Starting phenix.real_space_refine on Tue Sep 15 22:45:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ir9_9713/09_2026/6ir9_9713.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ir9_9713/09_2026/6ir9_9713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ir9_9713/09_2026/6ir9_9713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ir9_9713/09_2026/6ir9_9713.map" model { file = "/net/cci-nas-00/data/ceres_data/6ir9_9713/09_2026/6ir9_9713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ir9_9713/09_2026/6ir9_9713.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ir9_9713/09_2026/6ir9_9713.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ir9_9713/09_2026/6ir9_9713.cif" } resolution = 3.8 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= 0.003 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 10 6.06 5 P 266 5.49 5 Mg 1 5.21 5 S 214 5.16 5 C 28292 2.51 5 N 8212 2.21 5 O 9236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.21s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 46231 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 11123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1412, 11123 Classifications: {'peptide': 1412} Link IDs: {'PCIS': 3, 'PTRANS': 65, 'TRANS': 1343} Chain breaks: 5 Chain: "B" Number of atoms: 9228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1157, 9228 Classifications: {'peptide': 1157} Link IDs: {'PTRANS': 52, 'TRANS': 1104} 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: "P" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 341 Classifications: {'RNAv2': 16} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 5, 'rna3p_pyr': 9} Link IDs: {'rna2p': 2, 'rna3p': 13} Chain: "T" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2610 Classifications: {'DNA': 128} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 127} Chain: "N" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2527 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain breaks: 1 Chain: "M" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 505 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "V" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 792 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "W" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2226 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 4 Chain: "a" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 797 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "b" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "c" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 796 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "d" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "e" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} 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: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "h" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} 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} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" 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 73.622 61.614 137.424 1.00103.22 S ATOM 549 SG CYS A 70 77.089 60.752 138.399 1.00 94.73 S ATOM 594 SG CYS A 77 75.940 64.332 138.881 1.00 74.48 S ATOM 829 SG CYS A 107 78.544 83.381 94.410 1.00142.68 S ATOM 851 SG CYS A 110 79.933 80.030 93.777 1.00152.38 S ATOM 1229 SG CYS A 168 76.676 83.350 91.366 1.00155.44 S ATOM 19883 SG CYS B1163 87.532 61.334 124.895 1.00 76.06 S ATOM 19901 SG CYS B1166 85.696 64.686 123.711 1.00 77.90 S ATOM 20024 SG CYS B1182 83.729 61.187 124.841 1.00108.37 S ATOM 20047 SG CYS B1185 85.974 61.412 121.521 1.00109.59 S ATOM 20992 SG CYS C 85 85.222 77.309 204.161 1.00126.06 S ATOM 21040 SG CYS C 91 80.940 78.189 205.841 1.00108.11 S ATOM 21063 SG CYS C 94 82.478 80.560 202.346 1.00108.09 S ATOM 29171 SG CYS I 78 81.605 167.362 141.310 1.00173.59 S ATOM 29387 SG CYS I 103 81.862 163.727 140.808 1.00166.64 S ATOM 28787 SG CYS I 29 64.050 146.258 100.577 1.00154.71 S ATOM 28812 SG CYS I 32 61.079 148.528 98.884 1.00153.57 S ATOM 29528 SG CYS J 7 86.897 110.737 191.155 1.00 34.60 S ATOM 29551 SG CYS J 10 89.335 110.192 193.835 1.00 33.65 S ATOM 29827 SG CYS J 44 90.298 113.049 191.894 1.00 40.97 S ATOM 29833 SG CYS J 45 87.469 113.026 194.784 1.00 40.49 S ATOM 30995 SG CYS L 33 46.163 95.520 179.886 1.00114.61 S ATOM 31010 SG CYS L 36 44.093 95.899 183.064 1.00124.33 S ATOM 31120 SG CYS L 50 43.546 93.103 180.047 1.00122.63 S ATOM 31144 SG CYS L 53 43.068 97.088 178.900 1.00130.70 S ATOM 36879 SG CYS M 25 52.091 107.333 94.874 1.00198.31 S ATOM 36904 SG CYS M 28 52.062 103.870 94.583 1.00168.76 S ATOM 37062 SG CYS M 49 55.179 105.167 93.723 1.00180.55 S ATOM 37086 SG CYS M 52 52.443 105.565 91.212 1.00191.36 S ATOM 37323 SG CYS V 12 20.851 82.075 115.633 1.00 34.75 S ATOM 37345 SG CYS V 15 21.936 84.905 113.298 1.00 22.76 S ATOM 37447 SG CYS V 29 19.147 85.610 115.248 1.00 18.00 S ATOM 37468 SG CYS V 32 18.769 82.986 112.410 1.00 25.35 S Time building chain proxies: 8.26, per 1000 atoms: 0.18 Number of scatterers: 46231 At special positions: 0 Unit cell: (174.33, 178.8, 229.46, 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 10 29.99 S 214 16.00 P 266 15.00 Mg 1 11.99 O 9236 8.00 N 8212 7.00 C 28292 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: 3.34 Conformation dependent library (CDL) restraints added in 1.8 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 77 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 168 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 91 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 85 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 78 " pdb=" ZN I 202 " 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 7 " 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 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 50 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 53 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 33 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 52 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 25 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 49 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 28 " pdb=" ZN V 300 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 12 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 15 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 29 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 32 " Number of angles added : 33 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9588 Finding SS restraints... Secondary structure from input PDB file: 201 helices and 59 sheets defined 43.1% alpha, 17.3% beta 111 base pairs and 207 stacking pairs defined. Time for finding SS restraints: 5.51 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 removed outlier: 3.654A pdb=" N GLU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.560A pdb=" N VAL A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 223 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 279 removed outlier: 3.510A pdb=" N GLN A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 removed outlier: 3.622A pdb=" N MET A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 removed outlier: 3.585A pdb=" N LEU A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 385 through 396 removed outlier: 3.608A pdb=" N GLU A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 425 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: 3.718A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 506 removed outlier: 3.502A pdb=" N ALA A 500 " --> pdb=" O GLU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 525 through 536 removed outlier: 3.520A pdb=" N LYS A 534 " --> pdb=" O CYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.947A pdb=" N ASN A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.959A pdb=" N ALA A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 583 " --> pdb=" O LEU A 579 " (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: 3.753A pdb=" N PHE A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.711A 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 removed outlier: 3.582A pdb=" N LYS A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 738 removed outlier: 3.683A 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 removed outlier: 3.590A pdb=" N ILE A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 798 Processing helix chain 'A' and resid 810 through 847 removed outlier: 4.737A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 3.770A 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 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 904 through 908 Processing helix chain 'A' and resid 910 through 914 removed outlier: 3.627A pdb=" N VAL A 913 " --> pdb=" O LYS A 910 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 914 " --> pdb=" O PRO A 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 910 through 914' Processing helix chain 'A' and resid 923 through 947 removed outlier: 3.992A pdb=" N GLU A 929 " --> pdb=" O GLU A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 973 Processing helix chain 'A' and resid 984 through 996 Processing helix chain 'A' and resid 1006 through 1017 removed outlier: 3.633A pdb=" N THR A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1028 Processing helix chain 'A' and resid 1029 through 1035 Processing helix chain 'A' and resid 1040 through 1058 removed outlier: 3.602A pdb=" N GLN A1056 " --> pdb=" O GLU A1052 " (cutoff:3.500A) 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: 3.594A pdb=" N ARG A1102 " --> pdb=" O LEU A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 Processing helix chain 'A' and resid 1129 through 1141 Processing helix chain 'A' and resid 1145 through 1148 No H-bonds generated for 'chain 'A' and resid 1145 through 1148' Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 3.546A pdb=" N ALA A1174 " --> pdb=" O ASP A1170 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A1177 " --> pdb=" O GLU A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1207 Processing helix chain 'A' and resid 1210 through 1223 removed outlier: 3.726A pdb=" N VAL A1221 " --> pdb=" O LYS A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1272 removed outlier: 3.897A pdb=" N LYS A1264 " --> pdb=" O ASP A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1321 removed outlier: 3.630A pdb=" N ALA A1321 " --> pdb=" O ALA A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1343 removed outlier: 3.566A pdb=" N SER A1340 " --> pdb=" O VAL A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1362 removed outlier: 3.582A pdb=" N SER A1349 " --> pdb=" O GLU A1345 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASP A1362 " --> pdb=" O VAL A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1380 removed outlier: 4.107A 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 1404 Processing helix chain 'A' and resid 1407 through 1418 Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.664A 