Starting phenix.real_space_refine on Mon Aug 10 05:44:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jh3_36252/08_2026/8jh3_36252_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jh3_36252/08_2026/8jh3_36252.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/8jh3_36252/08_2026/8jh3_36252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jh3_36252/08_2026/8jh3_36252.map" model { file = "/net/cci-nas-00/data/ceres_data/8jh3_36252/08_2026/8jh3_36252_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jh3_36252/08_2026/8jh3_36252_neut.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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 312 5.49 5 Mg 1 5.21 5 S 200 5.16 5 C 26369 2.51 5 N 7718 2.21 5 O 8808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 337 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43416 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 11120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1412, 11120 Classifications: {'peptide': 1412} Link IDs: {'PCIS': 3, 'PTRANS': 65, 'TRANS': 1343} Chain breaks: 5 Chain: "B" Number of atoms: 9210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1155, 9210 Classifications: {'peptide': 1155} Link IDs: {'PTRANS': 52, 'TRANS': 1102} Chain breaks: 5 Chain: "C" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2098 Classifications: {'peptide': 263} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 249} Chain: "D" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1314 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 4, 'TRANS': 163} Chain breaks: 2 Chain: "E" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1740 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "F" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "G" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1324 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1052 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 917 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 545 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 932 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "N" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2897 Classifications: {'DNA': 141} Link IDs: {'rna3p': 140} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 281 Classifications: {'RNA': 13} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna3p': 12} Chain: "T" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3243 Classifications: {'DNA': 159} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 158} Chain: "a" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "b" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "c" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "d" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "e" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 746 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "f" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 720 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "h" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 685 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 527 SG CYS A 67 87.465 57.565 118.205 1.00 56.61 S ATOM 549 SG CYS A 70 90.752 57.042 120.042 1.00 49.09 S ATOM 594 SG CYS A 77 88.770 60.271 120.638 1.00 40.91 S ATOM 829 SG CYS A 107 100.420 86.727 81.557 1.00 95.18 S ATOM 851 SG CYS A 110 102.076 83.418 80.890 1.00 92.30 S ATOM 1157 SG CYS A 148 103.910 86.579 80.056 1.00102.85 S ATOM 1245 SG CYS A 168 100.954 85.595 77.911 1.00 90.43 S ATOM 19862 SG CYS B1163 104.008 61.398 110.969 1.00 50.40 S ATOM 19880 SG CYS B1166 101.900 64.373 109.787 1.00 53.42 S ATOM 20003 SG CYS B1182 100.620 60.867 109.662 1.00 71.56 S ATOM 20026 SG CYS B1185 103.342 61.989 107.184 1.00 76.29 S ATOM 20971 SG CYS C 85 76.115 63.802 186.119 1.00 93.30 S ATOM 20984 SG CYS C 87 74.405 63.510 182.932 1.00103.14 S ATOM 21019 SG CYS C 91 72.625 63.935 186.449 1.00 86.34 S ATOM 21042 SG CYS C 94 74.289 66.959 184.597 1.00 63.81 S ATOM 29128 SG CYS I 75 78.116 159.754 135.942 1.00108.75 S ATOM 29150 SG CYS I 78 74.697 161.152 137.064 1.00110.02 S ATOM 29366 SG CYS I 103 75.507 157.276 137.005 1.00 98.40 S ATOM 29388 SG CYS I 106 75.249 159.521 133.822 1.00105.79 S ATOM 28580 SG CYS I 7 71.221 146.989 91.450 1.00111.89 S ATOM 28766 SG CYS I 29 73.463 144.283 89.467 1.00110.40 S ATOM 28791 SG CYS I 32 71.682 146.030 88.223 1.00117.22 S ATOM 29507 SG CYS J 7 75.595 98.565 178.630 1.00 20.33 S ATOM 29530 SG CYS J 10 77.465 97.811 181.870 1.00 17.54 S ATOM 29806 SG CYS J 44 77.920 101.193 180.013 1.00 28.16 S ATOM 29812 SG CYS J 45 74.840 100.231 182.077 1.00 21.10 S ATOM 30974 SG CYS L 33 43.878 80.128 153.115 1.00 71.01 S ATOM 30989 SG CYS L 36 40.628 79.742 155.016 1.00 85.31 S ATOM 31099 SG CYS L 50 41.846 77.092 152.392 1.00 79.56 S ATOM 31123 SG CYS L 53 40.544 80.540 151.379 1.00 90.45 S Time building chain proxies: 7.98, per 1000 atoms: 0.18 Number of scatterers: 43416 At special positions: 0 Unit cell: (172.78, 173.84, 219.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 200 16.00 P 312 15.00 Mg 1 11.99 O 8808 8.00 N 7718 7.00 C 26369 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: 3.31 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 77 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 168 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 87 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 85 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 91 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 53 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 33 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 50 " Number of angles added : 39 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8718 Finding SS restraints... Secondary structure from input PDB file: 179 helices and 56 sheets defined 44.1% alpha, 16.0% beta 131 base pairs and 228 stacking pairs defined. Time for finding SS restraints: 5.32 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 130 through 143 removed outlier: 4.042A pdb=" N LEU A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.864A pdb=" N HIS A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.522A pdb=" N GLY A 224 " --> pdb=" O CYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 261 through 278 Processing helix chain 'A' and resid 289 through 306 removed outlier: 3.534A pdb=" N MET A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.503A pdb=" N LEU A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'A' and resid 421 through 425 removed outlier: 3.989A pdb=" N ILE A 425 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.609A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 507 through 512 removed outlier: 3.680A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 536 Processing helix chain 'A' and resid 543 through 554 removed outlier: 3.504A pdb=" N VAL A 554 " --> pdb=" O MET A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.756A pdb=" N ALA A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 639 through 662 removed outlier: 3.540A pdb=" N PHE A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 673 through 700 Processing helix chain 'A' and resid 710 through 738 removed outlier: 3.528A pdb=" N LEU A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 755 through 764 Processing helix chain 'A' and resid 810 through 847 removed outlier: 4.146A pdb=" N THR A 832 " --> pdb=" O THR A 828 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 910 through 914 removed outlier: 3.663A pdb=" N ILE A 914 " --> pdb=" O PRO A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 removed outlier: 3.993A pdb=" N LEU A 921 " --> pdb=" O ALA A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 947 Processing helix chain 'A' and resid 962 through 974 Processing helix chain 'A' and resid 984 through 997 Processing helix chain 'A' and resid 1006 through 1017 Processing helix chain 'A' and resid 1017 through 1028 Processing helix chain 'A' and resid 1029 through 1036 Processing helix chain 'A' and resid 1040 through 1058 Processing helix chain 'A' and resid 1065 through 1079 Proline residue: A1077 - end of helix Processing helix chain 'A' and resid 1098 through 1108 removed outlier: 3.935A pdb=" N ARG A1102 " --> pdb=" O LEU A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1129 removed outlier: 3.786A pdb=" N ASP A1129 " --> pdb=" O GLU A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1141 removed outlier: 3.631A pdb=" N ALA A1133 " --> pdb=" O ASP A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1175 Processing helix chain 'A' and resid 1200 through 1207 removed outlier: 3.626A pdb=" N MET A1204 " --> pdb=" O ASP A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1222 removed outlier: 3.635A pdb=" N