Starting phenix.real_space_refine on Tue Jul 7 03:49:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ii7_60593/07_2026/9ii7_60593_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ii7_60593/07_2026/9ii7_60593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ii7_60593/07_2026/9ii7_60593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ii7_60593/07_2026/9ii7_60593.map" model { file = "/net/cci-nas-00/data/ceres_data/9ii7_60593/07_2026/9ii7_60593_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ii7_60593/07_2026/9ii7_60593_neut.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 239 5.49 5 Mg 1 5.21 5 S 213 5.16 5 C 26781 2.51 5 N 7716 2.21 5 O 8726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 351 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43686 Number of models: 1 Model: "" Number of chains: 32 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: {'PTRANS': 12, 'TRANS': 250} 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: "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: "N" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 2242 Classifications: {'DNA': 109} Link IDs: {'rna3p': 108} Chain breaks: 1 Chain: "P" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 341 Classifications: {'RNA': 16} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, 'rna3p': 13} Chain: "T" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2326 Classifications: {'DNA': 114} Link IDs: {'rna3p': 113} 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: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 595 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "b" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "c" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 699 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "d" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 685 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "e" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 735 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "f" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} 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 72.943 60.667 133.076 1.00103.22 S ATOM 549 SG CYS A 70 76.378 59.464 133.755 1.00 94.73 S ATOM 594 SG CYS A 77 75.567 63.081 134.543 1.00 74.48 S ATOM 829 SG CYS A 107 77.003 84.910 91.313 1.00142.68 S ATOM 851 SG CYS A 110 78.063 81.511 90.373 1.00152.38 S ATOM 1229 SG CYS A 168 74.956 85.241 88.409 1.00155.44 S ATOM 19883 SG CYS B1163 85.975 60.148 119.642 1.00 76.06 S ATOM 19901 SG CYS B1166 84.360 63.710 118.803 1.00 77.90 S ATOM 20024 SG CYS B1182 82.177 60.309 119.837 1.00108.37 S ATOM 20047 SG CYS B1185 84.222 60.586 116.393 1.00109.59 S ATOM 20992 SG CYS C 85 89.943 70.701 199.745 1.00126.06 S ATOM 21040 SG CYS C 91 86.010 71.565 201.465 1.00108.11 S ATOM 21063 SG CYS C 94 87.376 74.279 198.332 1.00108.09 S ATOM 29171 SG CYS I 78 90.041 164.910 143.197 1.00173.59 S ATOM 29387 SG CYS I 103 89.958 161.309 142.448 1.00166.64 S ATOM 28624 SG CYS I 10 64.510 147.836 104.564 1.00133.80 S ATOM 28787 SG CYS I 29 68.275 148.163 102.472 1.00154.71 S ATOM 28812 SG CYS I 32 65.406 150.776 101.133 1.00153.57 S ATOM 29528 SG CYS J 7 93.621 104.712 188.829 1.00 34.60 S ATOM 29551 SG CYS J 10 96.166 103.788 191.299 1.00 33.65 S ATOM 29827 SG CYS J 44 97.245 106.686 189.485 1.00 40.97 S ATOM 29833 SG CYS J 45 94.608 106.690 192.552 1.00 40.49 S ATOM 30995 SG CYS L 33 51.128 93.623 179.384 1.00114.61 S ATOM 31010 SG CYS L 36 49.299 93.945 182.712 1.00124.33 S ATOM 31120 SG CYS L 50 48.332 91.417 179.566 1.00122.63 S ATOM 31144 SG CYS L 53 48.122 95.498 178.713 1.00130.70 S ATOM 31401 SG CYS M 25 52.745 110.810 95.103 1.00198.31 S ATOM 31426 SG CYS M 28 52.405 107.389 94.593 1.00168.76 S ATOM 31584 SG CYS M 49 56.044 108.045 93.588 1.00180.55 S ATOM 31608 SG CYS M 52 52.969 109.630 91.085 1.00191.36 S ATOM 36754 SG CYS V 12 20.835 86.750 116.259 1.00 34.75 S ATOM 36776 SG CYS V 15 22.008 89.639 114.042 1.00 22.76 S ATOM 36878 SG CYS V 29 19.354 89.904 116.254 1.00 18.00 S Time building chain proxies: 8.32, per 1000 atoms: 0.19 Number of scatterers: 43686 At special positions: 0 Unit cell: (177.02, 174.9, 224.72, 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 213 16.00 P 239 15.00 Mg 1 11.99 O 8726 8.00 N 7716 7.00 C 26781 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: 3.45 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 B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " 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 10 " 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 25 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 52 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 28 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 49 " pdb=" ZN V 300 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 29 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 12 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 15 " Number of angles added : 27 9588 Ramachandran restraints generated. 