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 1449 through 1454 removed outlier: 3.699A pdb=" N THR A1454 " --> pdb=" O GLU A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1456 No H-bonds generated for 'chain 'A' and resid 1455 through 1456' Processing helix chain 'A' and resid 1457 through 1461 removed outlier: 3.590A pdb=" N TYR A1460 " --> pdb=" O PRO A1457 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 29 Processing helix chain 'B' and resid 31 through 44 removed outlier: 3.714A pdb=" N SER B 37 " --> pdb=" O GLN B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 176 through 183 removed outlier: 3.603A pdb=" N LEU B 180 " --> pdb=" O ASP B 176 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 280 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 299 through 312 Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 318 through 328 Processing helix chain 'B' and resid 337 through 351 removed outlier: 3.642A pdb=" N ILE B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLN B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 383 removed outlier: 4.263A 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 429 removed outlier: 3.907A pdb=" N ARG B 427 " --> pdb=" O ARG B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 457 Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 480 through 489 removed outlier: 3.562A pdb=" N ARG B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 544 through 554 Processing helix chain 'B' and resid 558 through 562 removed outlier: 3.690A pdb=" N TYR B 562 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 600 removed outlier: 3.851A pdb=" N LEU B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER B 591 " --> pdb=" O SER B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 Processing helix chain 'B' and resid 677 through 683 removed outlier: 3.637A pdb=" N LEU B 681 " --> pdb=" O GLY B 677 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 682 " --> pdb=" O TRP B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.699A 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 GLN B 708 " --> pdb=" O GLU B 705 " (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: 3.909A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 768 " --> pdb=" O SER B 764 " (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 806 through 811 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1013 through 1017 Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.918A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.508A pdb=" N LEU B1058 " --> pdb=" O ALA B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1121 through 1125 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1151 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 removed outlier: 3.741A pdb=" N LEU C 68 " --> pdb=" O HIS C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'C' and resid 81 through 85 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 196 through 201 Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.695A pdb=" N GLU C 210 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 removed outlier: 3.504A pdb=" N GLU C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 72 removed outlier: 3.579A pdb=" N LEU D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) 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 removed outlier: 3.523A pdb=" N VAL D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 138 through 148 removed outlier: 3.506A pdb=" N ILE D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 160 removed outlier: 3.772A pdb=" N THR D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 167 removed outlier: 3.914A pdb=" N ALA D 164 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA D 165 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS D 166 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS D 167 " --> pdb=" O ALA D 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 161 through 167' Processing helix chain 'D' and resid 170 through 182 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 37 through 46 Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 64 through 71 Processing helix chain 'E' and resid 88 through 102 removed outlier: 3.506A pdb=" N ARG E 93 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 127 removed outlier: 3.723A pdb=" N ILE E 123 " --> pdb=" O ASN E 120 " (cutoff:3.500A) Proline residue: E 124 - end of helix removed outlier: 4.167A pdb=" N SER E 127 " --> pdb=" O PRO E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 156 through 168 Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.507A pdb=" N LEU E 174 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.596A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 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: 3.510A 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: 3.623A 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 61 through 65 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: 3.931A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.938A pdb=" N ARG J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.953A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 removed outlier: 3.616A pdb=" N ILE K 111 " --> pdb=" O GLU K 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 78 removed outlier: 3.656A pdb=" N ILE M 69 " --> pdb=" O GLN M 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 20 through 27 removed outlier: 3.725A pdb=" N PHE V 24 " --> pdb=" O PRO V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 32 through 37 Processing helix chain 'V' and resid 42 through 49 Processing helix chain 'V' and resid 66 through 72 Processing helix chain 'V' and resid 91 through 101 Processing helix chain 'W' and resid 213 through 218 removed outlier: 3.885A pdb=" N ILE W 218 " --> pdb=" O ARG W 215 " (cutoff:3.500A) Processing helix chain 'W' and resid 235 through 251 Processing helix chain 'W' and resid 278 through 287 removed outlier: 3.804A pdb=" N ILE W 282 " --> pdb=" O LYS W 278 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 304 No H-bonds generated for 'chain 'W' and resid 302 through 304' Processing helix chain 'W' and resid 305 through 310 removed outlier: 3.618A pdb=" N LEU W 309 " --> pdb=" O GLU W 305 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU W 310 " --> pdb=" O TYR W 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 305 through 310' Processing helix chain 'W' and resid 395 through 403 Processing helix chain 'W' and resid 443 through 450 Processing helix chain 'a' and resid 44 through 57 removed outlier: 3.816A pdb=" N LEU a 48 " --> pdb=" O GLY a 44 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 76 removed outlier: 3.976A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 removed outlier: 3.737A pdb=" N ILE a 89 " --> pdb=" O GLN a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 131 removed outlier: 3.853A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 29 Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 50 through 77 Processing helix chain 'b' and resid 82 through 94 Processing helix chain 'c' and resid 17 through 21 Processing helix chain 'c' and resid 26 through 36 removed outlier: 3.606A pdb=" N VAL c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 46 through 74 Processing helix chain 'c' and resid 79 through 90 removed outlier: 3.727A pdb=" N LEU c 83 " --> pdb=" O ILE c 79 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP c 90 " --> pdb=" O ALA c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'c' and resid 112 through 116 Processing helix chain 'd' and resid 34 through 46 Processing helix chain 'd' and resid 52 through 80 Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.667A pdb=" N ILE d 91 " --> pdb=" O THR d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 121 removed outlier: 3.901A pdb=" N ALA d 121 " --> pdb=" O LYS d 117 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 55 Processing helix chain 'e' and resid 63 through 76 removed outlier: 3.826A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 132 removed outlier: 3.651A pdb=" N ILE e 124 " --> pdb=" O MET e 120 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 42 Processing helix chain 'f' and resid 49 through 77 Processing helix chain 'f' and resid 82 through 93 Processing helix chain 'g' and resid 16 through 22 Processing helix chain 'g' and resid 26 through 36 removed outlier: 3.566A pdb=" N VAL g 30 " --> pdb=" O PRO g 26 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 72 removed outlier: 4.467A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU g 65 " --> pdb=" O GLU g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 90 Processing helix chain 'g' and resid 91 through 97 Processing helix chain 'h' and resid 34 through 46 Processing helix chain 'h' and resid 52 through 82 Processing helix chain 'h' and resid 87 through 99 removed outlier: 3.711A pdb=" N ILE h 91 " --> pdb=" O THR h 87 " (cutoff:3.500A) Processing helix chain 'h' and resid 100 through 121 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: 6.892A pdb=" N THR A 238 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.888A pdb=" N LYS A 88 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 10.402A pdb=" N ILE A 236 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 178 removed outlier: 3.763A pdb=" N GLY A 184 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 201 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TRP A 186 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU A 199 " --> pdb=" O TRP A 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 252 removed outlier: 3.588A pdb=" N ILE A 251 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.760A 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: 3.560A pdb=" N SER A 349 " --> pdb=" O ARG B1106 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 352 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL A 365 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET A 464 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL A 367 " --> pdb=" O MET A 464 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.834A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N HIS A 436 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA A 403 " --> pdb=" O HIS A 436 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 406 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 513 through 514 removed outlier: 3.756A pdb=" N LYS A 519 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AB1, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.467A pdb=" N VAL H 95 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE H 29 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE H 27 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LYS H 112 " --> pdb=" O PHE H 103 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE H 103 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR H 114 " --> pdb=" O TYR H 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 589 through 591 removed outlier: 7.037A pdb=" N LEU A 607 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 767 through 768 Processing sheet with id=AB4, first strand: chain 'A' and resid 850 through 851 removed outlier: 6.837A pdb=" N THR A 857 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 879 through 883 Processing sheet with id=AB6, first strand: chain 'A' and resid 1284 through 1295 removed outlier: 4.195A pdb=" N LYS A1284 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A1118 " --> pdb=" O THR A1311 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1143 through 1144 removed outlier: 7.228A pdb=" N THR A1143 " --> pdb=" O LEU A1276 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1226 through 1230 removed outlier: 3.582A pdb=" N ARG A1243 " --> pdb=" O PHE A1227 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU A1238 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL A1244 " --> pdb=" O TRP A1193 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TRP A1193 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N SER A1150 " --> pdb=" O GLU I 47 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU I 47 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR A1152 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARG I 45 " --> pdb=" O THR A1152 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE A1154 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1444 through 1448 Processing sheet with id=AC1, first strand: chain 'B' and resid 55 through 57 removed outlier: 5.189A pdb=" N ASP B 118 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE B 82 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TYR B 116 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU B 84 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY B 159 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU B 117 " --> pdb=" O HIS B 157 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N HIS B 157 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AC3, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC4, first strand: chain 'B' and resid 397 through 400 removed outlier: 3.513A pdb=" N ALA B 205 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 215 through 218 removed outlier: 4.037A pdb=" N HIS B 227 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 243 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 246 " --> pdb=" O THR B 264 " (cutoff:3.500A) 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 537 through 538 Processing sheet with id=AC8, first strand: chain 'B' and resid 578 through 583 removed outlier: 5.767A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.880A pdb=" N PHE B 963 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.880A pdb=" N PHE B 963 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL B 952 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE L 40 " --> pdb=" O TYR L 31 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD3, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.047A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 873 through 874 removed outlier: 3.555A pdb=" N ASP B 936 " --> pdb=" O LEU B 883 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.823A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD7, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AD8, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD9, first strand: chain 'C' and resid 6 through 12 removed outlier: 6.870A pdb=" N GLU C 18 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ALA C 12 " --> pdb=" O GLU C 16 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 233 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.926A pdb=" N GLU C 152 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN C 154 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LYS C 160 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY C 162 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU C 43 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE L 67 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.778A pdb=" N GLU C 131 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.553A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 4 through 6 removed outlier: 4.643A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILE G 45 " --> pdb=" O TRP G 79 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 50 through 51 removed outlier: 4.522A pdb=" N PHE G 2 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AE7, first strand: chain 'E' and resid 27 through 28 removed outlier: 4.228A pdb=" N ASN E 62 " --> pdb=" O PHE E 28 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 86 through 87 removed outlier: 3.638A pdb=" N VAL E 87 " --> pdb=" O ASN E 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'E' and resid 152 through 154 Processing sheet with id=AF1, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.865A pdb=" N VAL G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER G 162 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ASN G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLY G 161 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU G 106 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE G 100 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE G 90 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL G 143 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 120 through 122 removed outlier: 4.483A pdb=" N VAL G 120 " --> pdb=" O MET G 131 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET G 131 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF4, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.524A pdb=" N SER I 71 " --> pdb=" O CYS I 83 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N CYS I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF6, first strand: chain 'M' and resid 17 through 20 Processing sheet with id=AF7, first strand: chain 'V' and resid 18 through 19 Processing sheet with id=AF8, first strand: chain 'V' and resid 80 through 86 removed outlier: 7.010A pdb=" N GLY V 56 " --> pdb=" O VAL V 84 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL V 86 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE V 54 " --> pdb=" O VAL V 86 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU V 57 " --> pdb=" O GLN W 264 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER W 261 " --> pdb=" O GLU W 275 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 407 through 410 removed outlier: 6.542A pdb=" N PHE W 413 " --> pdb=" O ASP W 409 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU W 420 " --> pdb=" O TYR W 427 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS W 353 " --> pdb=" O VAL W 340 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL W 340 " --> pdb=" O LYS W 353 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 788 through 792 removed outlier: 6.692A pdb=" N ARG W 779 " --> pdb=" O LYS W 771 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THR W 755 " --> pdb=" O GLU W 799 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.673A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AG4, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.670A pdb=" N ARG g 42 " --> pdb=" O ILE h 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'g' and resid 77 through 78 1857 hydrogen bonds defined for protein. 5145 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 281 hydrogen bonds 558 hydrogen bond angles 0 basepair planarities 111 basepair parallelities 207 stacking parallelities Total time for adding SS restraints: 14.57 Time building geometry restraints manager: 4.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11178 1.33 - 1.45: 10728 1.45 - 1.57: 24825 1.57 - 1.70: 531 1.70 - 1.82: 342 Bond restraints: 47604 Sorted by residual: bond pdb=" C PHE e 84 " pdb=" N GLN e 85 " ideal model delta sigma weight residual 1.331 1.532 -0.201 1.33e-02 5.65e+03 2.29e+02 bond pdb=" C1' DA T 17 " pdb=" N9 DA T 17 " ideal model delta sigma weight residual 1.468 1.349 0.119 1.40e-02 5.10e+03 7.24e+01 bond pdb=" C CYS V 29 " pdb=" N PRO V 30 " ideal model delta sigma weight residual 1.335 1.432 -0.098 1.19e-02 7.06e+03 6.72e+01 bond pdb=" C1' DA N -15 " pdb=" N9 DA N -15 " ideal model delta sigma weight residual 1.468 1.358 0.110 1.40e-02 5.10e+03 6.17e+01 bond pdb=" CA ILE W 440 " pdb=" C ILE W 440 " ideal model delta sigma weight residual 1.521 1.432 0.089 1.21e-02 6.83e+03 5.47e+01 ... (remaining 47599 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.98: 64494 3.98 - 7.97: 839 7.97 - 11.95: 69 11.95 - 15.94: 8 15.94 - 19.92: 2 Bond angle restraints: 65412 Sorted by residual: angle pdb=" N GLN B 63 " pdb=" CA GLN B 63 " pdb=" C GLN B 63 " ideal model delta sigma weight residual 108.26 92.28 15.98 1.66e+00 3.63e-01 9.26e+01 angle pdb=" CA PRO W 389 " pdb=" N PRO W 389 " pdb=" CD PRO W 389 " ideal model delta sigma weight residual 112.00 99.50 12.50 1.40e+00 5.10e-01 7.97e+01 angle pdb=" N GLN B 63 " pdb=" CA GLN B 63 " pdb=" CB GLN B 63 " ideal model delta sigma weight residual 110.77 96.75 14.02 1.63e+00 3.76e-01 7.40e+01 angle pdb=" O CYS V 29 " pdb=" C CYS V 29 " pdb=" N PRO V 30 " ideal model delta sigma weight residual 121.31 114.30 7.01 8.50e-01 1.38e+00 6.80e+01 angle pdb=" C ARG W 388 " pdb=" N PRO W 389 " pdb=" CA PRO W 389 " ideal model delta sigma weight residual 119.84 128.76 -8.92 1.25e+00 6.40e-01 5.09e+01 ... (remaining 65407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 26783 34.98 - 69.95: 1488 69.95 - 104.93: 60 104.93 - 139.90: 4 139.90 - 174.88: 2 Dihedral angle restraints: 28337 sinusoidal: 13494 harmonic: 14843 Sorted by residual: dihedral pdb=" C4' G P 0 " pdb=" C3' G P 0 " pdb=" C2' G P 0 " pdb=" C1' G P 0 " ideal model delta sinusoidal sigma weight residual 36.34 -36.70 73.05 1 3.10e+00 1.04e-01 7.08e+02 dihedral pdb=" C4' G P -5 " pdb=" C3' G P -5 " pdb=" C2' G P -5 " pdb=" C1' G P -5 " ideal model delta sinusoidal sigma weight residual 36.35 -36.16 72.51 1 3.10e+00 1.04e-01 6.99e+02 dihedral pdb=" O4' G P -5 " pdb=" C4' G P -5 " pdb=" C3' G P -5 " pdb=" C2' G P -5 " ideal model delta sinusoidal sigma weight residual -35.15 27.75 -62.89 1 4.00e+00 6.25e-02 3.27e+02 ... (remaining 28334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 6881 0.131 - 0.261: 436 0.261 - 0.392: 15 0.392 - 0.523: 2 0.523 - 0.654: 2 Chirality restraints: 7336 Sorted by residual: chirality pdb=" CA GLN B 63 " pdb=" N GLN B 63 " pdb=" C GLN B 63 " pdb=" CB GLN B 63 " both_signs ideal model delta sigma weight residual False 2.51 3.16 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CB ILE B 336 " pdb=" CA ILE B 336 " pdb=" CG1 ILE B 336 " pdb=" CG2 ILE B 336 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.68e+00 chirality pdb=" CA TYR B 811 " pdb=" N TYR B 811 " pdb=" C TYR B 811 " pdb=" CB TYR B 811 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.54e+00 ... (remaining 