VAL A1214 " --> pdb=" O THR A1210 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A1221 " --> pdb=" O LYS A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1274 Processing helix chain 'A' and resid 1315 through 1322 Processing helix chain 'A' and resid 1334 through 1343 Processing helix chain 'A' and resid 1343 through 1361 Processing helix chain 'A' and resid 1367 through 1379 removed outlier: 4.070A pdb=" N MET A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1393 Processing helix chain 'A' and resid 1398 through 1406 removed outlier: 3.521A pdb=" N ARG A1402 " --> pdb=" O GLY A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1419 Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.973A pdb=" N ASN A1430 " --> pdb=" O GLY A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1442 Processing helix chain 'A' and resid 1452 through 1456 Processing helix chain 'A' and resid 1457 through 1461 removed outlier: 3.963A pdb=" N ALA A1461 " --> pdb=" O ALA A1458 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 29 Processing helix chain 'B' and resid 31 through 51 removed outlier: 5.568A pdb=" N ILE B 46 " --> pdb=" O MET B 42 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLN B 47 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 273 through 282 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 300 through 306 Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 318 through 328 removed outlier: 3.721A pdb=" N ALA B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 351 removed outlier: 3.772A pdb=" N GLN B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 383 removed outlier: 3.867A pdb=" N LYS B 367 " --> pdb=" O PHE B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 401 through 431 removed outlier: 4.079A pdb=" N ARG B 427 " --> pdb=" O ARG B 423 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 429 " --> pdb=" O MET B 425 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU B 430 " --> pdb=" O GLN B 426 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 457 removed outlier: 3.636A pdb=" N THR B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 522 through 526 removed outlier: 4.311A pdb=" N ALA B 525 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 555 Processing helix chain 'B' and resid 558 through 562 removed outlier: 3.687A pdb=" N TYR B 562 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 599 removed outlier: 3.904A pdb=" N LEU B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 removed outlier: 3.572A pdb=" N ILE B 652 " --> pdb=" O THR B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 684 Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.651A pdb=" N GLU B 696 " --> pdb=" O GLY B 692 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 692 through 696' Processing helix chain 'B' and resid 703 through 708 removed outlier: 3.576A pdb=" N LEU B 707 " --> pdb=" O PRO B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 removed outlier: 3.654A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 808 through 813 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1013 through 1017 Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.944A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.532A pdb=" N VAL B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 206 through 210 Processing helix chain 'C' and resid 239 through 264 Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.727A pdb=" N LEU D 28 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 72 Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 95 through 111 Processing helix chain 'D' and resid 117 through 129 removed outlier: 3.710A pdb=" N CYS D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 148 Processing helix chain 'D' and resid 152 through 160 removed outlier: 3.742A pdb=" N ALA D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 167 removed outlier: 3.940A pdb=" N LYS D 166 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS D 167 " --> pdb=" O ALA D 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 163 through 167' Processing helix chain 'D' and resid 170 through 182 Processing helix chain 'E' and resid 3 through 26 Processing helix chain 'E' and resid 30 through 35 removed outlier: 3.617A pdb=" N ASP E 35 " --> pdb=" O GLN E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 46 Processing helix chain 'E' and resid 64 through 71 Processing helix chain 'E' and resid 88 through 102 Processing helix chain 'E' and resid 116 through 121 Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 156 through 167 Processing helix chain 'E' and resid 170 through 174 Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'F' and resid 86 through 102 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.604A pdb=" N ILE G 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 87 through 92 removed outlier: 3.587A pdb=" N ASP H 91 " --> pdb=" O LEU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' Processing helix chain 'I' and resid 59 through 65 removed outlier: 4.079A pdb=" N GLY I 63 " --> pdb=" O ASP I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.556A pdb=" N VAL J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.782A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'a' and resid 45 through 56 Processing helix chain 'a' and resid 63 through 77 removed outlier: 3.607A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 Processing helix chain 'b' and resid 25 through 29 Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.501A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 Processing helix chain 'c' and resid 16 through 22 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 45 through 73 removed outlier: 3.638A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 89 Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'd' and resid 37 through 49 Processing helix chain 'd' and resid 55 through 84 Processing helix chain 'd' and resid 90 through 102 Processing helix chain 'd' and resid 103 through 123 Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 77 Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 131 Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.502A pdb=" N ASP f 68 " --> pdb=" O ASN f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 Processing helix chain 'g' and resid 18 through 22 Processing helix chain 'g' and resid 26 through 36 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.372A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 89 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'h' and resid 37 through 49 Processing helix chain 'h' and resid 55 through 84 Processing helix chain 'h' and resid 90 through 102 Processing helix chain 'h' and resid 103 through 123 removed outlier: 3.503A pdb=" N ALA h 107 " --> pdb=" O PRO h 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1421 through 1422 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 10.082A pdb=" N LEU A 86 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 10.556A pdb=" N LYS A 88 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A 239 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 178 removed outlier: 4.397A pdb=" N LEU A 182 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 252 removed outlier: 3.909A pdb=" N ILE A 251 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY A 259 " --> pdb=" O ILE A 251 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.682A pdb=" N LYS A 344 " --> pdb=" O PHE B1130 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B1128 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.673A pdb=" N THR A 352 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N PHE A 469 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL A 353 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU A 471 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER A 355 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.773A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N HIS A 436 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA A 403 " --> pdb=" O HIS A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA9, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.066A pdb=" N VAL H 95 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR H 56 " --> pdb=" O ARG H 144 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE H 29 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE H 27 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS H 102 " --> pdb=" O TYR H 114 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER H 116 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N VAL H 100 " --> pdb=" O SER H 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 589 through 591 removed outlier: 6.838A pdb=" N LEU A 607 