4794 Oldfield, 0 Emsley, 4794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9134 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 59 sheets defined 41.9% alpha, 17.9% beta 56 base pairs and 148 stacking pairs defined. Time for finding SS restraints: 5.35 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: 3.655A pdb=" N GLU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.603A 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 261 through 283 removed outlier: 3.771A pdb=" N MET A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 306 removed outlier: 3.532A pdb=" N GLU A 292 " --> pdb=" O HIS A 288 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) 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: 3.583A 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: 3.678A 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: 3.501A 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 526 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: 3.960A pdb=" N ALA A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 3.713A 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: 3.755A 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: 3.581A pdb=" N LYS A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 738 removed outlier: 3.681A 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: 4.739A 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: 3.628A 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: 3.994A pdb=" N GLU A 929 " --> pdb=" O GLU A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 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: 3.603A 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 1109 removed outlier: 3.595A 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: 3.545A 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: 3.727A 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 1316 through 1321 removed outlier: 3.629A pdb=" N ALA A1321 " --> pdb=" O ALA A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1343 removed outlier: 3.565A pdb=" N SER A1340 " --> pdb=" O VAL A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1362 removed outlier: 3.569A pdb=" N SER A1349 " --> pdb=" O GLU A1345 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP A1362 " --> pdb=" O VAL A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1380 removed outlier: 4.108A 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 108 removed outlier: 3.564A pdb=" N ALA B 104 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 181 removed outlier: 4.097A pdb=" N ASP B 179 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR B 181 " --> pdb=" O GLU B 177 " (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 300 through 305 Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'B' and resid 318 through 330 removed outlier: 3.597A pdb=" N GLY B 330 " --> pdb=" O ILE B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 351 removed outlier: 3.522A pdb=" N ILE B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 383 removed outlier: 4.264A 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 437 through 441 Processing helix chain 'B' and resid 443 through 457 Processing helix chain 'B' and resid 461 through 465 removed outlier: 3.602A pdb=" N ALA B 465 " --> pdb=" O GLN B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 removed outlier: 3.561A 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 555 Processing helix chain 'B' and resid 558 through 562 removed outlier: 3.688A 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: 3.771A 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: 3.507A pdb=" N VAL B 682 " --> pdb=" O TRP B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.698A 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: 3.575A 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 Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 808 through 813 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1013 through 1017 Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.917A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.509A 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: 3.744A 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: 3.651A 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: 4.039A pdb=" N ARG