7333 not shown) Planarity restraints: 7519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 336 " -0.030 2.00e-02 2.50e+03 6.07e-02 3.68e+01 pdb=" C ILE B 336 " 0.105 2.00e-02 2.50e+03 pdb=" O ILE B 336 " -0.039 2.00e-02 2.50e+03 pdb=" N ARG B 337 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 89 " -0.019 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C ASP C 89 " 0.064 2.00e-02 2.50e+03 pdb=" O ASP C 89 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR C 90 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 88 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C GLU C 88 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU C 88 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP C 89 " -0.022 2.00e-02 2.50e+03 ... (remaining 7516 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 671 2.64 - 3.20: 39278 3.20 - 3.77: 72403 3.77 - 4.33: 99235 4.33 - 4.90: 155469 Nonbonded interactions: 367056 Sorted by model distance: nonbonded pdb=" NH1 ARG V 85 " pdb=" OD1 ASP V 87 " model vdw 2.071 3.120 nonbonded pdb=" OE1 GLN M 57 " pdb=" N ASP e 81 " model vdw 2.073 3.120 nonbonded pdb=" O SER M 55 " pdb=" CG LYS f 79 " model vdw 2.074 3.440 nonbonded pdb=" CD1 LEU M 46 " pdb=" OD1 ASP e 81 " model vdw 2.113 3.460 nonbonded pdb=" O2 DC T 18 " pdb=" N2 DG N -18 " model vdw 2.122 3.120 ... (remaining 367051 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 39 through 134) selection = (chain 'e' and resid 39 through 134) } ncs_group { reference = (chain 'b' and resid 25 through 102) selection = chain 'f' } ncs_group { reference = chain 'c' selection = (chain 'g' and resid 16 through 118) } ncs_group { reference = (chain 'd' and resid 31 through 121) 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 50.750 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.110 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 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 : 0.012 0.662 47638 Z= 0.619 Angle : 1.274 27.612 65445 Z= 0.776 Chirality : 0.070 0.654 7336 Planarity : 0.007 0.064 7519 Dihedral : 17.860 174.876 18749 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.30 % Favored : 95.04 % Rotamer: Outliers : 0.74 % Allowed : 3.11 % Favored : 96.15 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.45 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.10), residues: 5043 helix: -1.29 (0.10), residues: 1856 sheet: -0.75 (0.18), residues: 716 loop : -0.96 (0.12), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 62 TYR 0.049 0.004 TYR d 80 PHE 0.052 0.004 PHE A1176 TRP 0.038 0.004 TRP G 79 HIS 0.014 0.003 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00949 / 0.57 (47604) covalent geometry : angle 1.23595 / 0.77 (65412) hydrogen bonds : bond 0.23043 / 15.34 ( 2107) hydrogen bonds : angle 7.32610 / 5.25 ( 5703) metal coordination : bond 0.26251 / 17.17 ( 34) metal coordination : angle 13.81170 / 8.97 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 4467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 810 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ASP cc_start: 0.8462 (t0) cc_final: 0.7824 (t0) REVERT: A 450 SER cc_start: 0.8604 (m) cc_final: 0.8085 (p) REVERT: B 472 VAL cc_start: 0.8999 (t) cc_final: 0.8681 (p) REVERT: B 702 MET cc_start: 0.8421 (tpp) cc_final: 0.7975 (tpp) REVERT: B 1082 MET cc_start: 0.7806 (tpp) cc_final: 0.7560 (tpp) REVERT: B 1136 ASP cc_start: 0.7216 (m-30) cc_final: 0.6703 (m-30) REVERT: C 157 CYS cc_start: 0.7377 (m) cc_final: 0.7120 (m) REVERT: D 170 ASN cc_start: 0.5565 (t0) cc_final: 0.5152 (t0) REVERT: G 29 LYS cc_start: 0.9361 (tptt) cc_final: 0.8923 (tttt) REVERT: G 52 MET cc_start: 0.7425 (mmp) cc_final: 0.6693 (pmm) REVERT: I 68 LEU cc_start: 0.8771 (mt) cc_final: 0.8510 (mm) REVERT: K 6 ARG cc_start: 0.8589 (mmm-85) cc_final: 0.7700 (mmm-85) REVERT: K 31 ILE cc_start: 0.8230 (pt) cc_final: 0.7818 (pt) REVERT: K 33 ILE cc_start: 0.8927 (mp) cc_final: 0.8696 (mp) REVERT: M 31 ASP cc_start: 0.6959 (p0) cc_final: 0.6720 (t0) REVERT: V 107 PRO cc_start: 0.0917 (Cg_exo) cc_final: 0.0477 (Cg_endo) REVERT: W 788 THR cc_start: 0.8449 (m) cc_final: 0.7890 (t) REVERT: W 802 HIS cc_start: 0.7407 (t70) cc_final: 0.6970 (p-80) REVERT: W 804 TRP cc_start: 0.6124 (m100) cc_final: 0.5357 (m100) outliers start: 33 outliers final: 4 residues processed: 838 average time/residue: 0.2990 time to fit residues: 402.2988 Evaluate side-chains 381 residues out of total 4467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 377 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain W residue 343 VAL Chi-restraints excluded: chain b residue 72 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 394 optimal weight: 50.0000 chunk 430 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 265 optimal weight: 5.9990 chunk 523 optimal weight: 8.9990 chunk 497 optimal weight: 40.0000 chunk 414 optimal weight: 30.0000 chunk 310 optimal weight: 10.0000 chunk 488 optimal weight: 10.0000 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN A 446 ASN ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 HIS A 971 GLN A1072 GLN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1435 GLN B 227 HIS ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 ASN ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS B 996 HIS C 8 ASN C 13 GLN ** C 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 ASN E 112 GLN E 145 HIS F 100 GLN G 122 ASN H 13 GLN I 12 ASN M 32 ASN M 65 GLN W 330 ASN W 339 GLN W 434 ASN c 38 ASN c 73 ASN d 64 ASN f 93 GLN ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.105055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.071934 restraints weight = 206096.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.071914 restraints weight = 111747.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.072776 restraints weight = 81450.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.072700 restraints weight = 55169.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.072833 restraints weight = 57031.155| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 47638 Z= 0.302 Angle : 0.886 21.598 65445 Z= 0.456 Chirality : 0.054 0.820 7336 Planarity : 0.006 0.063 7519 Dihedral : 21.931 175.032 8533 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.86 % Favored : 96.91 % Rotamer: Outliers : 1.99 % Allowed : 9.31 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.42 (0.11), residues: 5043 helix: 0.26 (0.11), residues: 1895 sheet: -0.43 (0.18), residues: 713 loop : -0.55 (0.12), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG V 73 TYR 0.026 0.002 TYR C 90 PHE 0.042 0.002 PHE J 59 TRP 0.019 0.003 TRP V 67 HIS 0.020 0.002 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.30 (47604) covalent geometry : angle 0.87444 / 0.46 (65412) hydrogen bonds : bond 0.06296 / 4.12 ( 2107) hydrogen bonds : angle 5.39703 / 3.86 ( 5703) metal coordination : bond 0.02212 / 1.28 ( 34) metal coordination : angle 6.54003 / 3.85 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 4467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 396 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8339 (m-80) cc_final: 0.8134 (m-80) REVERT: A 294 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8464 (pt0) REVERT: A 306 ASP cc_start: 0.8873 (t0) cc_final: 0.8557 (t0) REVERT: A 324 LYS cc_start: 0.9577 (mmmm) cc_final: 0.9309 (mmmm) REVERT: A 409 ASP cc_start: 0.8836 (p0) cc_final: 0.8630 (p0) REVERT: A 415 ASP cc_start: 0.8431 (t0) cc_final: 0.8150 (t0) REVERT: A 432 LYS cc_start: 0.9189 (mttp) cc_final: 0.8968 (mtpp) REVERT: A 450 SER cc_start: 0.8943 (m) cc_final: 0.8487 (p) REVERT: A 971 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: A 1105 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8315 (mp0) REVERT: A 1211 MET cc_start: 0.7892 (tpp) cc_final: 0.7608 (tpp) REVERT: A 1287 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7835 (tmm) REVERT: A 1411 ILE cc_start: 0.9583 (mm) cc_final: 0.9285 (mt) REVERT: B 183 MET cc_start: 0.8659 (mmt) cc_final: 0.8260 (mmm) REVERT: B 199 SER cc_start: 0.8893 (t) cc_final: 0.8421 (p) REVERT: B 391 ARG cc_start: 0.7378 (ttm170) cc_final: 0.7164 (ttm110) REVERT: B 503 LYS cc_start: 0.9431 (mmmt) cc_final: 0.8700 (tppt) REVERT: B 702 MET cc_start: 0.9131 (tpp) cc_final: 0.8362 (tpp) REVERT: B 908 ASP cc_start: 0.8245 (m-30) cc_final: 0.7954 (t70) REVERT: B 968 MET cc_start: 0.8298 (tmm) cc_final: 0.7969 (tmm) REVERT: B 1138 MET cc_start: 0.9060 (mmm) cc_final: 0.8627 (mmm) REVERT: C 59 ASP cc_start: 0.8044 (m-30) cc_final: 0.7807 (m-30) REVERT: C 66 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8888 (mm) REVERT: D 46 HIS cc_start: 0.7498 (t-170) cc_final: 0.7100 (t-90) REVERT: D 158 THR cc_start: 0.6659 (m) cc_final: 0.6351 (p) REVERT: F 100 GLN cc_start: 0.9161 (mt0) cc_final: 0.8878 (mp10) REVERT: G 29 LYS cc_start: 0.9502 (tptt) cc_final: 0.9178 (tttt) REVERT: G 52 MET cc_start: 0.7460 (mmp) cc_final: 0.6869 (pmm) REVERT: G 85 GLU cc_start: 0.6363 (mt-10) cc_final: 0.5716 (mp0) REVERT: G 167 PHE cc_start: 0.7967 (m-80) cc_final: 0.7083 (m-80) REVERT: H 38 LEU cc_start: 0.9245 (tp) cc_final: 0.8906 (tp) REVERT: K 6 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.7510 (mmm-85) REVERT: K 31 ILE cc_start: 0.9255 (pt) cc_final: 0.9013 (pt) REVERT: K 33 ILE cc_start: 0.9630 (OUTLIER) cc_final: 0.9207 (mp) REVERT: M 31 ASP cc_start: 0.7675 (p0) cc_final: 0.7332 (t0) REVERT: M 65 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7241 (mp10) REVERT: V 25 MET cc_start: 0.5969 (ptt) cc_final: 0.4711 (mmm) REVERT: W 444 LEU cc_start: 0.8083 (pt) cc_final: 0.7865 (tt) REVERT: W 802 HIS cc_start: 0.8553 (t70) cc_final: 0.7545 (p-80) REVERT: a 48 LEU cc_start: 0.3093 (mm) cc_final: 0.2772 (tp) REVERT: e 104 PHE cc_start: 0.6293 (OUTLIER) cc_final: 0.5860 (m-10) REVERT: f 37 LEU cc_start: 0.8568 (tp) cc_final: 0.8175 (tp) outliers start: 89 outliers final: 43 residues processed: 454 average time/residue: 0.2769 time to fit residues: 212.1200 Evaluate side-chains 368 residues out of total 4467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 319 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 971 GLN Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1287 MET Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain I residue 74 GLU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 65 GLN Chi-restraints excluded: chain W residue 232 ARG Chi-restraints excluded: chain W residue 343 VAL Chi-restraints excluded: chain W residue 384 THR Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 751 THR Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain e residue 104 PHE Chi-restraints excluded: chain h residue 66 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 95 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 390 optimal weight: 50.0000 chunk 339 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 344 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 404 optimal weight: 40.0000 chunk 211 optimal weight: 0.6980 chunk 304 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 GLN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 HIS D 170 ASN E 112 GLN G 122 ASN ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 43 GLN ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.106294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.073804 restraints weight = 202994.