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 767 through 768 Processing sheet with id=AB3, first strand: chain 'A' and resid 850 through 851 removed outlier: 6.835A pdb=" N THR A 857 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 879 through 883 Processing sheet with id=AB5, first strand: chain 'A' and resid 1284 through 1295 removed outlier: 4.037A pdb=" N LYS A1284 " --> pdb=" O ASP A1312 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1143 through 1144 removed outlier: 7.299A pdb=" N THR A1143 " --> pdb=" O LEU A1276 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1227 through 1230 removed outlier: 3.720A pdb=" N ARG A1196 " --> pdb=" O GLU A1153 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA A1151 " --> pdb=" O GLU A1198 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N SER A1150 " --> pdb=" O GLU I 47 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLU I 47 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR A1152 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG I 45 " --> pdb=" O THR A1152 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A1154 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 143 through 147 removed outlier: 3.511A pdb=" N VAL F 133 " --> pdb=" O MET A1447 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL A1446 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY G 59 " --> pdb=" O ILE A1448 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 55 through 60 removed outlier: 3.505A pdb=" N ILE B 77 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B 75 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 60 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASP B 118 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE B 82 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR B 116 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU B 84 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N SER B 113 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS B 160 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL B 115 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AC2, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC3, first strand: chain 'B' and resid 397 through 400 removed outlier: 3.523A pdb=" N ALA B 205 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 215 through 218 removed outlier: 3.990A pdb=" N HIS B 227 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 231 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER B 243 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN B 246 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC6, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC7, first strand: chain 'B' and resid 578 through 583 removed outlier: 5.542A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.615A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.615A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL B 952 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL L 29 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU L 42 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD2, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.521A pdb=" N MET B 839 " --> pdb=" O VAL B 992 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR B 994 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N MET B 841 " --> pdb=" O TYR B 994 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 873 through 874 removed outlier: 3.766A pdb=" N ASP B 936 " --> pdb=" O LEU B 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.538A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD6, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AD7, first strand: chain 'B' and resid 1171 through 1174 Processing sheet with id=AD8, first strand: chain 'C' and resid 6 through 12 removed outlier: 5.486A pdb=" N VAL C 7 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER C 22 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE C 9 " --> pdb=" O MET C 20 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N MET C 20 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 119 through 122 removed outlier: 6.956A pdb=" N VAL C 97 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU C 152 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN C 154 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS C 160 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLY C 162 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU C 43 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE L 67 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.769A pdb=" N GLU C 131 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.501A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 113 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.659A pdb=" N THR D 5 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AE5, first strand: chain 'E' and resid 59 through 61 removed outlier: 3.555A pdb=" N PHE E 59 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL E 79 " --> pdb=" O PHE E 59 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP E 78 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE E 110 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU E 80 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AE7, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.008A pdb=" N LYS E 151 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE E 198 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 169 through 170 removed outlier: 4.014A pdb=" N LYS G 146 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA G 159 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N VAL G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE G 100 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE G 90 " --> pdb=" O ASP G 102 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 14 through 18 removed outlier: 3.688A pdb=" N LYS I 17 " --> pdb=" O LEU I 26 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU I 36 " --> pdb=" O TYR I 27 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AF2, first strand: chain 'K' and resid 19 through 23 removed outlier: 3.589A pdb=" N PHE K 58 " --> pdb=" O GLN K 76 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.914A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AF5, first strand: chain 'b' and resid 96 through 98 Processing sheet with id=AF6, first strand: chain 'c' and resid 42 through 43 removed outlier: 6.989A pdb=" N ARG c 42 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AF8, first strand: chain 'c' and resid 100 through 102 Processing sheet with id=AF9, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.770A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AG2, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.015A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 1729 hydrogen bonds defined for protein. 4857 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 335 hydrogen bonds 666 hydrogen bond angles 0 basepair planarities 131 basepair parallelities 228 stacking parallelities Total time for adding SS restraints: 14.60 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6548 1.30 - 1.43: 12617 1.43 - 1.56: 24724 1.56 - 1.69: 624 1.69 - 1.82: 326 Bond restraints: 44839 Sorted by residual: bond pdb=" C ARG a 52 " pdb=" O ARG a 52 " ideal model delta sigma weight residual 1.236 1.165 0.071 1.15e-02 7.56e+03 3.81e+01 bond pdb=" C GLN c 112 " pdb=" O GLN c 112 " ideal model delta sigma weight residual 1.235 1.295 -0.060 1.20e-02 6.94e+03 2.53e+01 bond pdb=" C3' DC T 4 " pdb=" C2' DC T 4 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DG N 2 " pdb=" C2' DG N 2 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DT T -17 " pdb=" C2' DT T -17 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 44834 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 59490 1.84 - 3.67: 2232 3.67 - 5.51: 141 5.51 - 7.34: 22 7.34 - 9.18: 3 Bond angle restraints: 61888 Sorted by residual: angle pdb=" N VAL a 117 " pdb=" CA VAL a 117 " pdb=" C VAL a 117 " ideal model delta sigma weight residual 113.47 106.27 7.20 1.01e+00 9.80e-01 5.08e+01 angle pdb=" N VAL e 117 " pdb=" CA VAL e 117 " pdb=" C VAL e 117 " ideal model delta sigma weight residual 113.47 107.59 5.88 1.01e+00 9.80e-01 3.39e+01 angle pdb=" C ALA B 62 " pdb=" CA ALA B 62 " pdb=" CB ALA B 62 " ideal model delta sigma weight residual 116.63 110.94 5.69 1.16e+00 7.43e-01 2.40e+01 angle pdb=" C HIS h 49 " pdb=" N PRO h 50 " pdb=" CA PRO h 50 " ideal model delta sigma weight residual 119.47 125.15 -5.68 1.16e+00 7.43e-01 2.40e+01 angle pdb=" CA ALA B 62 " pdb=" C ALA B 62 " pdb=" N GLN B 63 " ideal model delta sigma weight residual 119.63 115.93 3.70 8.10e-01 1.52e+00 2.09e+01 ... (remaining 61883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 