C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 72 removed outlier: 3.580A 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: 3.521A 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: 3.872A 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: 3.786A pdb=" N LEU D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 167 removed outlier: 3.750A pdb=" N ALA D 165 " --> pdb=" O PRO D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 182 removed outlier: 4.166A pdb=" N ILE D 174 " --> pdb=" O ASN D 170 " (cutoff:3.500A) 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: 3.727A pdb=" N ILE E 123 " --> pdb=" O ASN E 120 " (cutoff:3.500A) Proline residue: E 124 - end of helix removed outlier: 4.166A 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 167 Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.508A 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: 3.930A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.714A 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: 3.954A 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: 3.803A pdb=" N ILE W 282 " --> pdb=" O LYS W 278 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 310 removed outlier: 5.106A pdb=" N LYS W 307 " --> pdb=" O VAL W 304 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP W 308 " --> pdb=" O GLU W 305 " (cutoff:3.500A) Processing helix chain 'W' and resid 330 through 334 removed outlier: 4.126A pdb=" N PHE W 333 " --> pdb=" O ASN W 330 " (cutoff:3.500A) Processing helix chain 'W' and resid 395 through 403 Processing helix chain 'W' and resid 431 through 433 No H-bonds generated for 'chain 'W' and resid 431 through 433' Processing helix chain 'W' and resid 443 through 450 Processing helix chain 'a' and resid 63 through 77 removed outlier: 3.606A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 Processing helix chain 'b' and resid 25 through 29 removed outlier: 3.628A pdb=" N GLY b 28 " --> pdb=" O ASN b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 42 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.627A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL b 60 " --> pdb=" O GLY b 56 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG b 67 " --> pdb=" O GLU b 63 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 92 removed outlier: 3.646A pdb=" N VAL b 86 " --> pdb=" O THR b 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 42 removed outlier: 3.721A pdb=" N VAL c 34 " --> pdb=" O SER c 30 " (cutoff:3.500A) Processing helix chain 'c' and resid 50 through 78 removed outlier: 3.867A pdb=" N GLU c 68 " --> pdb=" O ALA c 64 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU c 69 " --> pdb=" O LYS c 65 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN c 75 " --> pdb=" O GLY c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 83 through 93 removed outlier: 3.625A pdb=" N HIS c 92 " --> pdb=" O ASP c 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 37 through 49 removed outlier: 3.704A pdb=" N TYR d 42 " --> pdb=" O SER d 38 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS d 43 " --> pdb=" O ILE d 39 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN d 47 " --> pdb=" O LYS d 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 84 removed outlier: 3.610A pdb=" N GLY d 60 " --> pdb=" O SER d 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 90 through 102 removed outlier: 3.690A pdb=" N ILE d 94 " --> pdb=" O THR d 90 " (cutoff:3.500A) Processing helix chain 'd' and resid 104 through 123 removed outlier: 4.028A pdb=" N LYS d 120 " --> pdb=" O LYS d 116 " (cutoff:3.500A) Processing helix chain 'e' and resid 46 through 55 Processing helix chain 'e' and resid 63 through 77 Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 131 removed outlier: 3.624A pdb=" N ILE e 124 " --> pdb=" O MET e 120 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG e 129 " --> pdb=" O GLN e 125 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 29 removed outlier: 3.629A pdb=" N GLY f 28 " --> pdb=" O ASN f 25 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 42 Processing helix chain 'f' and resid 50 through 76 removed outlier: 3.544A pdb=" N VAL f 60 " --> pdb=" O GLY f 56 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG f 67 " --> pdb=" O GLU f 63 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP f 68 " --> pdb=" O ASN f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 92 removed outlier: 3.647A pdb=" N VAL f 86 " --> pdb=" O THR f 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1421 through 1422 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.890A pdb=" N THR A 238 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.890A