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.073368 restraints weight = 116126.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.074167 restraints weight = 81184.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.074315 restraints weight = 60015.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.074285 restraints weight = 61545.921| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 47638 Z= 0.140 Angle : 0.693 18.281 65445 Z= 0.360 Chirality : 0.047 0.591 7336 Planarity : 0.004 0.059 7519 Dihedral : 21.673 174.981 8532 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.72 % Favored : 97.05 % Rotamer: Outliers : 1.59 % Allowed : 10.23 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.19 (0.12), residues: 5043 helix: 0.93 (0.12), residues: 1902 sheet: -0.27 (0.19), residues: 718 loop : -0.31 (0.13), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG e 129 TYR 0.052 0.001 TYR h 80 PHE 0.028 0.001 PHE J 59 TRP 0.016 0.001 TRP C 209 HIS 0.013 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (47604) covalent geometry : angle 0.68404 / 0.36 (65412) hydrogen bonds : bond 0.05286 / 3.44 ( 2107) hydrogen bonds : angle 4.87811 / 3.49 ( 5703) metal coordination : bond 0.00576 / 0.37 ( 34) metal coordination : angle 4.94484 / 2.68 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 4467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 361 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8256 (m-80) cc_final: 0.7942 (m-80) REVERT: A 296 LEU cc_start: 0.9400 (tp) cc_final: 0.9115 (tt) REVERT: A 324 LYS cc_start: 0.9578 (mmmm) cc_final: 0.9345 (mmmm) REVERT: A 415 ASP cc_start: 0.8389 (t0) cc_final: 0.8041 (t0) REVERT: A 432 LYS cc_start: 0.9213 (mttp) cc_final: 0.8956 (mtpp) REVERT: A 450 SER cc_start: 0.8800 (m) cc_final: 0.8422 (p) REVERT: A 474 SER cc_start: 0.9329 (OUTLIER) cc_final: 0.8942 (t) REVERT: A 709 MET cc_start: 0.7846 (mmt) cc_final: 0.7273 (mpp) REVERT: A 971 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: A 975 LEU cc_start: 0.8839 (mt) cc_final: 0.8635 (mt) REVERT: A 1072 GLN cc_start: 0.8924 (mt0) cc_final: 0.8618 (mt0) REVERT: A 1073 SER cc_start: 0.9669 (m) cc_final: 0.9466 (p) REVERT: A 1105 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8324 (mt-10) REVERT: A 1287 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7811 (tmm) REVERT: A 1411 ILE cc_start: 0.9577 (mm) cc_final: 0.9325 (mt) REVERT: B 183 MET cc_start: 0.8610 (mmt) cc_final: 0.8357 (mmm) REVERT: B 503 LYS cc_start: 0.9369 (mmmt) cc_final: 0.8724 (tppt) REVERT: B 702 MET cc_start: 0.9169 (tpp) cc_final: 0.8470 (tpp) REVERT: B 903 VAL cc_start: 0.9250 (t) cc_final: 0.8725 (p) REVERT: B 908 ASP cc_start: 0.8372 (m-30) cc_final: 0.8135 (t70) REVERT: B 1138 MET cc_start: 0.9020 (mmm) cc_final: 0.8638 (mmm) REVERT: C 71 LEU cc_start: 0.8833 (mp) cc_final: 0.8546 (mt) REVERT: C 155 ILE cc_start: 0.9359 (pt) cc_final: 0.9011 (pt) REVERT: D 46 HIS cc_start: 0.7433 (t-170) cc_final: 0.7005 (t-90) REVERT: D 158 THR cc_start: 0.6671 (m) cc_final: 0.6349 (p) REVERT: F 100 GLN cc_start: 0.9028 (mt0) cc_final: 0.8570 (mp10) REVERT: F 110 ASP cc_start: 0.7928 (p0) cc_final: 0.7668 (p0) REVERT: G 29 LYS cc_start: 0.9586 (tptt) cc_final: 0.9259 (tttt) REVERT: G 52 MET cc_start: 0.7532 (mmp) cc_final: 0.6903 (pmm) REVERT: G 67 SER cc_start: 0.9163 (m) cc_final: 0.8931 (t) REVERT: G 85 GLU cc_start: 0.6388 (mt-10) cc_final: 0.5575 (mp0) REVERT: G 167 PHE cc_start: 0.8127 (m-80) cc_final: 0.7145 (m-80) REVERT: H 38 LEU cc_start: 0.9279 (tp) cc_final: 0.8914 (tp) REVERT: K 6 ARG cc_start: 0.8544 (mmm-85) cc_final: 0.8023 (mmm-85) REVERT: K 41 THR cc_start: 0.9355 (m) cc_final: 0.9102 (p) REVERT: M 31 ASP cc_start: 0.7448 (p0) cc_final: 0.7073 (t0) REVERT: V 25 MET cc_start: 0.6152 (ptt) cc_final: 0.4568 (mmm) REVERT: W 802 HIS cc_start: 0.8558 (t70) cc_final: 0.7556 (p-80) REVERT: e 104 PHE cc_start: 0.6218 (OUTLIER) cc_final: 0.5795 (m-10) REVERT: f 37 LEU cc_start: 0.8722 (tp) cc_final: 0.8327 (tp) outliers start: 71 outliers final: 37 residues processed: 409 average time/residue: 0.2440 time to fit residues: 172.8517 Evaluate side-chains 364 residues out of total 4467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 323 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 928 LYS Chi-restraints excluded: chain A residue 971 GLN Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1287 MET Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain I residue 74 GLU Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain W residue 343 VAL Chi-restraints excluded: chain W residue 384 THR Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 751 THR Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain e residue 104 PHE Chi-restraints excluded: chain h residue 66 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 46 optimal weight: 0.9990 chunk 173 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 396 optimal weight: 50.0000 chunk 308 optimal weight: 7.9990 chunk 406 optimal weight: 50.0000 chunk 466 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 318 optimal weight: 10.0000 chunk 208 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 GLN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 GLN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS H 44 ASN I 89 GLN ** M 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 GLN W 339 GLN ** d 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 31 HIS ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.103291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.066633 restraints weight = 206874.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.068457 restraints weight = 95657.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.069559 restraints weight = 60912.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.069918 restraints weight = 47538.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 77)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.070661 restraints weight = 43120.170| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 47638 Z= 0.236 Angle : 0.733 19.367 65445 Z= 0.373 Chirality : 0.047 0.440 7336 Planarity : 0.005 0.097 7519 Dihedral : 21.570 174.251 8530 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.17 % Favored : 96.59 % Rotamer: Outliers : 2.06 % Allowed : 10.63 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: 0.35 (0.12), residues: 5043 helix: 1.12 (0.12), residues: 1925 sheet: -0.24 (0.18), residues: 738 loop : -0.25 (0.13), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 176 TYR 0.021 0.002 TYR a 41 PHE 0.021 0.002 PHE J 59 TRP 0.016 0.002 TRP C 209 HIS 0.009 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.24 (47604) covalent geometry : angle 0.72410 / 0.37 (65412) hydrogen bonds : bond 0.05081 / 3.35 ( 2107) hydrogen bonds : angle 4.75578 / 3.41 ( 5703) metal coordination : bond 0.01365 / 0.72 ( 34) metal coordination : angle 5.13845 / 2.74 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 4467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 323 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8227 (m-80) cc_final: 0.7900 (m-80) REVERT: A 108 MET cc_start: 0.7214 (mmt) cc_final: 0.6809 (mmp) REVERT: A 282 MET cc_start: 0.6293 (ptm) cc_final: 0.6078 (ppp) REVERT: A 296 LEU cc_start: 0.9445 (tp) cc_final: 0.9187 (tt) REVERT: A 301 VAL cc_start: 0.9220 (t) cc_final: 0.8983 (p) REVERT: A 306 ASP cc_start: 0.9058 (t0) cc_final: 0.8643 (t0) REVERT: A 432 LYS cc_start: 0.9223 (mttp) cc_final: 0.8951 (mtpp) REVERT: A 839 GLN cc_start: 0.9095 (tp40) cc_final: 0.8689 (tm-30) REVERT: A 863 ASP cc_start: 0.8845 (m-30) cc_final: 0.8609 (t0) REVERT: A 1105 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8302 (mt-10) REVERT: A 1411 ILE cc_start: 0.9615 (mm) cc_final: 0.9400 (mt) REVERT: B 215 GLN cc_start: 0.8246 (mp10) cc_final: 0.8043 (mp10) REVERT: B 283 VAL cc_start: 0.8479 (OUTLIER) cc_final: 0.8225 (p) REVERT: B 391 ARG cc_start: 0.7506 (ttm170) cc_final: 0.7143 (ttm-80) REVERT: B 503 LYS cc_start: 0.9332 (mmmt) cc_final: 0.8681 (tppt) REVERT: B 702 MET cc_start: 0.9184 (tpp) cc_final: 0.8495 (tpp) REVERT: B 903 VAL cc_start: 0.9557 (t) cc_final: 0.9228 (p) REVERT: B 1138 MET cc_start: 0.9073 (mmm) cc_final: 0.8619 (mmm) REVERT: B 1217 TYR cc_start: 0.8648 (m-80) cc_final: 0.8374 (m-80) REVERT: C 79 MET cc_start: 0.7841 (tpp) cc_final: 0.7558 (tpp) REVERT: D 46 HIS cc_start: 0.7403 (t-90) cc_final: 0.7195 (t-90) REVERT: D 158 THR cc_start: 0.6930 (m) cc_final: 0.6630 (p) REVERT: G 29 LYS cc_start: 0.9557 (tptt) cc_final: 0.9235 (tttt) REVERT: G 52 MET cc_start: 0.7552 (mmp) cc_final: 0.7088 (pmm) REVERT: G 85 GLU cc_start: 0.6538 (mt-10) cc_final: 0.5570 (mp0) REVERT: G 167 PHE cc_start: 0.8516 (m-80) cc_final: 0.7631 (m-80) REVERT: W 771 LYS cc_start: 0.9353 (mtpt) cc_final: 0.9130 (ptmt) REVERT: W 802 HIS cc_start: 0.8268 (t70) cc_final: 0.7415 (p-80) REVERT: e 104 PHE cc_start: 0.6323 (OUTLIER) cc_final: 0.6048 (m-10) REVERT: f 37 LEU cc_start: 0.8897 (tp) cc_final: 0.8574 (tp) outliers start: 92 outliers final: 49 residues processed: 392 average time/residue: 0.2474 time to fit residues: 166.9718 Evaluate side-chains 343 residues out of total 4467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 292 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 928 LYS Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain I residue 74 GLU Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain V residue 85 ARG Chi-restraints excluded: chain W residue 343 VAL Chi-restraints excluded: chain W residue 384 THR Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 751 THR Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain e residue 104 PHE Chi-restraints excluded: chain g residue 31 HIS Chi-restraints excluded: chain g residue 76 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 338 optimal weight: 0.0980 chunk 297 optimal weight: 8.9990 chunk 235 optimal weight: 6.9990 chunk 320 optimal weight: 2.9990 chunk 316 optimal weight: 2.9990 chunk 255 optimal weight: 0.9990 chunk 372 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 502 optimal weight: 0.4980 chunk 294 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1190 GLN A1213 GLN ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 38 ASN ** d 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 64 ASN d 79 HIS e 68 GLN ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.104607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.070800 restraints weight = 204574.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.071599 restraints weight = 103194.