24985 35.86 - 71.73: 1542 71.73 - 107.59: 53 107.59 - 143.46: 1 143.46 - 179.32: 2 Dihedral angle restraints: 26583 sinusoidal: 13089 harmonic: 13494 Sorted by residual: dihedral pdb=" C4' DC T 4 " pdb=" C3' DC T 4 " pdb=" O3' DC T 4 " pdb=" P DC T 5 " ideal model delta sinusoidal sigma weight residual -140.00 39.32 -179.32 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC T 45 " pdb=" C3' DC T 45 " pdb=" O3' DC T 45 " pdb=" P DA T 46 " ideal model delta sinusoidal sigma weight residual -140.00 35.09 -175.09 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA ASP B 176 " pdb=" C ASP B 176 " pdb=" N GLU B 177 " pdb=" CA GLU B 177 " ideal model delta harmonic sigma weight residual -180.00 -160.28 -19.72 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 26580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4877 0.045 - 0.090: 1609 0.090 - 0.134: 427 0.134 - 0.179: 39 0.179 - 0.224: 3 Chirality restraints: 6955 Sorted by residual: chirality pdb=" CA LYS g 74 " pdb=" N LYS g 74 " pdb=" C LYS g 74 " pdb=" CB LYS g 74 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE c 111 " pdb=" N ILE c 111 " pdb=" C ILE c 111 " pdb=" CB ILE c 111 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.98e-01 chirality pdb=" CA VAL e 117 " pdb=" N VAL e 117 " pdb=" C VAL e 117 " pdb=" CB VAL e 117 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.29e-01 ... (remaining 6952 not shown) Planarity restraints: 6891 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR d 37 " -0.070 2.00e-02 2.50e+03 4.01e-02 3.22e+01 pdb=" CG TYR d 37 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR d 37 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR d 37 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR d 37 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR d 37 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR d 37 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR d 37 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN c 73 " -0.015 2.00e-02 2.50e+03 3.00e-02 8.99e+00 pdb=" CG ASN c 73 " 0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN c 73 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN c 73 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL c 43 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.30e+00 pdb=" C VAL c 43 " -0.050 2.00e-02 2.50e+03 pdb=" O VAL c 43 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY c 44 " 0.017 2.00e-02 2.50e+03 ... (remaining 6888 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 6 1.90 - 2.65: 565 2.65 - 3.40: 56527 3.40 - 4.15: 108927 4.15 - 4.90: 189296 Nonbonded interactions: 355321 Sorted by model distance: nonbonded pdb=" OP2 DA T -44 " pdb=" NH2 ARG c 32 " model vdw 1.149 3.120 nonbonded pdb=" OP2 DA T -44 " pdb=" CZ ARG c 32 " model vdw 1.258 3.270 nonbonded pdb=" P DA T -44 " pdb=" NH2 ARG c 32 " model vdw 1.483 3.480 nonbonded pdb=" OP2 DA T -44 " pdb=" NH1 ARG c 32 " model vdw 1.486 3.120 nonbonded pdb=" SD MET A 253 " pdb=" N3 DC T 42 " model vdw 1.757 3.480 ... (remaining 355316 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and resid 43 through 133) selection = (chain 'e' and resid 43 through 133) } ncs_group { reference = chain 'b' selection = (chain 'f' and resid 25 through 101) } ncs_group { reference = (chain 'c' and resid 17 through 109) selection = chain 'g' } ncs_group { reference = (chain 'd' and resid 36 through 123) selection = chain 'h' } 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: 3.910 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: 0.050 Extract box with map and model: 0.690 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 48.910 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.100 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 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 : 0.005 0.071 44870 Z= 0.341 Angle : 0.768 12.113 61927 Z= 0.538 Chirality : 0.047 0.224 6955 Planarity : 0.004 0.062 6891 Dihedral : 19.209 179.320 17865 Min Nonbonded Distance : 1.149 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.20 % Favored : 96.73 % Rotamer: Outliers : 0.35 % Allowed : 0.86 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % 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: -0.79 (0.12), residues: 4589 helix: 0.14 (0.12), residues: 1833 sheet: -1.12 (0.20), residues: 636 loop : -0.82 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG a 63 TYR 0.070 0.002 TYR d 37 PHE 0.031 0.002 PHE B 217 TRP 0.026 0.003 TRP C 201 HIS 0.007 0.001 HIS B 996 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.34 (44839) covalent geometry : angle 0.76018 / 0.54 (61888) hydrogen bonds : bond 0.15699 / 10.60 ( 2043) hydrogen bonds : angle 6.50197 / 4.64 ( 5523) metal coordination : bond 0.00649 / 0.38 ( 31) metal coordination : angle 4.32144 / 2.94 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 484 time to evaluate : 1.074 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 253 MET cc_start: 0.3187 (tmm) cc_final: 0.2746 (mtm) REVERT: A 282 MET cc_start: 0.5370 (mmp) cc_final: 0.5051 (ppp) REVERT: B 35 LEU cc_start: 0.6786 (mt) cc_final: 0.6583 (mp) REVERT: B 860 MET cc_start: 0.6093 (tmm) cc_final: 0.5718 (tmm) REVERT: B 1082 MET cc_start: 0.8042 (tpp) cc_final: 0.7782 (tpt) REVERT: B 1152 MET cc_start: 0.7166 (mmm) cc_final: 0.6907 (mmm) REVERT: C 81 TYR cc_start: 0.6838 (m-80) cc_final: 0.6609 (m-80) REVERT: D 24 ASN cc_start: 0.3706 (t0) cc_final: 0.3229 (p0) REVERT: h 59 MET cc_start: 0.4852 (tpt) cc_final: 0.4324 (tmm) outliers start: 14 outliers final: 0 residues processed: 496 average time/residue: 0.2846 time to fit residues: 222.4738 Evaluate side-chains 203 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.1980 chunk 470 optimal weight: 0.6980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1393 ASN B 72 ASN ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 996 HIS D 46 HIS D 144 GLN E 112 GLN E 113 ASN G 41 GLN I 12 ASN I 31 ASN K 29 ASN b 93 GLN c 110 ASN d 82 HIS d 84 ASN ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.079476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.061584 restraints weight = 287667.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.061311 restraints weight = 185253.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.061397 restraints weight = 138283.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.061493 restraints weight = 126728.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.061508 restraints weight = 114063.187| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 44870 Z= 0.190 Angle : 0.654 13.841 61927 Z= 0.349 Chirality : 0.044 0.255 6955 Planarity : 0.005 0.069 6891 Dihedral : 21.511 178.665 8585 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.81 % Favored : 97.15 % Rotamer: Outliers : 0.79 % Allowed : 6.41 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % 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: 4589 helix: 1.08 (0.12), residues: 1853 sheet: -0.80 (0.19), residues: 650 loop : -0.49 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG c 32 TYR 0.023 0.002 TYR I 27 PHE 0.024 0.002 PHE e 67 TRP 0.012 0.002 TRP C 192 HIS 0.009 0.001 HIS D 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (44839) covalent geometry : angle 0.64808 / 0.35 (61888) hydrogen bonds : bond 0.05032 / 3.37 ( 2043) hydrogen bonds : angle 4.93927 / 3.51 ( 5523) metal coordination : bond 0.00733 / 0.48 ( 31) metal coordination : angle 3.66924 / 2.44 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 1.433 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 253 MET cc_start: 0.4561 (tmm) cc_final: 0.3633 (mtm) REVERT: A 282 MET cc_start: 0.6485 (mmp) cc_final: 0.5485 (ppp) REVERT: A 548 MET cc_start: 0.7685 (mtm) cc_final: 0.7455 (mtp) REVERT: A 920 ILE cc_start: 0.8689 (mm) cc_final: 0.8474 (mm) REVERT: A 1439 MET cc_start: 0.8386 (ptp) cc_final: 0.7937 (ptp) REVERT: A 1447 MET cc_start: 0.7777 (mmm) cc_final: 0.6951 (mmm) REVERT: B 556 MET cc_start: 0.6357 (tmm) cc_final: 0.6053 (tmm) REVERT: B 860 MET cc_start: 0.7026 (tmm) cc_final: 0.6803 (tmm) REVERT: B 1082 MET cc_start: 0.8491 (tpp) cc_final: 0.7978 (tpt) REVERT: B 1152 MET cc_start: 0.8081 (mmm) cc_final: 0.7503 (mmm) REVERT: C 81 TYR cc_start: 0.7489 (m-80) cc_final: 0.7182 (m-80) REVERT: D 24 ASN cc_start: 0.4502 (t0) cc_final: 0.3864 (p0) REVERT: D 144 GLN cc_start: 0.1025 (mt0) cc_final: 0.0757 (mm-40) REVERT: G 35 GLU cc_start: 0.4175 (mt-10) cc_final: 0.2864 (tp30) REVERT: G 38 CYS cc_start: 0.4404 (OUTLIER) cc_final: 0.4177 (p) REVERT: G 153 ASP cc_start: 0.0333 (t0) cc_final: 0.0110 (t0) REVERT: K 5 ASP cc_start: 0.7539 (m-30) cc_final: 0.7267 (t0) REVERT: c 41 GLU cc_start: 0.4467 (OUTLIER) cc_final: 0.4174 (pt0) REVERT: d 59 MET cc_start: 0.5841 (mtt) cc_final: 0.5579 (mtm) REVERT: d 62 MET cc_start: 0.7795 (mmm) cc_final: 0.7272 (mtp) REVERT: h 59 MET cc_start: 0.5806 (tpt) cc_final: 0.5007 (tmm) outliers start: 32 outliers final: 18 residues processed: 252 average time/residue: 0.2379 time to fit residues: 100.7876 Evaluate side-chains 205 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1392 ILE Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain b residue 91 LYS Chi-restraints excluded: chain c residue 41 GLU Chi-restraints excluded: chain d residue 82 HIS Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain f residue 59 LYS Chi-restraints excluded: chain h residue 65 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 476 optimal weight: 40.0000 chunk 429 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 412 optimal weight: 40.0000 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 145 optimal weight: 0.2980 chunk 14 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 377 optimal weight: 5.