pdb=" N LYS A 88 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 10.403A 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: 3.761A pdb=" N GLY A 184 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 201 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.762A pdb=" N LEU B1128 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.559A pdb=" N SER A 349 " --> pdb=" O ARG B1106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 352 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 6.134A 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=AA6, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.832A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.273A 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: 3.508A pdb=" N VAL A 406 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 513 through 514 removed outlier: 3.758A pdb=" N LYS A 519 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AA9, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.465A 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: 4.175A 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: 5.507A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR H 114 " --> pdb=" O TYR H 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 589 through 591 removed outlier: 7.036A pdb=" N LEU A 607 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 767 through 768 Processing sheet with id=AB3, first strand: chain 'A' and resid 850 through 851 removed outlier: 6.837A pdb=" N THR A 857 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 879 through 883 Processing sheet with id=AB5, first strand: chain 'A' and resid 1285 through 1295 Processing sheet with id=AB6, first strand: chain 'A' and resid 1143 through 1144 removed outlier: 7.230A pdb=" N THR A1143 " --> pdb=" O LEU A1276 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1226 through 1230 removed outlier: 3.677A pdb=" N ARG A1243 " --> pdb=" O PHE A1227 " (cutoff:3.500A) removed outlier: 4.427A 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: 6.930A pdb=" N TRP A1193 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N SER A1150 " --> pdb=" O GLU I 47 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLU I 47 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR A1152 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ARG I 45 " --> pdb=" O THR A1152 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE A1154 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1444 through 1448 Processing sheet with id=AB9, 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: 4.928A pdb=" N ILE B 82 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.199A 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: 5.953A pdb=" N SER B 113 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYS B 160 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 115 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AC2, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC3, first strand: chain 'B' and resid 397 through 400 removed outlier: 3.513A pdb=" N ALA B 205 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 215 through 218 removed outlier: 4.036A pdb=" N HIS B 227 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.743A 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=AC5, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC6, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC7, first strand: chain 'B' and resid 579 through 583 removed outlier: 5.937A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.880A pdb=" N PHE B 963 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 4.555A 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: 4.467A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 7.005A 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: 8.804A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (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: 4.555A 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: 4.467A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 7.005A 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: 8.804A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL B 952 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE L 40 " --> pdb=" O TYR L 31 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD2, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.048A 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: 4.326A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 873 through 874 removed outlier: 3.554A pdb=" N ASP B 936 " --> pdb=" O LEU B 