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.072134 restraints weight = 67854.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.072001 restraints weight = 58284.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.072122 restraints weight = 56253.194| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 47638 Z= 0.128 Angle : 0.634 17.582 65445 Z= 0.327 Chirality : 0.045 0.299 7336 Planarity : 0.004 0.039 7519 Dihedral : 21.451 174.010 8530 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.86 % Favored : 96.95 % Rotamer: Outliers : 1.84 % Allowed : 11.73 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: 0.62 (0.12), residues: 5043 helix: 1.40 (0.12), residues: 1928 sheet: -0.13 (0.19), residues: 728 loop : -0.14 (0.13), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 904 TYR 0.022 0.001 TYR a 41 PHE 0.021 0.001 PHE J 59 TRP 0.011 0.001 TRP A 139 HIS 0.017 0.001 HIS g 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (47604) covalent geometry : angle 0.62687 / 0.33 (65412) hydrogen bonds : bond 0.04244 / 2.75 ( 2107) hydrogen bonds : angle 4.46881 / 3.20 ( 5703) metal coordination : bond 0.00617 / 0.36 ( 34) metal coordination : angle 4.31218 / 2.32 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 4467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 333 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8250 (m-80) cc_final: 0.7934 (m-80) REVERT: A 296 LEU cc_start: 0.9446 (tp) cc_final: 0.9213 (tt) REVERT: A 306 ASP cc_start: 0.8954 (t0) cc_final: 0.8692 (t0) REVERT: A 432 LYS cc_start: 0.9201 (mttp) cc_final: 0.8941 (mtpp) REVERT: A 473 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8897 (tt) REVERT: A 474 SER cc_start: 0.9202 (OUTLIER) cc_final: 0.8921 (t) REVERT: A 497 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7676 (tm-30) REVERT: A 635 MET cc_start: 0.8829 (tpt) cc_final: 0.8526 (tpt) REVERT: A 709 MET cc_start: 0.7681 (mmt) cc_final: 0.7086 (mpp) REVERT: A 839 GLN cc_start: 0.9038 (tp40) cc_final: 0.8682 (tm-30) REVERT: A 971 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: A 1411 ILE cc_start: 0.9610 (mm) cc_final: 0.9372 (mt) REVERT: B 283 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.8122 (p) REVERT: B 702 MET cc_start: 0.9105 (tpp) cc_final: 0.8613 (tpp) REVERT: B 860 MET cc_start: 0.7698 (tmm) cc_final: 0.7441 (tmm) REVERT: B 893 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8207 (mm) REVERT: B 903 VAL cc_start: 0.9403 (t) cc_final: 0.8954 (p) REVERT: B 1122 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8643 (ttt180) REVERT: B 1138 MET cc_start: 0.8907 (mmm) cc_final: 0.8539 (mmm) REVERT: B 1217 TYR cc_start: 0.8560 (m-80) cc_final: 0.8278 (m-80) REVERT: C 20 MET cc_start: 0.8685 (tmm) cc_final: 0.8468 (tmm) REVERT: C 79 MET cc_start: 0.7746 (tpp) cc_final: 0.7440 (tpp) REVERT: D 46 HIS cc_start: 0.7529 (t-90) cc_final: 0.7272 (t-90) REVERT: D 158 THR cc_start: 0.6821 (m) cc_final: 0.6447 (p) REVERT: E 122 MET cc_start: 0.7990 (tpp) cc_final: 0.6835 (ttt) REVERT: F 100 GLN cc_start: 0.8863 (mt0) cc_final: 0.8434 (mp10) REVERT: F 110 ASP cc_start: 0.7983 (p0) cc_final: 0.7753 (p0) REVERT: G 29 LYS cc_start: 0.9502 (tptt) cc_final: 0.9190 (tttt) REVERT: G 52 MET cc_start: 0.7448 (mmp) cc_final: 0.7007 (pmm) REVERT: G 85 GLU cc_start: 0.6568 (mt-10) cc_final: 0.5586 (mp0) REVERT: G 167 PHE cc_start: 0.8215 (m-80) cc_final: 0.7398 (m-80) REVERT: I 65 ASP cc_start: 0.8495 (p0) cc_final: 0.8293 (p0) REVERT: I 89 GLN cc_start: 0.8183 (pm20) cc_final: 0.7873 (pm20) REVERT: L 66 MET cc_start: 0.8674 (ppp) cc_final: 0.8329 (ppp) REVERT: L 68 GLN cc_start: 0.6776 (tp40) cc_final: 0.6558 (tp40) REVERT: W 771 LYS cc_start: 0.9311 (mtpt) cc_final: 0.9106 (ptmt) REVERT: W 802 HIS cc_start: 0.8470 (t70) cc_final: 0.7579 (p-80) REVERT: e 89 ILE cc_start: 0.4385 (mm) cc_final: 0.4146 (mt) REVERT: f 37 LEU cc_start: 0.8725 (tp) cc_final: 0.8350 (tp) outliers start: 82 outliers final: 49 residues processed: 395 average time/residue: 0.2398 time to fit residues: 161.3479 Evaluate side-chains 356 residues out of total 4467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 301 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 928 LYS Chi-restraints excluded: chain A residue 971 GLN Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1122 ARG Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain V residue 85 ARG Chi-restraints excluded: chain W residue 384 THR Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 751 THR Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain g residue 31 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 424 optimal weight: 40.0000 chunk 14 optimal weight: 30.0000 chunk 338 optimal weight: 4.9990 chunk 270 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 299 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 431 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 310 optimal weight: 0.0010 chunk 246 optimal weight: 9.9990 overall best weight: 2.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 57 GLN ** d 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 31 HIS ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.103664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.067117 restraints weight = 204225.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.068997 restraints weight = 93780.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.070164 restraints weight = 59398.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.070824 restraints weight = 46164.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.071289 restraints weight = 40461.120| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 47638 Z= 0.158 Angle : 0.635 15.068 65445 Z= 0.327 Chirality : 0.044 0.310 7336 Planarity : 0.004 0.044 7519 Dihedral : 21.366 173.846 8529 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.21 % Favored : 96.65 % Rotamer: Outliers : 1.86 % Allowed : 11.84 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: 0.76 (0.12), residues: 5043 helix: 1.52 (0.12), residues: 1929 sheet: -0.11 (0.19), residues: 724 loop : -0.05 (0.13), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG I 24 TYR 0.020 0.001 TYR a 41 PHE 0.028 0.001 PHE G 70 TRP 0.015 0.001 TRP A 139 HIS 0.007 0.001 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (47604) covalent geometry : angle 0.62860 / 0.33 (65412) hydrogen bonds : bond 0.04200 / 2.73 ( 2107) hydrogen bonds : angle 4.40618 / 3.15 ( 5703) metal coordination : bond 0.00851 / 0.47 ( 34) metal coordination : angle 4.02435 / 2.13 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 4467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 316 time to evaluate : 1.592 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 37 TYR cc_start: 0.8043 (m-80) cc_final: 0.7671 (m-80) REVERT: A 108 MET cc_start: 0.7615 (mmt) cc_final: 0.7171 (mmp) REVERT: A 296 LEU cc_start: 0.9497 (tp) cc_final: 0.9270 (tt) REVERT: A 306 ASP cc_start: 0.9035 (t0) cc_final: 0.8803 (t0) REVERT: A 324 LYS cc_start: 0.9618 (mmmm) cc_final: 0.9314 (mmmm) REVERT: A 432 LYS cc_start: 0.9225 (mttp) cc_final: 0.8949 (mtpp) REVERT: A 473 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8937 (tt) REVERT: A 474 SER cc_start: 0.9298 (OUTLIER) cc_final: 0.9053 (t) REVERT: A 497 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7709 (tm-30) REVERT: A 839 GLN cc_start: 0.9048 (tp40) cc_final: 0.8675 (tm-30) REVERT: A 960 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8586 (t) REVERT: A 971 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: A 1411 ILE cc_start: 0.9611 (OUTLIER) cc_final: 0.9391 (mt) REVERT: B 283 VAL cc_start: 0.8259 (OUTLIER) cc_final: 0.8000 (p) REVERT: B 702 MET cc_start: 0.9156 (tpp) cc_final: 0.8588 (tpp) REVERT: B 893 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8336 (mm) REVERT: B 1122 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8507 (ttt180) REVERT: B 1138 MET cc_start: 0.8960 (mmm) cc_final: 0.8608 (mmm) REVERT: B 1217 TYR cc_start: 0.8646 (m-80) cc_final: 0.8353 (m-80) REVERT: C 52 MET cc_start: 0.7991 (ttp) cc_final: 0.7386 (tmm) REVERT: C 79 MET cc_start: 0.7855 (tpp) cc_final: 0.7562 (tpp) REVERT: D 46 HIS cc_start: 0.7594 (t-90) cc_final: 0.7310 (t-90) REVERT: D 158 THR cc_start: 0.6766 (m) cc_final: 0.6477 (p) REVERT: E 3 ASP cc_start: 0.7847 (t0) cc_final: 0.7496 (t0) REVERT: F 110 ASP cc_start: 0.7879 (p0) cc_final: 0.7488 (p0) REVERT: G 1 MET cc_start: 0.8539 (tpp) cc_final: 0.8291 (tpp) REVERT: G 29 LYS cc_start: 0.9444 (tptt) cc_final: 0.9118 (tttt) REVERT: G 52 MET cc_start: 0.7471 (mmp) cc_final: 0.7009 (pmm) REVERT: G 85 GLU cc_start: 0.6582 (mt-10) cc_final: 0.5586 (mp0) REVERT: G 167 PHE cc_start: 0.8485 (m-80) cc_final: 0.7622 (m-80) REVERT: I 37 LEU cc_start: 0.7791 (mm) cc_final: 0.7459 (pt) REVERT: I 97 MET cc_start: 0.8476 (mmt) cc_final: 0.8257 (mmp) REVERT: W 802 HIS cc_start: 0.8198 (t70) cc_final: 0.7465 (p-80) REVERT: g 57 TYR cc_start: 0.6298 (t80) cc_final: 0.5470 (m-80) outliers start: 83 outliers final: 47 residues processed: 374 average time/residue: 0.2060 time to fit residues: 133.2823 Evaluate side-chains 351 residues out of total 4467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 296 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 971 GLN Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1411 ILE Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 613 ARG Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1122 ARG Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain V residue 85 ARG Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 751 THR Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain g residue 31 HIS Chi-restraints excluded: chain g residue 76 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 412 optimal weight: 50.0000 chunk 276 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 209 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 203 optimal weight: 6.9990 chunk 409 optimal weight: 50.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 967 GLN ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 843 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 GLN I 89 GLN ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 57 GLN ** d 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.102429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.067123 restraints weight = 203026.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.069045 restraints weight = 99817.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.068982 restraints weight = 65398.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.069606 restraints weight = 54645.