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN A 314 GLN A 769 GLN B 356 HIS B 761 HIS B 932 HIS B1104 HIS C 264 ASN E 113 ASN G 21 GLN c 73 ASN d 84 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.077602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.059968 restraints weight = 290626.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.059022 restraints weight = 225696.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.059181 restraints weight = 180160.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.059193 restraints weight = 176329.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.059360 restraints weight = 136011.389| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 44870 Z= 0.217 Angle : 0.636 10.386 61927 Z= 0.342 Chirality : 0.044 0.377 6955 Planarity : 0.005 0.087 6891 Dihedral : 21.551 177.177 8585 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.51 % Favored : 96.47 % Rotamer: Outliers : 1.16 % Allowed : 8.16 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % 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: 0.36 (0.12), residues: 4589 helix: 1.33 (0.12), residues: 1859 sheet: -0.62 (0.20), residues: 629 loop : -0.40 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 42 TYR 0.019 0.002 TYR B 116 PHE 0.023 0.002 PHE C 178 TRP 0.013 0.002 TRP A 956 HIS 0.027 0.002 HIS d 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.22 (44839) covalent geometry : angle 0.63191 / 0.34 (61888) hydrogen bonds : bond 0.04786 / 3.22 ( 2043) hydrogen bonds : angle 4.67723 / 3.32 ( 5523) metal coordination : bond 0.00877 / 0.51 ( 31) metal coordination : angle 2.83536 / 1.85 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 1.491 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 253 MET cc_start: 0.4969 (tmm) cc_final: 0.4193 (mtm) REVERT: A 282 MET cc_start: 0.6392 (mmp) cc_final: 0.5851 (ppp) REVERT: A 548 MET cc_start: 0.7903 (mtm) cc_final: 0.7628 (mtp) REVERT: A 1270 MET cc_start: 0.7857 (mtp) cc_final: 0.7652 (mtp) REVERT: A 1439 MET cc_start: 0.8577 (ptp) cc_final: 0.8119 (ptp) REVERT: B 245 MET cc_start: 0.7916 (ptm) cc_final: 0.7637 (ptp) REVERT: B 556 MET cc_start: 0.6541 (tmm) cc_final: 0.6214 (tmm) REVERT: B 699 MET cc_start: 0.9009 (tpp) cc_final: 0.8769 (tpp) REVERT: B 702 MET cc_start: 0.8400 (tpp) cc_final: 0.7878 (tpp) REVERT: B 1082 MET cc_start: 0.8490 (tpp) cc_final: 0.8152 (tpt) REVERT: B 1152 MET cc_start: 0.8191 (mmm) cc_final: 0.7635 (mmm) REVERT: C 81 TYR cc_start: 0.7514 (m-80) cc_final: 0.7253 (m-80) REVERT: D 24 ASN cc_start: 0.4466 (t0) cc_final: 0.3819 (p0) REVERT: D 138 HIS cc_start: 0.5824 (m-70) cc_final: 0.5089 (t70) REVERT: G 21 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: G 22 MET cc_start: 0.8373 (tpp) cc_final: 0.7867 (mmm) REVERT: G 35 GLU cc_start: 0.4543 (mt-10) cc_final: 0.4168 (tp30) REVERT: L 66 MET cc_start: 0.7190 (tpp) cc_final: 0.6819 (tpt) REVERT: d 62 MET cc_start: 0.7755 (mmm) cc_final: 0.7294 (mtp) REVERT: d 71 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8536 (tp30) REVERT: g 41 GLU cc_start: 0.0982 (OUTLIER) cc_final: 0.0772 (mt-10) outliers start: 47 outliers final: 23 residues processed: 228 average time/residue: 0.2330 time to fit residues: 90.5985 Evaluate side-chains 196 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 1204 MET Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 21 GLN Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain a residue 49 ARG Chi-restraints excluded: chain b residue 91 LYS Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain f residue 59 LYS Chi-restraints excluded: chain g residue 41 GLU Chi-restraints excluded: chain h residue 65 PHE Chi-restraints excluded: chain h residue 105 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 277 optimal weight: 6.9990 chunk 210 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 343 optimal weight: 20.0000 chunk 413 optimal weight: 40.0000 chunk 281 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 363 optimal weight: 8.9990 chunk 205 optimal weight: 0.0980 chunk 18 optimal weight: 8.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN A 140 GLN A 265 HIS A 518 ASN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.077603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.060045 restraints weight = 288569.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.059037 restraints weight = 207311.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.059331 restraints weight = 167201.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.059444 restraints weight = 134340.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.059460 restraints weight = 124106.332| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 44870 Z= 0.156 Angle : 0.558 10.135 61927 Z= 0.301 Chirality : 0.042 0.251 6955 Planarity : 0.004 0.076 6891 Dihedral : 21.570 178.663 8585 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.94 % Favored : 97.04 % Rotamer: Outliers : 1.31 % Allowed : 8.95 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % 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: 0.61 (0.12), residues: 4589 helix: 1.52 (0.12), residues: 1860 sheet: -0.44 (0.20), residues: 623 loop : -0.27 (0.14), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 55 TYR 0.021 0.001 TYR a 99 PHE 0.027 0.002 PHE G 3 TRP 0.011 0.001 TRP C 192 HIS 0.008 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (44839) covalent geometry : angle 0.55425 / 0.30 (61888) hydrogen bonds : bond 0.04137 / 2.78 ( 2043) hydrogen bonds : angle 4.45981 / 3.16 ( 5523) metal coordination : bond 0.00660 / 0.39 ( 31) metal coordination : angle 2.69395 / 1.73 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 174 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7356 (pt0) REVERT: A 253 MET cc_start: 0.5452 (tmm) cc_final: 0.4215 (mtm) REVERT: A 282 MET cc_start: 0.6350 (mmp) cc_final: 0.5493 (ppp) REVERT: A 305 MET cc_start: 0.8363 (mmt) cc_final: 0.8142 (mmt) REVERT: A 548 MET cc_start: 0.7825 (mtm) cc_final: 0.7564 (mtp) REVERT: A 1270 MET cc_start: 0.8001 (mtp) cc_final: 0.7788 (mtp) REVERT: A 1439 MET cc_start: 0.8605 (ptp) cc_final: 0.8119 (ptp) REVERT: B 245 MET cc_start: 0.7919 (ptm) cc_final: 0.7653 (ptp) REVERT: B 702 MET cc_start: 0.8411 (tpp) cc_final: 0.8100 (tpp) REVERT: B 1082 MET cc_start: 0.8422 (tpp) cc_final: 0.8117 (tpt) REVERT: C 23 ASP cc_start: 0.7566 (t0) cc_final: 0.7354 (t0) REVERT: C 81 TYR cc_start: 0.7536 (m-80) cc_final: 0.7272 (m-80) REVERT: D 24 ASN cc_start: 0.4370 (t0) cc_final: 0.3650 (p0) REVERT: D 138 HIS cc_start: 0.5765 (m-70) cc_final: 0.5090 (t70) REVERT: E 34 MET cc_start: 0.7576 (mtp) cc_final: 0.7191 (mmp) REVERT: G 22 MET cc_start: 0.8555 (tpp) cc_final: 0.8099 (mmm) REVERT: G 35 GLU cc_start: 0.4614 (mt-10) cc_final: 0.4148 (tp30) REVERT: L 66 MET cc_start: 0.7268 (tpp) cc_final: 0.6989 (tpt) REVERT: d 59 MET cc_start: 0.5982 (mtt) cc_final: 0.5674 (mtm) REVERT: d 71 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8572 (tp30) REVERT: g 41 GLU cc_start: 0.1140 (OUTLIER) cc_final: 0.0863 (mt-10) outliers start: 53 outliers final: 29 residues processed: 213 average time/residue: 0.2231 time to fit residues: 81.8668 Evaluate side-chains 199 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1204 MET Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain a residue 49 ARG Chi-restraints excluded: chain b residue 39 ARG Chi-restraints excluded: chain b residue 91 LYS Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain f residue 59 LYS Chi-restraints excluded: chain g residue 41 GLU Chi-restraints excluded: chain h residue 65 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 301 optimal weight: 7.9990 chunk 232 optimal weight: 6.9990 chunk 354 optimal weight: 10.0000 chunk 480 optimal weight: 20.0000 chunk 417 optimal weight: 50.0000 chunk 319 optimal weight: 6.9990 chunk 346 optimal weight: 9.9990 chunk 448 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 268 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 ASN A 651 GLN A1370 HIS A1435 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN B 984 HIS C 64 HIS ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN J 52 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.075638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.058936 restraints weight = 294665.