT: A 908 MET cc_start: 0.2778 (mmt) cc_final: 0.2164 (mmm) REVERT: A 939 MET cc_start: 0.6277 (mmm) cc_final: 0.5722 (tpt) REVERT: A 1494 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8105 (pmm) REVERT: A 1602 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8352 (mmm) REVERT: A 1681 MET cc_start: 0.8260 (tmm) cc_final: 0.7472 (tmm) REVERT: B 348 GLU cc_start: 0.8221 (mp0) cc_final: 0.7214 (pt0) REVERT: C 230 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8260 (t80) REVERT: C 267 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8646 (tp) REVERT: C 285 CYS cc_start: 0.8659 (m) cc_final: 0.8149 (p) REVERT: C 304 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.8446 (p0) REVERT: D 208 MET cc_start: 0.8955 (tpp) cc_final: 0.8353 (mmm) REVERT: D 250 ASP cc_start: 0.9021 (m-30) cc_final: 0.8688 (m-30) REVERT: D 360 MET cc_start: 0.8493 (tmm) cc_final: 0.8142 (tpp) REVERT: D 487 MET cc_start: 0.8607 (tmm) cc_final: 0.8348 (tmm) REVERT: D 527 ASP cc_start: 0.8691 (m-30) cc_final: 0.8429 (m-30) REVERT: D 589 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.6735 (t80) REVERT: D 864 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8499 (pm20) REVERT: D 893 MET cc_start: 0.6938 (ttt) cc_final: 0.6674 (ttt) REVERT: D 922 MET cc_start: 0.9190 (mpp) cc_final: 0.8849 (mtt) REVERT: D 939 MET cc_start: 0.3741 (tpp) cc_final: 0.3226 (tpp) REVERT: D 967 MET cc_start: 0.6900 (tmm) cc_final: 0.5317 (ptp) REVERT: D 1237 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7526 (tm-30) REVERT: D 1681 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8182 (mmm) REVERT: F 191 GLU cc_start: 0.9011 (tt0) cc_final: 0.8275 (mp0) REVERT: G 17 ASP cc_start: 0.9163 (m-30) cc_final: 0.8719 (m-30) REVERT: G 75 MET cc_start: 0.8706 (mmm) cc_final: 0.8463 (mmm) REVERT: G 270 ASP cc_start: 0.7185 (p0) cc_final: 0.6699 (p0) REVERT: G 393 GLU cc_start: 0.8612 (tp30) cc_final: 0.8330 (tm-30) REVERT: G 464 LEU cc_start: 0.8279 (tt) cc_final: 0.7814 (mm) REVERT: G 484 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8840 (p) REVERT: G 682 HIS cc_start: 0.6809 (p90) cc_final: 0.6348 (p90) REVERT: G 744 MET cc_start: 0.1629 (ttt) cc_final: 0.1040 (mmp) REVERT: G 818 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7829 (t80) REVERT: G 1040 LYS cc_start: 0.7835 (pptt) cc_final: 0.7364 (mptt) REVERT: G 1215 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8689 (mp) REVERT: G 1388 LYS cc_start: 0.6805 (tttt) cc_final: 0.6566 (tttt) REVERT: G 1528 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8189 (tm-30) REVERT: G 1617 GLU cc_start: 0.9373 (tp30) cc_final: 0.8961 (tp30) REVERT: G 1658 ARG cc_start: 0.7125 (mmm160) cc_final: 0.6554 (ptm160) REVERT: G 1665 HIS cc_start: 0.8308 (m-70) cc_final: 0.8016 (t70) REVERT: G 1689 MET cc_start: 0.2627 (mmt) cc_final: 0.1863 (mmt) REVERT: G 1707 LEU cc_start: 0.9442 (tt) cc_final: 0.9080 (pp) REVERT: I 204 TYR cc_start: 0.7736 (m-80) cc_final: 0.7382 (m-80) REVERT: I 223 ARG cc_start: 0.8272 (ttt-90) cc_final: 0.7751 (ttt-90) REVERT: I 226 TYR cc_start: 0.8711 (t80) cc_final: 0.8345 (t80) REVERT: I 263 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6776 (mp) outliers start: 87 outliers final: 55 residues processed: 452 average time/residue: 0.2364 time to fit residues: 184.9291 Evaluate side-chains 431 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 364 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR 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 882 VAL Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1494 MET Chi-restraints excluded: chain A residue 1602 MET Chi-restraints excluded: chain A residue 1608 VAL Chi-restraints excluded: chain A residue 1620 ILE Chi-restraints excluded: chain A residue 1654 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 281 VAL Chi-restraints excluded: chain C residue 296 THR 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 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 589 PHE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 864 GLN Chi-restraints excluded: chain D residue 918 TYR Chi-restraints excluded: chain D residue 1333 GLU Chi-restraints excluded: chain D residue 1669 VAL Chi-restraints excluded: chain D residue 1681 