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.069708 restraints weight = 48392.640| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 47638 Z= 0.206 Angle : 0.657 16.060 65445 Z= 0.336 Chirality : 0.044 0.317 7336 Planarity : 0.004 0.064 7519 Dihedral : 21.357 174.311 8529 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.45 % Favored : 96.45 % Rotamer: Outliers : 1.90 % Allowed : 12.45 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: 0.74 (0.12), residues: 5043 helix: 1.54 (0.12), residues: 1928 sheet: -0.19 (0.19), residues: 733 loop : -0.06 (0.14), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 328 TYR 0.019 0.001 TYR a 41 PHE 0.020 0.001 PHE B 325 TRP 0.015 0.002 TRP A 139 HIS 0.021 0.001 HIS g 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 (47604) covalent geometry : angle 0.64983 / 0.34 (65412) hydrogen bonds : bond 0.04298 / 2.79 ( 2107) hydrogen bonds : angle 4.42719 / 3.16 ( 5703) metal coordination : bond 0.01195 / 0.65 ( 34) metal coordination : angle 4.27969 / 2.28 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 4467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 302 time to evaluate : 1.352 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: 0.7725 (mmt) cc_final: 0.7221 (mmm) REVERT: A 306 ASP cc_start: 0.9067 (t0) cc_final: 0.8841 (t0) REVERT: A 324 LYS cc_start: 0.9631 (mmmm) cc_final: 0.9365 (mmmm) REVERT: A 432 LYS cc_start: 0.9267 (mttp) cc_final: 0.8948 (mtpp) REVERT: A 473 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9029 (tt) REVERT: A 474 SER cc_start: 0.9406 (OUTLIER) cc_final: 0.9152 (t) REVERT: A 497 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7845 (tm-30) REVERT: A 709 MET cc_start: 0.8305 (mmm) cc_final: 0.7377 (mpp) REVERT: A 839 GLN cc_start: 0.9077 (tp40) cc_final: 0.8717 (tm-30) REVERT: A 960 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8624 (t) REVERT: A 971 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7989 (tm-30) REVERT: A 1411 ILE cc_start: 0.9586 (OUTLIER) cc_final: 0.9367 (mt) REVERT: B 245 MET cc_start: 0.7901 (tmm) cc_final: 0.7436 (tmm) REVERT: B 283 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8406 (p) REVERT: B 702 MET cc_start: 0.9250 (tpp) cc_final: 0.8700 (tpp) REVERT: B 860 MET cc_start: 0.7969 (tmm) cc_final: 0.7691 (tmm) REVERT: B 893 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8465 (mm) REVERT: B 904 ARG cc_start: 0.6553 (ttp80) cc_final: 0.6300 (ttp80) REVERT: B 1122 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8527 (ttt180) REVERT: B 1138 MET cc_start: 0.8984 (mmm) cc_final: 0.8613 (mmm) REVERT: B 1217 TYR cc_start: 0.8718 (m-80) cc_final: 0.8381 (m-80) REVERT: C 20 MET cc_start: 0.8680 (tmm) cc_final: 0.8351 (tmm) REVERT: C 52 MET cc_start: 0.8140 (ttp) cc_final: 0.7547 (tmm) REVERT: C 79 MET cc_start: 0.7804 (tpp) cc_final: 0.7499 (tpp) REVERT: D 46 HIS cc_start: 0.7904 (t-90) cc_final: 0.7648 (t-90) REVERT: D 158 THR cc_start: 0.6768 (m) cc_final: 0.6471 (p) REVERT: F 110 ASP cc_start: 0.8192 (p0) cc_final: 0.7888 (p0) REVERT: G 29 LYS cc_start: 0.9411 (tptt) cc_final: 0.9091 (tttt) REVERT: G 52 MET cc_start: 0.7683 (mmp) cc_final: 0.6985 (pmm) REVERT: G 167 PHE cc_start: 0.8612 (m-80) cc_final: 0.7947 (m-80) REVERT: I 37 LEU cc_start: 0.8581 (mm) cc_final: 0.7720 (pt) REVERT: W 310 LEU cc_start: 0.8003 (tp) cc_final: 0.7428 (pt) REVERT: W 771 LYS cc_start: 0.9080 (ptmt) cc_final: 0.8500 (mtmm) REVERT: W 802 HIS cc_start: 0.8542 (t70) cc_final: 0.7690 (p-80) REVERT: g 31 HIS cc_start: 0.3475 (OUTLIER) cc_final: 0.3186 (t-170) REVERT: g 57 TYR cc_start: 0.5994 (t80) cc_final: 0.5031 (m-80) outliers start: 85 outliers final: 58 residues processed: 363 average time/residue: 0.1798 time to fit residues: 114.1557 Evaluate side-chains 352 residues out of total 4467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 285 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 928 LYS Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 971 GLN Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1411 ILE Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 300 TRP Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1122 ARG Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain W residue 343 VAL Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 447 LEU Chi-restraints excluded: chain W residue 751 THR Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain g residue 31 HIS Chi-restraints excluded: chain g residue 76 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 454 optimal weight: 5.9990 chunk 442 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 317 optimal weight: 0.9990 chunk 326 optimal weight: 1.9990 chunk 210 optimal weight: 0.7980 chunk 329 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 425 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 134 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.103515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.068808 restraints weight = 206342.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.071406 restraints weight = 102455.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.070838 restraints weight = 56186.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.071075 restraints weight = 50410.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.071189 restraints weight = 48443.462| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 47638 Z= 0.135 Angle : 0.627 14.364 65445 Z= 0.322 Chirality : 0.044 0.319 7336 Planarity : 0.004 0.044 7519 Dihedral : 21.292 174.179 8529 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.35 % Favored : 96.55 % Rotamer: Outliers : 1.70 % Allowed : 12.81 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: 0.83 (0.12), residues: 5043 helix: 1.63 (0.12), residues: 1936 sheet: -0.19 (0.19), residues: 743 loop : -0.01 (0.14), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG V 85 TYR 0.027 0.001 TYR I 34 PHE 0.015 0.001 PHE K 7 TRP 0.016 0.001 TRP A 139 HIS 0.007 0.001 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (47604) covalent geometry : angle 0.62110 / 0.32 (65412) hydrogen bonds : bond 0.03934 / 2.53 ( 2107) hydrogen bonds : angle 4.31402 / 3.09 ( 5703) metal coordination : bond 0.00682 / 0.39 ( 34) metal coordination : angle 3.88916 / 2.11 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 4467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 307 time to evaluate : 0.980 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 37 TYR cc_start: 0.7891 (m-80) cc_final: 0.7562 (m-80) REVERT: A 108 MET cc_start: 0.7551 (mmt) cc_final: 0.7025 (mmm) REVERT: A 306 ASP cc_start: 0.9056 (t0) cc_final: 0.8831 (t0) REVERT: A 324 LYS cc_start: 0.9585 (mmmm) cc_final: 0.9373 (mmmm) REVERT: A 432 LYS cc_start: 0.9234 (mttp) cc_final: 0.8978 (mtpp) REVERT: A 473 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8935 (tt) REVERT: A 474 SER cc_start: 0.9305 (OUTLIER) cc_final: 0.9048 (t) REVERT: A 497 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7913 (tm-30) REVERT: A 635 MET cc_start: 0.8819 (tpt) cc_final: 0.8465 (tpt) REVERT: A 839 GLN cc_start: 0.8995 (tp40) cc_final: 0.8622 (tm-30) REVERT: A 960 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8641 (t) REVERT: A 971 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7904 (tm-30) REVERT: A 1411 ILE cc_start: 0.9610 (mm) cc_final: 0.9393 (mt) REVERT: A 1429 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: B 283 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8133 (p) REVERT: B 702 MET cc_start: 0.9120 (tpp) cc_final: 0.8725 (tpp) REVERT: B 860 MET cc_start: 0.7954 (tmm) cc_final: 0.7694 (tmm) REVERT: B 893 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8413 (mm) REVERT: B 1122 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8523 (ttt180) REVERT: B 1138 MET cc_start: 0.8853 (mmm) cc_final: 0.8493 (mmm) REVERT: B 1217 TYR cc_start: 0.8634 (m-80) cc_final: 0.8352 (m-80) REVERT: C 20 MET cc_start: 0.8602 (tmm) cc_final: 0.8238 (tmm) REVERT: C 52 MET cc_start: 0.7993 (ttp) cc_final: 0.7495 (tmm) REVERT: C 79 MET cc_start: 0.7767 (tpp) cc_final: 0.7462 (tpp) REVERT: D 46 HIS cc_start: 0.7678 (t-90) cc_final: 0.7429 (t-90) REVERT: D 158 THR cc_start: 0.6794 (m) cc_final: 0.6467 (p) REVERT: F 110 ASP cc_start: 0.8170 (p0) cc_final: 0.7890 (p0) REVERT: G 29 LYS cc_start: 0.9448 (tptt) cc_final: 0.9131 (tttt) REVERT: G 52 MET cc_start: 0.7588 (mmp) cc_final: 0.6916 (pmm) REVERT: G 85 GLU cc_start: 0.6410 (mt-10) cc_final: 0.5472 (mp0) REVERT: G 167 PHE cc_start: 0.8456 (m-80) cc_final: 0.7829 (m-80) REVERT: I 37 LEU cc_start: 0.8451 (mm) cc_final: 0.7665 (pt) REVERT: J 48 MET cc_start: 0.8974 (mmm) cc_final: 0.8244 (mpp) REVERT: W 310 LEU cc_start: 0.7836 (tp) cc_final: 0.7271 (pt) REVERT: W 444 LEU cc_start: 0.8008 (pt) cc_final: 0.7652 (tp) REVERT: W 771 LYS cc_start: 0.8985 (ptmt) cc_final: 0.8477 (mtmm) REVERT: W 802 HIS cc_start: 0.8506 (t70) cc_final: 0.7682 (p-80) REVERT: g 57 TYR cc_start: 0.5905 (t80) cc_final: 0.4806 (m-80) outliers start: 76 outliers final: 56 residues processed: 365 average time/residue: 0.1633 time to fit residues: 103.5868 Evaluate side-chains 356 residues out of total 4467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 292 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 928 LYS Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 971 GLN Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1429 GLU Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1122 ARG Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain I residue 65 ASP Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain W residue 343 VAL Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 447 LEU Chi-restraints excluded: chain W residue 751 THR Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain g residue 76 THR Chi-restraints excluded: chain h residue 80 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 129 optimal weight: 0.8980 chunk 249 optimal weight: 2.9990 chunk 164 optimal weight: 0.4980 chunk 122 optimal weight: 0.7980 chunk 201 optimal weight: 9.9990 chunk 341 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 322 optimal weight: 0.5980 chunk 418 optimal weight: 0.4980 chunk 299 optimal weight: 2.9990 chunk 246 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 GLN ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 GLN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 GLN I 105 ASN ** d 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.104209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.069343 restraints weight = 205800.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.070985 restraints weight = 96337.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.071758 restraints weight = 60527.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.071878 restraints weight = 45646.