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.825A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD6, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AD7, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD8, first strand: chain 'C' and resid 6 through 12 removed outlier: 6.872A pdb=" N GLU C 18 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA C 12 " --> pdb=" O GLU C 16 " (cutoff:3.500A) removed outlier: 7.013A 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: 4.925A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 119 through 122 removed outlier: 6.679A pdb=" N VAL C 97 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.927A 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: 6.806A 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: 6.722A pdb=" N GLY C 162 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU C 43 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE L 67 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.200A pdb=" N GLU C 131 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.554A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 4 through 6 removed outlier: 4.642A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE G 45 " --> pdb=" O TRP G 79 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 50 through 51 removed outlier: 4.521A pdb=" N PHE G 2 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AE6, first strand: chain 'E' and resid 27 through 28 removed outlier: 4.230A pdb=" N ASN E 62 " --> pdb=" O PHE E 28 " (cutoff:3.500A) Processing sheet with id=AE7, 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=AE7 Processing sheet with id=AE8, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.249A pdb=" N LYS E 151 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE E 198 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AE9, 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: 7.010A pdb=" N SER G 162 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ASN G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 8.055A 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: 3.776A pdb=" N LEU G 106 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL G 108 " --> pdb=" O ALA G 101 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA G 101 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL G 110 " --> pdb=" O PHE G 99 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN G 93 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASP G 102 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL G 91 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL G 143 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 121 through 122 removed outlier: 3.812A pdb=" N ALA G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF3, 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: 4.020A pdb=" N CYS I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF5, first strand: chain 'M' and resid 17 through 20 Processing sheet with id=AF6, first strand: chain 'V' and resid 18 through 19 Processing sheet with id=AF7, first strand: chain 'V' and resid 80 through 86 removed outlier: 7.009A pdb=" N GLY V 56 " --> pdb=" O VAL V 84 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL V 86 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE V 54 " --> pdb=" O VAL V 86 " (cutoff:3.500A) removed outlier: 3.621A 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=AF8, first strand: chain 'W' and resid 407 through 410 removed outlier: 6.791A 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: 6.795A pdb=" N LYS W 353 " --> pdb=" O VAL W 340 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL W 340 " --> pdb=" O LYS W 353 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 788 through 792 removed outlier: 6.691A pdb=" N ARG W 779 " --> pdb=" O LYS W 771 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N THR W 755 " --> pdb=" O GLU W 799 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'a' and resid 83 through 84 removed outlier: 7.183A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'c' and resid 46 through 47 removed outlier: 7.186A pdb=" N ARG c 46 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'c' and resid 104 through 106 Processing sheet with id=AG4, first strand: chain 'e' and resid 83 through 84 removed outlier: 7.549A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'e' and resid 118 through 119 1712 hydrogen bonds defined for protein. 