MET Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 237 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 916 THR Chi-restraints excluded: chain G residue 922 MET Chi-restraints excluded: chain G residue 933 VAL Chi-restraints excluded: chain G residue 1183 LYS Chi-restraints excluded: chain G residue 1215 LEU Chi-restraints excluded: chain G residue 1275 TYR 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 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 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: 10.0000 chunk 10 optimal weight: 10.0000 chunk 419 optimal weight: 20.0000 chunk 378 optimal weight: 0.6980 chunk 385 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 296 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 313 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1353 ASN ** A1548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1439 ASN ** D1712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 ASN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1519 HIS ** G1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.076523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.056719 restraints weight = 230455.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.057919 restraints weight = 125206.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.058933 restraints weight = 83913.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.059544 restraints weight = 63534.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.060043 restraints weight = 52849.868| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 43395 Z= 0.160 Angle : 0.668 14.306 58957 Z= 0.328 Chirality : 0.043 0.260 6663 Planarity : 0.004 0.052 7333 Dihedral : 6.587 60.693 6226 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.96 % Favored : 96.02 % Rotamer: Outliers : 1.86 % Allowed : 18.27 % Favored : 79.87 % 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: 0.35 (0.12), residues: 5049 helix: 0.96 (0.11), residues: 2445 sheet: -0.25 (0.24), residues: 466 loop : -0.39 (0.14), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 99 TYR 0.033 0.001 TYR I 231 PHE 0.040 0.001 PHE G1393 TRP 0.015 0.001 TRP G 986 HIS 0.005 0.001 HIS D1519 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (43395) covalent geometry : angle 0.66807 / 0.33 (58957) hydrogen bonds : bond 0.03751 / 2.51 ( 2059) hydrogen bonds : angle 4.64521 / 3.34 ( 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 451 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 366 time to evaluate : 1.502 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 122 MET cc_start: 0.9351 (tmm) cc_final: 0.9147 (tmm) REVERT: A 222 MET cc_start: 0.7446 (tpt) cc_final: 0.7027 (tmm) REVERT: A 372 MET cc_start: 0.7010 (ttt) cc_final: 0.6740 (ptm) REVERT: A 424 MET cc_start: 0.8165 (ppp) cc_final: 0.7199 (ppp) REVERT: A 635 MET cc_start: 0.7862 (mmm) cc_final: 0.7421 (mmm) REVERT: A 744 MET cc_start: 0.8723 (tpp) cc_final: 0.8465 (tpp) REVERT: A 747 ASN cc_start: 0.8906 (m110) cc_final: 0.8627 (t0) REVERT: A 748 LEU cc_start: 0.9058 (mt) cc_final: 0.8814 (mt) REVERT: A 891 LYS cc_start: 0.9081 (tttt) cc_final: 0.8769 (tttp) REVERT: A 908 MET cc_start: 0.2986 (mmt) cc_final: 0.2364 (mmm) REVERT: A 939 MET cc_start: 0.6278 (mmm) cc_final: 0.5771 (tpt) REVERT: A 1494 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8101 (pmm) REVERT: A 1602 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8019 (mmm) REVERT: A 1681 MET cc_start: 0.8462 (tmm) cc_final: 0.7727 (tmm) REVERT: C 218 MET cc_start: 0.7561 (mtm) cc_final: 0.6716 (ptm) REVERT: C 230 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8290 (t80) REVERT: C 267 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8666 (tp) REVERT: C 285 CYS cc_start: 0.8678 (m) cc_final: 0.7886 (p) REVERT: C 304 ASP cc_start: 0.8971 (OUTLIER) cc_final: 0.8533 (p0) REVERT: D 208 MET cc_start: 0.8918 (tpp) cc_final: 0.8300 (mmm) REVERT: D 250 ASP cc_start: 0.9055 (m-30) cc_final: 0.8702 (m-30) REVERT: D 360 MET cc_start: 0.8538 (tmm) cc_final: 0.8216 (tpp) REVERT: D 527 ASP cc_start: 0.8724 (m-30) cc_final: 0.8469 (m-30) REVERT: D 589 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6989 (t80) REVERT: D 625 MET cc_start: 0.8262 (mmm) cc_final: 0.7969 (mmm) REVERT: D 922 MET cc_start: 0.9203 (mpp) cc_final: 0.8825 (mtt) REVERT: D 1237 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7557 (tm-30) REVERT: D 1333 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8796 (pt0) REVERT: D 1681 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8194 (mmm) REVERT: G 17 ASP cc_start: 0.9177 (m-30) cc_final: 0.8770 (m-30) REVERT: G 75 MET cc_start: 0.8697 (mmm) cc_final: 0.8432 (mmm) REVERT: G 180 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8608 (mp0) REVERT: G 270 ASP cc_start: 0.7265 (p0) cc_final: 0.6762 (p0) REVERT: G 484 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8912 (p) REVERT: G 682 HIS cc_start: 0.6851 (p90) cc_final: 0.6389 (p90) REVERT: G 744 MET cc_start: 0.1642 (ttt) cc_final: 0.0822 (mmp) REVERT: G 1040 LYS cc_start: 0.7902 (pptt) cc_final: 0.7384 (mptt) REVERT: G 1209 MET cc_start: 0.5171 (OUTLIER) cc_final: 0.4936 (mtm) REVERT: G 1455 THR cc_start: 0.9116 (m) cc_final: 0.8572 (p) REVERT: G 1617 GLU cc_start: 0.9405 (tp30) cc_final: 0.8935 (tp30) REVERT: G 1658 ARG cc_start: 0.7104 (mmm160) cc_final: 0.6552 (ptm160) REVERT: G 1665 HIS cc_start: 0.8401 (m-70) cc_final: 0.8063 (t70) REVERT: G 1689 MET cc_start: 0.2766 (mmt) cc_final: 0.2066 (mmt) REVERT: G 1707 LEU cc_start: 0.9499 (tt) cc_final: 0.9116 (pp) REVERT: I 214 ASP cc_start: 0.8501 (t0) cc_final: 0.8212 (t0) REVERT: I 223 ARG cc_start: 0.8298 (ttt-90) cc_final: 0.7656 (ttt-90) REVERT: I 226 TYR cc_start: 0.8737 (t80) cc_final: 0.8367 (t80) REVERT: I 263 ILE cc_start: 0.7112 (OUTLIER) cc_final: 0.6823 (mp) outliers start: 85 outliers final: 65 residues processed: 417 average time/residue: 0.2293 time to fit residues: 166.8881 Evaluate side-chains 433 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 357 time to evaluate : 1.542 ------------------------------------------------------------------------------- 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 482 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 946 THR 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 1494 MET Chi-restraints excluded: chain A residue 1602 MET 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 281 VAL Chi-restraints excluded: chain C residue 304 ASP 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 589 PHE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 745 TYR Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 932 VAL 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 D residue 1681 MET Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 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 566 LEU Chi-restraints excluded: chain G residue 584 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 916 THR Chi-restraints excluded: chain G residue 922 MET 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 1209 MET 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 1532 LEU Chi-restraints excluded: chain G residue 1600 PHE Chi-restraints excluded: chain G residue 1654 ILE Chi-restraints excluded: chain G residue 1671 SER Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 263 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 190 optimal weight: 7.9990 chunk 423 optimal weight: 20.0000 chunk 292 optimal weight: 6.9990 chunk 413 optimal weight: 0.8980 chunk 404 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 158 optimal weight: 0.9990 chunk 489 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 497 optimal weight: 5.9990 chunk 234 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 747 ASN ** A1548 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 ** D1712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 743 HIS G 747 ASN ** G1191 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.076156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.056193 restraints weight = 231515.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.057706 restraints weight = 126835.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.058692 restraints weight = 84505.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.059320 restraints weight = 64121.