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.071988 restraints weight = 40631.021| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 47638 Z= 0.113 Angle : 0.616 14.941 65445 Z= 0.316 Chirality : 0.043 0.326 7336 Planarity : 0.003 0.042 7519 Dihedral : 21.164 173.802 8529 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.05 % Favored : 96.87 % Rotamer: Outliers : 0.99 % Allowed : 13.63 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: 0.93 (0.12), residues: 5043 helix: 1.68 (0.12), residues: 1942 sheet: -0.13 (0.19), residues: 746 loop : 0.07 (0.14), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG A 977 TYR 0.021 0.001 TYR I 34 PHE 0.015 0.001 PHE K 7 TRP 0.016 0.001 TRP A 139 HIS 0.007 0.001 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (47604) covalent geometry : angle 0.61232 / 0.32 (65412) hydrogen bonds : bond 0.03684 / 2.36 ( 2107) hydrogen bonds : angle 4.20836 / 3.01 ( 5703) metal coordination : bond 0.00357 / 0.23 ( 34) metal coordination : angle 3.20143 / 1.79 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 4467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 322 time to evaluate : 1.050 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 37 TYR cc_start: 0.8043 (m-80) cc_final: 0.7719 (m-80) REVERT: A 306 ASP cc_start: 0.9004 (t0) cc_final: 0.8777 (t0) REVERT: A 362 LEU cc_start: 0.9494 (tp) cc_final: 0.9230 (tp) REVERT: A 415 ASP cc_start: 0.8418 (t0) cc_final: 0.8021 (t0) REVERT: A 432 LYS cc_start: 0.9258 (mttp) cc_final: 0.8977 (mtpp) REVERT: A 473 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8851 (tt) REVERT: A 474 SER cc_start: 0.9332 (OUTLIER) cc_final: 0.9069 (t) REVERT: A 635 MET cc_start: 0.8862 (tpt) cc_final: 0.8583 (tpt) REVERT: A 677 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8411 (mpp) REVERT: A 709 MET cc_start: 0.7889 (mmp) cc_final: 0.7642 (mmp) REVERT: A 839 GLN cc_start: 0.8991 (tp40) cc_final: 0.8640 (tm-30) REVERT: A 971 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: A 1411 ILE cc_start: 0.9607 (mm) cc_final: 0.9390 (mt) REVERT: B 283 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.7914 (p) REVERT: B 702 MET cc_start: 0.9102 (tpp) cc_final: 0.8781 (tpp) REVERT: B 860 MET cc_start: 0.7901 (tmm) cc_final: 0.7669 (tmm) REVERT: B 893 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8389 (mm) REVERT: B 1122 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8572 (ttt180) REVERT: B 1138 MET cc_start: 0.8823 (mmm) cc_final: 0.8495 (mmm) REVERT: B 1217 TYR cc_start: 0.8588 (m-80) cc_final: 0.8292 (m-80) REVERT: C 20 MET cc_start: 0.8539 (tmm) cc_final: 0.8168 (tmm) REVERT: C 79 MET cc_start: 0.7783 (tpp) cc_final: 0.7424 (tpp) REVERT: D 158 THR cc_start: 0.6791 (m) cc_final: 0.6487 (p) REVERT: F 100 GLN cc_start: 0.9149 (mt0) cc_final: 0.8849 (pt0) REVERT: G 29 LYS cc_start: 0.9343 (tptt) cc_final: 0.9044 (ttmt) REVERT: G 52 MET cc_start: 0.7498 (mmp) cc_final: 0.6819 (pmm) REVERT: G 85 GLU cc_start: 0.6366 (mt-10) cc_final: 0.5456 (mp0) REVERT: G 167 PHE cc_start: 0.8583 (m-80) cc_final: 0.7931 (m-80) REVERT: I 37 LEU cc_start: 0.8400 (mm) cc_final: 0.7623 (pt) REVERT: I 97 MET cc_start: 0.7600 (mmp) cc_final: 0.6898 (tpp) REVERT: J 48 MET cc_start: 0.8866 (mmm) cc_final: 0.8109 (mpp) REVERT: W 310 LEU cc_start: 0.7707 (tp) cc_final: 0.7120 (pt) REVERT: W 444 LEU cc_start: 0.8074 (pt) cc_final: 0.7684 (tp) REVERT: W 771 LYS cc_start: 0.8948 (ptmt) cc_final: 0.8627 (mtmm) REVERT: W 802 HIS cc_start: 0.8389 (t70) cc_final: 0.7600 (p-80) REVERT: g 57 TYR cc_start: 0.6374 (t80) cc_final: 0.5397 (m-80) outliers start: 44 outliers final: 30 residues processed: 354 average time/residue: 0.1709 time to fit residues: 105.8994 Evaluate side-chains 329 residues out of total 4467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 292 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 928 LYS Chi-restraints excluded: chain A residue 971 GLN Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1122 ARG Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain f residue 82 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 484 optimal weight: 50.0000 chunk 30 optimal weight: 4.9990 chunk 483 optimal weight: 0.9990 chunk 451 optimal weight: 30.0000 chunk 192 optimal weight: 8.9990 chunk 452 optimal weight: 20.0000 chunk 377 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 235 optimal weight: 0.9980 chunk 476 optimal weight: 10.0000 chunk 448 optimal weight: 30.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 GLN ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 113 HIS ** d 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.104074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.069098 restraints weight = 206257.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.071665 restraints weight = 102958.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.070983 restraints weight = 58809.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.071456 restraints weight = 50301.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.071524 restraints weight = 48021.991| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.271 47638 Z= 0.180 Angle : 0.696 59.200 65445 Z= 0.371 Chirality : 0.044 0.326 7336 Planarity : 0.004 0.068 7519 Dihedral : 21.161 173.825 8529 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.17 % Favored : 96.75 % Rotamer: Outliers : 1.16 % Allowed : 13.90 % Favored : 84.93 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.25 % 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: 0.93 (0.12), residues: 5043 helix: 1.69 (0.12), residues: 1936 sheet: -0.12 (0.19), residues: 746 loop : 0.07 (0.14), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.000 ARG B 904 TYR 0.021 0.001 TYR I 34 PHE 0.016 0.001 PHE K 7 TRP 0.061 0.002 TRP A 557 HIS 0.009 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (47604) covalent geometry : angle 0.69249 / 0.37 (65412) hydrogen bonds : bond 0.03721 / 2.38 ( 2107) hydrogen bonds : angle 4.21857 / 3.02 ( 5703) metal coordination : bond 0.00424 / 0.25 ( 34) metal coordination : angle 3.16861 / 1.77 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10086 Ramachandran restraints generated. 5043 Oldfield, 0 Emsley, 5043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 4467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 292 time to evaluate : 0.932 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 37 TYR cc_start: 0.8136 (m-80) cc_final: 0.7755 (m-80) REVERT: A 306 ASP cc_start: 0.9033 (t0) cc_final: 0.8813 (t0) REVERT: A 362 LEU cc_start: 0.9497 (tp) cc_final: 0.9252 (tp) REVERT: A 415 ASP cc_start: 0.8417 (t0) cc_final: 0.8046 (t0) REVERT: A 432 LYS cc_start: 0.9307 (mttp) cc_final: 0.8978 (mtpp) REVERT: A 473 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8875 (tt) REVERT: A 474 SER cc_start: 0.9419 (OUTLIER) cc_final: 0.9142 (t) REVERT: A 635 MET cc_start: 0.8934 (tpt) cc_final: 0.8619 (tpt) REVERT: A 677 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8554 (mpp) REVERT: A 839 GLN cc_start: 0.9053 (tp40) cc_final: 0.8649 (tm-30) REVERT: A 971 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: A 1411 ILE cc_start: 0.9607 (mm) cc_final: 0.9370 (mt) REVERT: A 1447 MET cc_start: 0.8701 (mmm) cc_final: 0.8270 (mmm) REVERT: B 283 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.7936 (p) REVERT: B 702 MET cc_start: 0.9176 (tpp) cc_final: 0.8817 (tpp) REVERT: B 860 MET cc_start: 0.7906 (tmm) cc_final: 0.7684 (tmm) REVERT: B 893 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8404 (mm) REVERT: B 1122 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8547 (ttt180) REVERT: B 1138 MET cc_start: 0.8854 (mmm) cc_final: 0.8528 (mmm) REVERT: B 1217 TYR cc_start: 0.8611 (m-80) cc_final: 0.8278 (m-80) REVERT: C 20 MET cc_start: 0.8569 (tmm) cc_final: 0.8205 (tmm) REVERT: C 79 MET cc_start: 0.7800 (tpp) cc_final: 0.7424 (tpp) REVERT: D 158 THR cc_start: 0.6793 (m) cc_final: 0.6475 (p) REVERT: G 29 LYS cc_start: 0.9316 (tptt) cc_final: 0.9016 (ttmt) REVERT: G 52 MET cc_start: 0.7537 (mmp) cc_final: 0.6858 (pmm) REVERT: G 85 GLU cc_start: 0.6399 (mt-10) cc_final: 0.5470 (mp0) REVERT: G 167 PHE cc_start: 0.8544 (m-80) cc_final: 0.7897 (m-80) REVERT: I 37 LEU cc_start: 0.8505 (mm) cc_final: 0.7754 (pt) REVERT: I 97 MET cc_start: 0.7499 (mmp) cc_final: 0.6848 (tpp) REVERT: J 48 MET cc_start: 0.8890 (mmm) cc_final: 0.8135 (mpp) REVERT: W 310 LEU cc_start: 0.7710 (tp) cc_final: 0.7123 (pt) REVERT: W 444 LEU cc_start: 0.8072 (pt) cc_final: 0.7682 (tp) REVERT: W 771 LYS cc_start: 0.8936 (ptmt) cc_final: 0.8560 (mtmm) REVERT: W 802 HIS cc_start: 0.8564 (t70) cc_final: 0.7730 (p-80) REVERT: g 57 TYR cc_start: 0.6339 (t80) cc_final: 0.5316 (m-80) outliers start: 52 outliers final: 40 residues processed: 328 average time/residue: 0.1618 time to fit residues: 93.5278 Evaluate side-chains 333 residues out of total 4467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 286 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 928 LYS Chi-restraints excluded: chain A residue 971 GLN Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1122 ARG Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain W residue 343 VAL Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain c residue 116 LEU Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain h residue 80 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 497 optimal weight: 40.0000 chunk 405 optimal weight: 50.0000 chunk 417 optimal weight: 20.0000 chunk 287 optimal weight: 7.9990 chunk 197 optimal weight: 0.0030 chunk 195 optimal weight: 0.8980 chunk 509 optimal weight: 5.9990 chunk 515 optimal weight: 40.0000 chunk 47 optimal weight: 0.4980 chunk 333 optimal weight: 1.9990 chunk 377 optimal weight: 3.9990 overall best weight: 1.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.104058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.068944 restraints weight = 205843.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.071325 restraints weight = 100848.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.070792 restraints weight = 65379.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.071369 restraints weight = 51114.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.071515 restraints weight = 46701.161| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.271 47638 Z= 0.180 Angle : 0.696 59.198 65445 Z= 0.371 Chirality : 0.044 0.326 7336 Planarity : 0.004 0.068 7519 Dihedral : 21.161 173.825 8529 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.17 % Favored : 96.75 % Rotamer: Outliers : 1.05 % Allowed : 14.04 % Favored : 84.91 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.25 % 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: 0.93 (0.12), residues: 5043 helix: 1.69 (0.12), residues: 1936 sheet: -0.12 (0.19), residues: 746 loop : 0.07 (0.14), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.000 ARG B 904 TYR 0.021 0.001 TYR I 34 PHE 0.016 0.001 PHE K 7 TRP 0.061 0.002 TRP A 557 HIS 0.009 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (47604) covalent geometry : angle 0.69248 / 0.37 (65412) hydrogen bonds : bond 0.03721 / 2.38 ( 2107) hydrogen bonds : angle 4.21857 / 3.02 ( 5703) metal coordination : bond 0.00424 / 0.25 ( 34) metal coordination : angle 3.16861 / 1.77 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7258.70 seconds wall clock time: 125 minutes 44.21 seconds (7544.21 seconds total)