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.058078 restraints weight = 245643.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.058275 restraints weight = 208453.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.058293 restraints weight = 173929.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.058302 restraints weight = 160986.364| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 44870 Z= 0.271 Angle : 0.702 13.351 61927 Z= 0.370 Chirality : 0.045 0.248 6955 Planarity : 0.005 0.062 6891 Dihedral : 21.715 176.078 8585 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.38 % Favored : 95.60 % Rotamer: Outliers : 1.70 % Allowed : 10.28 % Favored : 88.02 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % 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: 0.24 (0.12), residues: 4589 helix: 1.14 (0.12), residues: 1860 sheet: -0.57 (0.20), residues: 625 loop : -0.40 (0.14), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 460 TYR 0.021 0.002 TYR C 81 PHE 0.038 0.002 PHE C 178 TRP 0.026 0.002 TRP A 139 HIS 0.009 0.002 HIS J 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.27 (44839) covalent geometry : angle 0.69688 / 0.37 (61888) hydrogen bonds : bond 0.05327 / 3.56 ( 2043) hydrogen bonds : angle 4.74072 / 3.37 ( 5523) metal coordination : bond 0.01211 / 0.64 ( 31) metal coordination : angle 3.48134 / 2.20 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 169 time to evaluate : 1.208 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: A 140 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7411 (pt0) REVERT: A 253 MET cc_start: 0.4905 (tmm) cc_final: 0.4114 (mtt) REVERT: A 282 MET cc_start: 0.6312 (mmp) cc_final: 0.5537 (ppp) REVERT: A 383 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7407 (pp30) REVERT: A 522 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7977 (mtm) REVERT: A 1270 MET cc_start: 0.7979 (mtp) cc_final: 0.7771 (mtp) REVERT: A 1439 MET cc_start: 0.8732 (ptp) cc_final: 0.8317 (ptp) REVERT: B 245 MET cc_start: 0.7775 (ptm) cc_final: 0.7419 (ptp) REVERT: B 702 MET cc_start: 0.8400 (tpp) cc_final: 0.8178 (tpp) REVERT: B 1082 MET cc_start: 0.8495 (tpp) cc_final: 0.8164 (tpt) REVERT: C 81 TYR cc_start: 0.7910 (m-80) cc_final: 0.7549 (m-10) REVERT: D 24 ASN cc_start: 0.3862 (t0) cc_final: 0.3547 (t0) REVERT: D 138 HIS cc_start: 0.5636 (m-70) cc_final: 0.5150 (t-90) REVERT: E 57 MET cc_start: 0.6746 (mmm) cc_final: 0.6526 (mmm) REVERT: E 64 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7930 (p) REVERT: G 35 GLU cc_start: 0.4878 (mt-10) cc_final: 0.4600 (tp30) REVERT: K 5 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7279 (t0) REVERT: b 39 ARG cc_start: 0.1091 (OUTLIER) cc_final: 0.0716 (mmp-170) REVERT: d 59 MET cc_start: 0.6149 (mtt) cc_final: 0.5947 (mtm) REVERT: d 71 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8534 (tp30) REVERT: f 58 LEU cc_start: 0.7960 (pp) cc_final: 0.7757 (pp) REVERT: h 59 MET cc_start: 0.4993 (tmm) cc_final: 0.4407 (tmm) outliers start: 69 outliers final: 37 residues processed: 228 average time/residue: 0.2097 time to fit residues: 83.4248 Evaluate side-chains 206 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1216 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 121 CYS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain a residue 49 ARG Chi-restraints excluded: chain b residue 39 ARG Chi-restraints excluded: chain b residue 91 LYS Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain f residue 59 LYS Chi-restraints excluded: chain h residue 105 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 451 optimal weight: 10.0000 chunk 330 optimal weight: 30.0000 chunk 136 optimal weight: 8.9990 chunk 477 optimal weight: 30.0000 chunk 48 optimal weight: 0.9990 chunk 458 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 289 optimal weight: 30.0000 chunk 428 optimal weight: 30.0000 chunk 326 optimal weight: 9.9990 chunk 214 optimal weight: 3.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 140 GLN A 769 GLN A1112 ASN A1261 GLN A1435 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 GLN I 79 HIS L 55 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.074571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.057145 restraints weight = 286363.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.056066 restraints weight = 218360.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.056290 restraints weight = 185445.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.056414 restraints weight = 150166.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.056422 restraints weight = 137937.101| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 44870 Z= 0.301 Angle : 0.735 14.235 61927 Z= 0.385 Chirality : 0.047 0.333 6955 Planarity : 0.006 0.067 6891 Dihedral : 22.009 176.798 8585 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.27 % Favored : 95.71 % Rotamer: Outliers : 1.73 % Allowed : 11.83 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.12), residues: 4589 helix: 0.79 (0.12), residues: 1868 sheet: -0.65 (0.20), residues: 616 loop : -0.65 (0.14), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG B 385 TYR 0.022 0.002 TYR H 140 PHE 0.035 0.003 PHE C 178 TRP 0.032 0.002 TRP A 139 HIS 0.010 0.002 HIS A1290 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.30 (44839) covalent geometry : angle 0.72748 / 0.38 (61888) hydrogen bonds : bond 0.05374 / 3.57 ( 2043) hydrogen bonds : angle 4.91123 / 3.48 ( 5523) metal coordination : bond 0.01442 / 0.75 ( 31) metal coordination : angle 4.21628 / 2.72 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 173 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7222 (tptp) REVERT: A 140 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7782 (mm110) REVERT: A 253 MET cc_start: 0.5249 (tmm) cc_final: 0.4172 (mtm) REVERT: A 282 MET cc_start: 0.6157 (mmp) cc_final: 0.5385 (ppp) REVERT: A 305 MET cc_start: 0.8628 (mmt) cc_final: 0.8394 (mmt) REVERT: A 383 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7438 (pp30) REVERT: A 457 MET cc_start: 0.8243 (mtt) cc_final: 0.7937 (mtt) REVERT: A 550 MET cc_start: 0.7834 (mtt) cc_final: 0.7364 (mtt) REVERT: A 1439 MET cc_start: 0.8676 (ptp) cc_final: 0.8248 (ptp) REVERT: B 245 MET cc_start: 0.7740 (ptm) cc_final: 0.7477 (ptp) REVERT: B 374 MET cc_start: 0.7975 (ptm) cc_final: 0.7717 (tmm) REVERT: B 699 MET cc_start: 0.8986 (tpp) cc_final: 0.8633 (tpp) REVERT: B 702 MET cc_start: 0.8428 (tpp) cc_final: 0.8033 (tpp) REVERT: B 968 MET cc_start: 0.8097 (ttp) cc_final: 0.7882 (ttt) REVERT: B 997 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7469 (pm20) REVERT: C 81 TYR cc_start: 0.7911 (m-80) cc_final: 0.7581 (m-10) REVERT: D 24 ASN cc_start: 0.3788 (t0) cc_final: 0.3522 (t0) REVERT: D 138 HIS cc_start: 0.5688 (m-70) cc_final: 0.5122 (t-90) REVERT: E 34 MET cc_start: 0.7854 (mtp) cc_final: 0.7542 (mmt) REVERT: G 22 MET cc_start: 0.8514 (tpp) cc_final: 0.8185 (mmt) REVERT: G 35 GLU cc_start: 0.4802 (mt-10) cc_final: 0.3786 (tp30) REVERT: K 5 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7407 (t0) REVERT: d 71 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8635 (tp30) REVERT: f 59 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6850 (mmmt) outliers start: 70 outliers final: 40 residues processed: 233 average time/residue: 0.2244 time to fit residues: 90.0926 Evaluate side-chains 206 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 997 GLU Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1186 LYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain b residue 91 LYS Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain e residue 94 GLU Chi-restraints excluded: chain f residue 59 LYS Chi-restraints excluded: chain h residue 65 PHE Chi-restraints excluded: chain h residue 105 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 394 optimal weight: 40.0000 chunk 66 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 399 optimal weight: 50.0000 chunk 40 optimal weight: 4.9990 chunk 427 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 245 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 320 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.075289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.058459 restraints weight = 291067.