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.059780 restraints weight = 53201.978| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 43395 Z= 0.158 Angle : 0.670 16.851 58957 Z= 0.328 Chirality : 0.043 0.266 6663 Planarity : 0.004 0.050 7333 Dihedral : 6.612 60.889 6226 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.78 % Favored : 96.20 % Rotamer: Outliers : 1.99 % Allowed : 18.35 % Favored : 79.65 % 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: 0.96 (0.11), residues: 2432 sheet: -0.27 (0.24), residues: 466 loop : -0.42 (0.14), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 577 TYR 0.026 0.001 TYR I 231 PHE 0.036 0.001 PHE G1393 TRP 0.016 0.001 TRP G 986 HIS 0.006 0.001 HIS G 743 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (43395) covalent geometry : angle 0.66955 / 0.33 (58957) hydrogen bonds : bond 0.03776 / 2.54 ( 2059) hydrogen bonds : angle 4.64217 / 3.34 ( 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 459 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 368 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8593 (mmm) cc_final: 0.8217 (tpt) REVERT: A 122 MET cc_start: 0.9357 (tmm) cc_final: 0.9131 (tmm) REVERT: A 222 MET cc_start: 0.7427 (tpt) cc_final: 0.7139 (tmm) REVERT: A 424 MET cc_start: 0.8202 (ppp) cc_final: 0.7249 (ppp) REVERT: A 635 MET cc_start: 0.7827 (mmm) cc_final: 0.7378 (mmm) REVERT: A 744 MET cc_start: 0.8749 (tpp) cc_final: 0.8469 (tpp) REVERT: A 747 ASN cc_start: 0.8944 (m-40) cc_final: 0.8597 (t0) REVERT: A 748 LEU cc_start: 0.9053 (mt) cc_final: 0.8790 (mt) REVERT: A 768 MET cc_start: 0.8482 (tpp) cc_final: 0.8213 (tpp) REVERT: A 891 LYS cc_start: 0.9091 (tttt) cc_final: 0.8799 (tttm) REVERT: A 908 MET cc_start: 0.2909 (mmt) cc_final: 0.2377 (mmm) REVERT: A 1494 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8180 (pmm) REVERT: A 1602 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.7920 (mmm) REVERT: A 1681 MET cc_start: 0.8458 (tmm) cc_final: 0.7731 (tmm) REVERT: C 218 MET cc_start: 0.7571 (mtm) cc_final: 0.6715 (ptm) REVERT: C 230 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8290 (t80) REVERT: C 267 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8692 (tp) REVERT: C 285 CYS cc_start: 0.8691 (m) cc_final: 0.8152 (p) REVERT: C 304 ASP cc_start: 0.9000 (OUTLIER) cc_final: 0.8566 (p0) REVERT: D 208 MET cc_start: 0.8930 (tpp) cc_final: 0.8322 (mmm) REVERT: D 250 ASP cc_start: 0.9087 (m-30) cc_final: 0.8770 (m-30) REVERT: D 360 MET cc_start: 0.8523 (tmm) cc_final: 0.8209 (tpp) REVERT: D 527 ASP cc_start: 0.8730 (m-30) cc_final: 0.8474 (m-30) REVERT: D 589 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.7016 (t80) REVERT: D 893 MET cc_start: 0.6576 (ttt) cc_final: 0.6256 (ttm) REVERT: D 922 MET cc_start: 0.9217 (mpp) cc_final: 0.8840 (mtt) REVERT: D 967 MET cc_start: 0.6702 (tmm) cc_final: 0.6063 (ptp) REVERT: D 1237 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7603 (tm-30) REVERT: D 1261 ASP cc_start: 0.8751 (t0) cc_final: 0.8485 (t0) REVERT: D 1333 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8791 (pt0) REVERT: D 1681 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8263 (mmm) REVERT: F 218 MET cc_start: 0.8120 (pmm) cc_final: 0.7668 (ptt) REVERT: G 17 ASP cc_start: 0.9204 (m-30) cc_final: 0.8810 (m-30) REVERT: G 75 MET cc_start: 0.8701 (mmm) cc_final: 0.8429 (mmm) REVERT: G 270 ASP cc_start: 0.7031 (p0) cc_final: 0.6576 (p0) REVERT: G 306 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8891 (tp30) REVERT: G 393 GLU cc_start: 0.8658 (tp30) cc_final: 0.8379 (tm-30) REVERT: G 633 ASP cc_start: 0.8746 (t0) cc_final: 0.8464 (p0) REVERT: G 682 HIS cc_start: 0.6743 (p90) cc_final: 0.6295 (p90) REVERT: G 744 MET cc_start: 0.1600 (ttt) cc_final: 0.1288 (mmp) REVERT: G 1040 LYS cc_start: 0.7743 (pptt) cc_final: 0.7196 (mptt) REVERT: G 1209 MET cc_start: 0.5461 (OUTLIER) cc_final: 0.5213 (mtm) REVERT: G 1371 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.7460 (pt0) REVERT: G 1388 LYS cc_start: 0.7051 (tttt) cc_final: 0.6639 (tttt) REVERT: G 1455 THR cc_start: 0.9138 (m) cc_final: 0.8611 (p) REVERT: G 1528 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8233 (tm-30) REVERT: G 1617 GLU cc_start: 0.9408 (tp30) cc_final: 0.8957 (tp30) REVERT: G 1658 ARG cc_start: 0.7117 (mmm160) cc_final: 0.6576 (ptm160) REVERT: G 1665 HIS cc_start: 0.8365 (m-70) cc_final: 0.7997 (t70) REVERT: G 1689 MET cc_start: 