4719 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 144 hydrogen bonds 284 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 148 stacking parallelities Total time for adding SS restraints: 12.99 Time building geometry restraints manager: 4.73 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: 11289 1.33 - 1.45: 9481 1.45 - 1.57: 23374 1.57 - 1.70: 475 1.70 - 1.82: 340 Bond restraints: 44959 Sorted by residual: bond pdb=" N GLN W 339 " pdb=" CA GLN W 339 " ideal model delta sigma weight residual 1.456 1.507 -0.051 1.29e-02 6.01e+03 1.55e+01 bond pdb=" CA ARG a 63 " pdb=" C ARG a 63 " ideal model delta sigma weight residual 1.523 1.577 -0.054 1.42e-02 4.96e+03 1.47e+01 bond pdb=" C3' DT T 4 " pdb=" C2' DT T 4 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C3' DA T 18 " pdb=" C2' DA T 18 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" N CYS M 49 " pdb=" CA CYS M 49 " ideal model delta sigma weight residual 1.454 1.414 0.040 1.21e-02 6.83e+03 1.08e+01 ... (remaining 44954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 60332 3.14 - 6.28: 1273 6.28 - 9.42: 112 9.42 - 12.55: 13 12.55 - 15.69: 1 Bond angle restraints: 61731 Sorted by residual: angle pdb=" N SER L 45 " pdb=" CA SER L 45 " pdb=" C SER L 45 " ideal model delta sigma weight residual 111.28 120.93 -9.65 1.09e+00 8.42e-01 7.84e+01 angle pdb=" C ARG A 47 " pdb=" N PRO A 48 " pdb=" CA PRO A 48 " ideal model delta sigma weight residual 119.84 130.46 -10.62 1.25e+00 6.40e-01 7.22e+01 angle pdb=" N ASP H 109 " pdb=" CA ASP H 109 " pdb=" C ASP H 109 " ideal model delta sigma weight residual 111.36 120.34 -8.98 1.09e+00 8.42e-01 6.78e+01 angle pdb=" N THR b 30 " pdb=" CA THR b 30 " pdb=" C THR b 30 " ideal model delta sigma weight residual 110.24 119.38 -9.14 1.30e+00 5.92e-01 4.94e+01 angle pdb=" N SER A 467 " pdb=" CA SER A 467 " pdb=" C SER A 467 " ideal model delta sigma weight residual 112.59 120.67 -8.08 1.22e+00 6.72e-01 4.39e+01 ... (remaining 61726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 25760 35.39 - 70.77: 1065 70.77 - 106.16: 32 106.16 - 141.54: 1 141.54 - 176.93: 3 Dihedral angle restraints: 26861 sinusoidal: 12734 harmonic: 14127 Sorted by residual: dihedral pdb=" N TYR A 466 " pdb=" C TYR A 466 " pdb=" CA TYR A 466 " pdb=" CB TYR A 466 " ideal model delta harmonic sigma weight residual 122.80 134.84 -12.04 0 2.50e+00 1.60e-01 2.32e+01 dihedral pdb=" C TYR A 466 " pdb=" N TYR A 466 " pdb=" CA TYR A 466 " pdb=" CB TYR A 466 " ideal model delta harmonic sigma weight residual -122.60 -133.90 11.30 0 2.50e+00 1.60e-01 2.04e+01 dihedral pdb=" C ASN E 103 " pdb=" N ASN E 103 " pdb=" CA ASN E 103 " pdb=" CB ASN E 103 " ideal model delta harmonic sigma weight residual -122.60 -133.68 11.08 0 2.50e+00 1.60e-01 1.97e+01 ... (remaining 26858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 6130 0.103 - 0.206: 723 0.206 - 0.309: 63 0.309 - 0.412: 11 0.412 - 0.514: 4 Chirality restraints: 6931 Sorted by residual: chirality pdb=" P G P 10 " pdb=" OP1 G P 10 " pdb=" OP2 G P 10 " pdb=" O5' G P 10 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.62e+00 chirality pdb=" CA ASN D 170 " pdb=" N ASN D 170 " pdb=" C ASN D 170 " pdb=" CB ASN D 170 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" CA ASN E 103 " pdb=" N ASN E 103 " pdb=" C ASN E 103 " pdb=" CB ASN E 103 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.02e+00 ... (remaining 6928 not shown) Planarity restraints: 7138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU a 65 " -0.073 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO a 66 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO a 66 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO a 66 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN d 67 " -0.021 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C ASN d 67 " 0.072 2.00e-02 2.50e+03 pdb=" O ASN d 67 " -0.027 2.00e-02 2.50e+03 pdb=" N ASP d 68 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE d 69 " 0.019 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C ILE d 69 " -0.067 2.00e-02 2.50e+03 pdb=" O ILE d 69 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE d 70 " 0.023 2.00e-02 2.50e+03 ... (remaining 7135 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 9 2.17 - 2.85: 13925 2.85 - 3.54: 57465 3.54 - 4.22: 101936 4.22 - 4.90: 169992 Nonbonded interactions: 343327 Sorted by model distance: nonbonded pdb=" C ALA a 111 " pdb=" O ARG a 116 " model vdw 1.489 3.270 nonbonded pdb=" OG SER C 116 " pdb=" NH1 ARG C 134 " model vdw 1.692 3.120 nonbonded pdb=" N ILE a 112 " pdb=" O ARG a 116 " model vdw 1.794 3.120 nonbonded pdb=" O ALA a 111 " pdb=" N ARG a 116 " model vdw 1.916 3.120 nonbonded pdb=" CB ALA a 111 " pdb=" O ARG a 116 " model vdw 1.976 3.460 ... (remaining 343322 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 'b' selection = chain 'f' } 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: 0.010 Normalize map: mean=0, sd=1: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 50.550 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 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 : 0.011 0.660 44993 Z= 0.499 Angle : 1.169 27.947 61758 Z= 0.717 Chirality : 0.070 0.514 6931 Planarity : 0.007 0.108 7138 Dihedral : 16.257 176.929 17727 Min Nonbonded Distance : 1.489 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.80 % Favored : 96.08 % Rotamer: Outliers : 0.70 % Allowed : 3.58 % Favored : 95.71 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.11), residues: 4794 helix: -1.50 (0.11), residues: 1682 sheet: -0.88 (0.18), residues: 718 loop : -0.87 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 25 TYR 0.033 0.004 TYR B 769 PHE 0.052 0.004 PHE A1176 TRP 0.032 0.004 TRP C 192 HIS 0.013 0.002 HIS K 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00819 / 0.42 (44959) covalent geometry : angle 1.12751 / 0.71 (61731) hydrogen bonds : bond 0.23959 / 15.81 ( 1825) hydrogen bonds : angle 7.79593 / 5.46 ( 5003) metal coordination : bond 0.28217 / 17.95 ( 34) metal coordination : angle 14.87281 / 9.51 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9588 Ramachandran restraints generated. 4794 Oldfield, 0 Emsley, 4794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9588 Ramachandran restraints generated. 4794 Oldfield, 0 Emsley, 4794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 647 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 40 ILE cc_start: 0.7605 (mt) cc_final: 0.7379 (mm) REVERT: A 54 ASN cc_start: 0.7954 (m-40) cc_final: 0.7749 (p0) REVERT: B 510 THR cc_start: 0.8397 (p) cc_final: 0.7959 (t) REVERT: B 944 THR cc_start: 0.8208 (p) cc_final: 0.7934 (t) REVERT: B 1082 MET cc_start: 0.7444 (tpp) cc_final: 0.7146 (mmm) REVERT: B 1152 MET cc_start: 0.7698 (mmm) cc_final: 0.7487 (mmm) REVERT: G 25 TYR cc_start: 0.8008 (t80) cc_final: 0.7777 (t80) REVERT: G 142 LYS cc_start: 0.7022 (mttp) cc_final: 0.6663 (tttm) REVERT: G 156 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6336 (tm-30) REVERT: I 84 VAL cc_start: 0.8012 (m) cc_final: 0.7760 (m) REVERT: M 39 ASP cc_start: 0.7288 (t0) cc_final: 0.6951 (t70) REVERT: W 782 LEU cc_start: 0.8459 (mt) cc_final: 0.8235 (mp) REVERT: c 39 ARG cc_start: 0.4220 (OUTLIER) cc_final: 0.3700 (mmt180) REVERT: f 43 VAL cc_start: 0.0844 (OUTLIER) cc_final: 0.0643 (m) outliers start: 30 outliers final: 4 residues processed: 674 average time/residue: 0.2935 time to fit residues: 308.8915 Evaluate side-chains 296 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 290 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain W residue 264 GLN Chi-restraints excluded: chain c residue 39 ARG Chi-restraints excluded: chain e residue 65 LEU Chi-restraints excluded: chain f residue 43 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.8980 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 494 optimal weight: 8.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN A 287 GLN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 GLN A 651 GLN A 787 HIS A1112 ASN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1393 ASN B 102 GLN B 359 GLN B 438 ASN B 776 GLN B 932 HIS ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 996 HIS B1093 GLN C 8 ASN C 13 GLN C 188 HIS C 242 GLN D 170 ASN E 4 ASN E 120 ASN E 145 HIS E 193 GLN I 31 ASN I 105 ASN ** M 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 264 GLN W 339 GLN W 434 ASN a 108 ASN c 81 ASN c 93 ASN ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.102100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.066068 restraints weight = 186569.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.067874 restraints weight = 77266.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.068977 restraints weight = 46103.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.069597 restraints weight = 34357.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.069917 restraints weight = 29478.306| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 44993 Z= 0.173 Angle : 0.715 13.681 61758 Z= 0.380 Chirality : 0.045 0.291 6931 Planarity : 0.006 0.136 7138 Dihedral : 19.502 171.221 8018 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.23 % Favored : 97.73 % Rotamer: Outliers : 1.64 % Allowed : 8.06 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.12), residues: 4794 helix: 0.31 (0.12), residues: 1719 sheet: -0.49 (0.18), residues: 746 loop : -0.34 (0.13), residues: 2329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG I 81 TYR 0.023 0.002 TYR G 130 PHE 0.038 0.002 PHE a 67 TRP 0.028 0.002 TRP B 579 HIS 0.011 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (44959) covalent geometry : angle 0.70487 / 0.38 (61731) hydrogen bonds : bond 0.06277 / 4.18 ( 1825) hydrogen bonds : angle 5.51783 / 3.87 ( 5003) metal coordination : bond 0.01499 / 0.86 ( 34) metal coordination : angle 5.68222 / 3.72 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9588 Ramachandran restraints generated. 