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.057868 restraints weight = 221795.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.058033 restraints weight = 184003.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.058047 restraints weight = 156604.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.058059 restraints weight = 145963.244| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 44870 Z= 0.158 Angle : 0.598 13.408 61927 Z= 0.318 Chirality : 0.043 0.255 6955 Planarity : 0.004 0.068 6891 Dihedral : 21.923 177.499 8585 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.40 % Favored : 96.58 % Rotamer: Outliers : 1.18 % Allowed : 12.72 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % 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: 0.30 (0.12), residues: 4589 helix: 1.24 (0.12), residues: 1860 sheet: -0.61 (0.20), residues: 631 loop : -0.40 (0.14), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 807 TYR 0.013 0.001 TYR f 72 PHE 0.018 0.001 PHE C 178 TRP 0.013 0.001 TRP C 192 HIS 0.006 0.001 HIS C 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (44839) covalent geometry : angle 0.59140 / 0.32 (61888) hydrogen bonds : bond 0.04352 / 2.90 ( 2043) hydrogen bonds : angle 4.57381 / 3.23 ( 5523) metal coordination : bond 0.00720 / 0.40 ( 31) metal coordination : angle 3.45547 / 2.24 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.4050 (tmm) cc_final: 0.3503 (tmm) REVERT: A 253 MET cc_start: 0.5255 (tmm) cc_final: 0.4179 (mtm) REVERT: A 282 MET cc_start: 0.6167 (mmp) cc_final: 0.5351 (ppp) REVERT: A 305 MET cc_start: 0.8669 (mmt) cc_final: 0.8099 (mmt) REVERT: A 383 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7363 (pp30) REVERT: A 457 MET cc_start: 0.8337 (mtt) cc_final: 0.8003 (mtt) REVERT: A 548 MET cc_start: 0.7913 (mtm) cc_final: 0.7555 (mtp) REVERT: A 550 MET cc_start: 0.7992 (mtt) cc_final: 0.7476 (mtt) REVERT: B 245 MET cc_start: 0.7567 (ptm) cc_final: 0.7341 (ptp) REVERT: B 699 MET cc_start: 0.8893 (tpp) cc_final: 0.8517 (tpp) REVERT: B 702 MET cc_start: 0.8311 (tpp) cc_final: 0.8024 (tpp) REVERT: C 81 TYR cc_start: 0.7895 (m-80) cc_final: 0.7551 (m-10) REVERT: D 17 GLN cc_start: 0.4922 (mm-40) cc_final: 0.4652 (mp10) REVERT: D 24 ASN cc_start: 0.3803 (t0) cc_final: 0.3533 (t0) REVERT: D 138 HIS cc_start: 0.5637 (m-70) cc_final: 0.5148 (t-90) REVERT: E 34 MET cc_start: 0.7771 (mtp) cc_final: 0.7491 (mmt) REVERT: G 22 MET cc_start: 0.8358 (tpp) cc_final: 0.8147 (mmm) REVERT: G 35 GLU cc_start: 0.4721 (mt-10) cc_final: 0.3397 (tp30) REVERT: G 69 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8110 (tm-30) REVERT: I 81 ARG cc_start: 0.4515 (tpt170) cc_final: 0.2778 (tmm160) REVERT: d 62 MET cc_start: 0.7638 (mtp) cc_final: 0.7105 (mmm) REVERT: d 71 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8577 (tp30) REVERT: d 111 VAL cc_start: 0.1981 (OUTLIER) cc_final: 0.1764 (t) REVERT: h 119 THR cc_start: 0.3136 (OUTLIER) cc_final: 0.2858 (m) outliers start: 48 outliers final: 32 residues processed: 211 average time/residue: 0.2253 time to fit residues: 81.7826 Evaluate side-chains 199 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain b residue 91 LYS Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain f residue 59 LYS Chi-restraints excluded: chain h residue 65 PHE Chi-restraints excluded: chain h residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 53 optimal weight: 4.9990 chunk 272 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 211 optimal weight: 0.8980 chunk 444 optimal weight: 9.9990 chunk 380 optimal weight: 7.9990 chunk 265 optimal weight: 10.0000 chunk 210 optimal weight: 0.7980 chunk 390 optimal weight: 50.0000 chunk 409 optimal weight: 50.0000 chunk 394 optimal weight: 40.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.075775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.058785 restraints weight = 288087.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.057559 restraints weight = 210040.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.057820 restraints weight = 186928.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.058014 restraints weight = 143829.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.058033 restraints weight = 130389.192| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 44870 Z= 0.128 Angle : 0.572 17.058 61927 Z= 0.304 Chirality : 0.042 0.259 6955 Planarity : 0.004 0.074 6891 Dihedral : 21.834 177.695 8585 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.99 % Favored : 96.99 % Rotamer: Outliers : 1.08 % Allowed : 12.65 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % 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: 0.58 (0.13), residues: 4589 helix: 1.48 (0.12), residues: 1854 sheet: -0.41 (0.20), residues: 622 loop : -0.28 (0.14), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG f 55 TYR 0.041 0.001 TYR B 931 PHE 0.016 0.001 PHE K 71 TRP 0.014 0.001 TRP A1307 HIS 0.004 0.001 HIS B 932 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (44839) covalent geometry : angle 0.56688 / 0.30 (61888) hydrogen bonds : bond 0.04028 / 2.69 ( 2043) hydrogen bonds : angle 4.41811 / 3.14 ( 5523) metal coordination : bond 0.00481 / 0.28 ( 31) metal coordination : angle 2.97218 / 1.89 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 1.429 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 108 MET cc_start: 0.3924 (tmm) cc_final: 0.3383 (tmm) REVERT: A 122 MET cc_start: 0.5529 (mtt) cc_final: 0.4825 (mtm) REVERT: A 253 MET cc_start: 0.5291 (tmm) cc_final: 0.4199 (mtm) REVERT: A 282 MET cc_start: 0.6144 (mmp) cc_final: 0.5335 (ppp) REVERT: A 305 MET cc_start: 0.8650 (mmt) cc_final: 0.8262 (mmt) REVERT: A 383 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7342 (pp30) REVERT: A 457 MET cc_start: 0.8311 (mtt) cc_final: 0.7963 (mtt) REVERT: A 550 MET cc_start: 0.8008 (mtt) cc_final: 0.7717 (mtt) REVERT: B 245 MET cc_start: 0.7594 (ptm) cc_final: 0.7375 (ptp) REVERT: B 699 MET cc_start: 0.8816 (tpp) cc_final: 0.8469 (tpp) REVERT: C 81 TYR cc_start: 0.7854 (m-80) cc_final: 0.7566 (m-10) REVERT: D 17 GLN cc_start: 0.4944 (mm-40) cc_final: 0.4675 (mp10) REVERT: D 24 ASN cc_start: 0.3663 (t0) cc_final: 0.3404 (t0) REVERT: E 92 MET cc_start: 0.6794 (mmm) cc_final: 0.6533 (mmm) REVERT: G 22 MET cc_start: 0.8391 (tpp) cc_final: 0.8077 (mmm) REVERT: G 35 GLU cc_start: 0.4216 (mt-10) cc_final: 0.3407 (tp30) REVERT: I 81 ARG cc_start: 0.4566 (tpt170) cc_final: 0.2738 (tmm160) REVERT: d 62 MET cc_start: 0.7714 (mtp) cc_final: 0.7221 (mmm) REVERT: d 71 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8586 (tp30) REVERT: d 111 VAL cc_start: 0.2077 (OUTLIER) cc_final: 0.1875 (t) REVERT: e 94 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7930 (pp20) REVERT: h 59 MET cc_start: 0.4751 (tmm) cc_final: 0.2996 (mtt) REVERT: h 119 THR cc_start: 0.3186 (OUTLIER) cc_final: 0.2937 (m) outliers start: 44 outliers final: 33 residues processed: 206 average time/residue: 0.2382 time to fit residues: 83.8911 Evaluate side-chains 200 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1186 LYS Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain b residue 39 ARG Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain e residue 94 GLU Chi-restraints excluded: chain f residue 59 LYS Chi-restraints excluded: chain h residue 65 PHE Chi-restraints excluded: chain h residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 281 optimal weight: 0.8980 chunk 256 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 412 optimal weight: 40.0000 chunk 174 optimal weight: 0.9980 chunk 246 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 360 optimal weight: 7.9990 chunk 480 optimal weight: 20.0000 chunk 460 optimal weight: 40.0000 chunk 285 optimal weight: 20.0000 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 GLN h 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.075552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.058496 restraints weight = 285152.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.057274 restraints weight = 222332.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.057413 restraints weight = 190803.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.057629 restraints weight = 152999.