0.3003 (mmt) cc_final: 0.2278 (mmt) REVERT: G 1707 LEU cc_start: 0.9510 (tt) cc_final: 0.9121 (pp) REVERT: I 214 ASP cc_start: 0.8505 (t0) cc_final: 0.8211 (t0) REVERT: I 223 ARG cc_start: 0.8279 (ttt-90) cc_final: 0.7637 (ttt-90) REVERT: I 263 ILE cc_start: 0.7193 (OUTLIER) cc_final: 0.6891 (mp) outliers start: 91 outliers final: 67 residues processed: 428 average time/residue: 0.2291 time to fit residues: 170.7240 Evaluate side-chains 433 residues out of total 4571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 355 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU 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 482 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1494 MET Chi-restraints excluded: chain A residue 1602 MET Chi-restraints excluded: chain A residue 1608 VAL Chi-restraints excluded: chain A residue 1620 ILE Chi-restraints excluded: chain A residue 1654 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 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 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 589 PHE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 918 TYR Chi-restraints excluded: chain D residue 932 VAL 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 D residue 1681 MET Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 264 THR 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 37 VAL 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 566 LEU Chi-restraints excluded: chain G residue 584 THR 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 916 THR Chi-restraints excluded: chain G residue 922 MET 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 1209 MET Chi-restraints excluded: chain G residue 1275 TYR Chi-restraints excluded: chain G residue 1282 ILE Chi-restraints excluded: chain G residue 1371 GLU 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 1532 LEU Chi-restraints excluded: chain G residue 1600 PHE Chi-restraints excluded: chain G residue 1654 ILE Chi-restraints excluded: chain G residue 1671 SER Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain I residue 279 LEU 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 497 optimal weight: 5.9990 chunk 377 optimal weight: 0.9980 chunk 491 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 480 optimal weight: 0.0040 chunk 203 optimal weight: 0.0060 chunk 507 optimal weight: 9.9990 chunk 454 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 400 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.5810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN ** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1439 ASN ** D1712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 HIS ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1267 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.077734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.057922 restraints weight = 228723.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.059372 restraints weight = 124492.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.060379 restraints weight = 83145.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.061069 restraints weight = 63225.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.061456 restraints weight = 52255.971| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 43395 Z= 0.116 Angle : 0.667 14.972 58957 Z= 0.321 Chirality : 0.043 0.256 6663 Planarity : 0.004 0.050 7333 Dihedral : 6.489 60.135 6226 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.45 % Favored : 96.53 % Rotamer: Outliers : 1.71 % Allowed : 18.68 % Favored : 79.61 % 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: 0.36 (0.12), residues: 5049 helix: 0.96 (0.11), residues: 2431 sheet: -0.12 (0.24), residues: 465 loop : -0.40 (0.14), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 99 TYR 0.032 0.001 TYR I 231 PHE 0.036 0.001 PHE G1393 TRP 0.038 0.002 TRP A 442 HIS 0.017 0.001 HIS G 743 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (43395) covalent geometry : angle 0.66703 / 0.32 (58957) hydrogen bonds : bond 0.03573 / 2.40 ( 2059) hydrogen bonds : angle 4.53009 / 3.25 ( 5864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10194.11 seconds wall clock time: 176 minutes 31.52 seconds (10591.52 seconds total)