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.057637 restraints weight = 134600.490| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 44870 Z= 0.145 Angle : 0.573 14.668 61927 Z= 0.304 Chirality : 0.041 0.259 6955 Planarity : 0.004 0.071 6891 Dihedral : 21.796 177.104 8585 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.53 % Favored : 96.45 % Rotamer: Outliers : 1.08 % Allowed : 12.97 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % 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: 0.66 (0.13), residues: 4589 helix: 1.55 (0.12), residues: 1856 sheet: -0.35 (0.20), residues: 622 loop : -0.24 (0.14), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1203 TYR 0.026 0.001 TYR e 54 PHE 0.016 0.001 PHE C 178 TRP 0.011 0.001 TRP C 192 HIS 0.004 0.001 HIS A 660 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (44839) covalent geometry : angle 0.56826 / 0.30 (61888) hydrogen bonds : bond 0.04063 / 2.71 ( 2043) hydrogen bonds : angle 4.34799 / 3.09 ( 5523) metal coordination : bond 0.00576 / 0.31 ( 31) metal coordination : angle 2.91657 / 1.80 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 1.600 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 108 MET cc_start: 0.3819 (tmm) cc_final: 0.3341 (tmm) REVERT: A 122 MET cc_start: 0.5520 (mtt) cc_final: 0.4807 (mtm) REVERT: A 253 MET cc_start: 0.5335 (tmm) cc_final: 0.4231 (mtm) REVERT: A 282 MET cc_start: 0.6230 (mmp) cc_final: 0.5413 (ppp) REVERT: A 305 MET cc_start: 0.8647 (mmt) cc_final: 0.8234 (mmt) REVERT: A 383 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7283 (pp30) REVERT: A 457 MET cc_start: 0.8356 (mtt) cc_final: 0.8014 (mtt) REVERT: A 550 MET cc_start: 0.8008 (mtt) cc_final: 0.7751 (mtt) REVERT: A 770 MET cc_start: 0.7928 (tpp) cc_final: 0.7692 (tpp) REVERT: A 1432 MET cc_start: 0.7633 (ptp) cc_final: 0.7382 (ptp) REVERT: B 245 MET cc_start: 0.7597 (ptm) cc_final: 0.7363 (ptp) REVERT: C 81 TYR cc_start: 0.7845 (m-80) cc_final: 0.7521 (m-10) REVERT: D 17 GLN cc_start: 0.4921 (mm-40) cc_final: 0.4663 (mp10) REVERT: D 24 ASN cc_start: 0.3667 (t0) cc_final: 0.3404 (t0) REVERT: E 92 MET cc_start: 0.6988 (mmm) cc_final: 0.6661 (mmm) REVERT: G 35 GLU cc_start: 0.4141 (mt-10) cc_final: 0.3805 (tp30) REVERT: I 81 ARG cc_start: 0.4600 (tpt170) cc_final: 0.2762 (tmm160) REVERT: d 71 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8593 (tp30) REVERT: e 94 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7925 (pp20) REVERT: h 59 MET cc_start: 0.4698 (tmm) cc_final: 0.2974 (mtt) REVERT: h 119 THR cc_start: 0.3162 (OUTLIER) cc_final: 0.2898 (m) outliers start: 44 outliers final: 34 residues processed: 201 average time/residue: 0.2200 time to fit residues: 76.5557 Evaluate side-chains 200 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1186 LYS Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain b residue 39 ARG Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain e residue 94 GLU Chi-restraints excluded: chain f residue 59 LYS Chi-restraints excluded: chain h residue 65 PHE Chi-restraints excluded: chain h residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 486 optimal weight: 4.9990 chunk 283 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 317 optimal weight: 5.9990 chunk 482 optimal weight: 10.0000 chunk 452 optimal weight: 20.0000 chunk 251 optimal weight: 4.9990 chunk 272 optimal weight: 8.9990 chunk 400 optimal weight: 50.0000 chunk 44 optimal weight: 2.9990 chunk 190 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 GLN ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.075119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.057819 restraints weight = 286453.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.057294 restraints weight = 196486.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.057404 restraints weight = 181246.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.057541 restraints weight = 144374.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.057586 restraints weight = 132261.705| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 44870 Z= 0.183 Angle : 0.608 14.832 61927 Z= 0.320 Chirality : 0.042 0.261 6955 Planarity : 0.004 0.073 6891 Dihedral : 21.844 176.595 8585 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.68 % Favored : 96.30 % Rotamer: Outliers : 1.21 % Allowed : 13.12 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % 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: 0.56 (0.13), residues: 4589 helix: 1.47 (0.12), residues: 1862 sheet: -0.43 (0.20), residues: 625 loop : -0.30 (0.14), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1203 TYR 0.024 0.002 TYR B 931 PHE 0.024 0.002 PHE C 178 TRP 0.019 0.001 TRP A1307 HIS 0.004 0.001 HIS A 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (44839) covalent geometry : angle 0.60318 / 0.32 (61888) hydrogen bonds : bond 0.04338 / 2.89 ( 2043) hydrogen bonds : angle 4.40561 / 3.14 ( 5523) metal coordination : bond 0.00717 / 0.39 ( 31) metal coordination : angle 3.08883 / 2.00 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.3965 (tmm) cc_final: 0.3500 (tmm) REVERT: A 122 MET cc_start: 0.5556 (mtt) cc_final: 0.4832 (mtm) REVERT: A 132 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7272 (tptp) REVERT: A 253 MET cc_start: 0.5396 (tmm) cc_final: 0.4197 (mtm) REVERT: A 282 MET cc_start: 0.6112 (mmp) cc_final: 0.5395 (ppp) REVERT: A 305 MET cc_start: 0.8675 (mmt) cc_final: 0.8312 (mmt) REVERT: A 383 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7328 (pp30) REVERT: A 457 MET cc_start: 0.8392 (mtt) cc_final: 0.8048 (mtt) REVERT: A 550 MET cc_start: 0.8051 (mtt) cc_final: 0.7843 (mtt) REVERT: A 770 MET cc_start: 0.7942 (tpp) cc_final: 0.7682 (tpp) REVERT: A 1432 MET cc_start: 0.7667 (ptp) cc_final: 0.7390 (ptp) REVERT: B 245 MET cc_start: 0.7425 (ptm) cc_final: 0.7136 (ptp) REVERT: D 24 ASN cc_start: 0.3644 (t0) cc_final: 0.3332 (t0) REVERT: D 138 HIS cc_start: 0.5553 (m-70) cc_final: 0.5025 (t-90) REVERT: E 92 MET cc_start: 0.7184 (mmm) cc_final: 0.6760 (mmm) REVERT: G 22 MET cc_start: 0.8346 (tpp) cc_final: 0.7720 (mmm) REVERT: G 35 GLU cc_start: 0.4136 (mt-10) cc_final: 0.3848 (tp30) REVERT: I 81 ARG cc_start: 0.5008 (tpt170) cc_final: 0.2982 (tmm160) REVERT: L 66 MET cc_start: 0.7044 (tpp) cc_final: 0.6749 (tpt) REVERT: d 62 MET cc_start: 0.7584 (mtp) cc_final: 0.7166 (mmm) REVERT: d 71 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8538 (tp30) REVERT: d 111 VAL cc_start: 0.2185 (OUTLIER) cc_final: 0.1978 (t) REVERT: h 119 THR cc_start: 0.3163 (OUTLIER) cc_final: 0.2868 (m) outliers start: 49 outliers final: 35 residues processed: 206 average time/residue: 0.2236 time to fit residues: 79.3549 Evaluate side-chains 202 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 1186 LYS Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain b residue 39 ARG Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain e residue 94 GLU Chi-restraints excluded: chain f residue 59 LYS Chi-restraints excluded: chain h residue 65 PHE Chi-restraints excluded: chain h residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 183 optimal weight: 10.0000 chunk 361 optimal weight: 0.0060 chunk 350 optimal weight: 0.5980 chunk 482 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 360 optimal weight: 9.9990 chunk 346 optimal weight: 10.0000 chunk 321 optimal weight: 0.9980 chunk 353 optimal weight: 0.3980 chunk 431 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 GLN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.075842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.058768 restraints weight = 287607.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.057649 restraints weight = 223713.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.057840 restraints weight = 180604.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.058067 restraints weight = 146169.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.058135 restraints weight = 130109.438| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 44870 Z= 0.114 Angle : 0.554 15.472 61927 Z= 0.295 Chirality : 0.041 0.331 6955 Planarity : 0.004 0.072 6891 Dihedral : 21.783 177.292 8585 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.96 % Favored : 97.01 % Rotamer: Outliers : 0.84 % Allowed : 13.66 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.49 % Cis-general : 0.02 % 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: 0.81 (0.13), residues: 4589 helix: 1.71 (0.12), residues: 1856 sheet: -0.27 (0.20), residues: 637 loop : -0.20 (0.14), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1203 TYR 0.024 0.001 TYR B 931 PHE 0.024 0.001 PHE J 8 TRP 0.013 0.001 TRP A1307 HIS 0.003 0.001 HIS A 895 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (44839) covalent geometry : angle 0.55007 / 0.29 (61888) hydrogen bonds : bond 0.03723 / 2.48 ( 2043) hydrogen bonds : angle 4.20945 / 3.00 ( 5523) metal coordination : bond 0.00356 / 0.21 ( 31) metal coordination : angle 2.82987 / 1.80 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6030.73 seconds wall clock time: 105 minutes 43.56 seconds (6343.56 seconds total)