4794 Oldfield, 0 Emsley, 4794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9588 Ramachandran restraints generated. 4794 Oldfield, 0 Emsley, 4794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 343 time to evaluate : 1.601 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: A 40 ILE cc_start: 0.8201 (mt) cc_final: 0.7909 (mm) REVERT: A 54 ASN cc_start: 0.9033 (m-40) cc_final: 0.8027 (p0) REVERT: A 74 MET cc_start: 0.8338 (ttp) cc_final: 0.8115 (ttp) REVERT: A 122 MET cc_start: 0.9157 (tpp) cc_final: 0.8604 (tpp) REVERT: A 262 ASP cc_start: 0.9254 (OUTLIER) cc_final: 0.8952 (p0) REVERT: A 306 ASP cc_start: 0.8005 (t0) cc_final: 0.7644 (t0) REVERT: A 470 ARG cc_start: 0.8584 (mmt-90) cc_final: 0.8349 (mmt90) REVERT: A 635 MET cc_start: 0.9189 (tpt) cc_final: 0.8611 (tpt) REVERT: A 677 MET cc_start: 0.9352 (tpp) cc_final: 0.8977 (tpp) REVERT: A 830 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.8100 (p) REVERT: A 843 VAL cc_start: 0.9160 (t) cc_final: 0.8936 (p) REVERT: A 979 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6787 (ptpp) REVERT: A 1270 MET cc_start: 0.9045 (ttp) cc_final: 0.8831 (tmm) REVERT: A 1274 ILE cc_start: 0.8838 (mm) cc_final: 0.8588 (mm) REVERT: B 510 THR cc_start: 0.9600 (p) cc_final: 0.9368 (p) REVERT: B 593 MET cc_start: 0.9175 (tpp) cc_final: 0.8803 (tpp) REVERT: B 699 MET cc_start: 0.8476 (tpp) cc_final: 0.8182 (tpp) REVERT: B 944 THR cc_start: 0.9243 (p) cc_final: 0.8955 (t) REVERT: B 1082 MET cc_start: 0.8484 (tpp) cc_final: 0.8250 (tpp) REVERT: C 32 LEU cc_start: 0.9129 (tp) cc_final: 0.8743 (tt) REVERT: E 92 MET cc_start: 0.8487 (mmm) cc_final: 0.8067 (tpp) REVERT: E 157 ASP cc_start: 0.8951 (m-30) cc_final: 0.8541 (t0) REVERT: F 110 ASP cc_start: 0.8393 (p0) cc_final: 0.8035 (p0) REVERT: F 149 ASP cc_start: 0.8998 (p0) cc_final: 0.8737 (p0) REVERT: G 142 LYS cc_start: 0.7240 (mttp) cc_final: 0.6796 (tttm) REVERT: G 156 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6682 (tm-30) REVERT: H 122 MET cc_start: 0.7735 (tmm) cc_final: 0.7361 (tmm) REVERT: I 68 LEU cc_start: 0.8175 (mt) cc_final: 0.7879 (mt) REVERT: K 39 ASP cc_start: 0.8217 (t0) cc_final: 0.7985 (t70) REVERT: M 39 ASP cc_start: 0.8085 (t0) cc_final: 0.7800 (t0) REVERT: W 214 GLN cc_start: 0.0444 (tp40) cc_final: -0.1136 (mp10) REVERT: d 62 MET cc_start: 0.5803 (mmt) cc_final: 0.5570 (mmt) REVERT: f 58 LEU cc_start: 0.8420 (tp) cc_final: 0.7875 (pp) outliers start: 70 outliers final: 29 residues processed: 392 average time/residue: 0.2586 time to fit residues: 169.0290 Evaluate side-chains 310 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 979 LYS Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain W residue 286 LEU Chi-restraints excluded: chain c residue 81 ASN Chi-restraints excluded: chain f residue 46 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 272 optimal weight: 6.9990 chunk 186 optimal weight: 0.0770 chunk 48 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 278 optimal weight: 0.6980 chunk 261 optimal weight: 4.9990 overall best weight: 1.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 971 GLN A1190 GLN B 356 HIS ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN E 94 ASN H 44 ASN M 57 GLN c 81 ASN e 68 GLN ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.101417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.065030 restraints weight = 185333.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.066804 restraints weight = 77599.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.067891 restraints weight = 46559.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.068483 restraints weight = 34813.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.068851 restraints weight = 29953.999| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 44993 Z= 0.139 Angle : 0.606 14.660 61758 Z= 0.323 Chirality : 0.043 0.221 6931 Planarity : 0.004 0.100 7138 Dihedral : 19.475 171.026 8006 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.54 % Favored : 97.41 % Rotamer: Outliers : 1.45 % Allowed : 8.92 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.12), residues: 4794 helix: 0.99 (0.12), residues: 1739 sheet: -0.28 (0.18), residues: 754 loop : -0.14 (0.13), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 81 TYR 0.021 0.001 TYR M 70 PHE 0.023 0.001 PHE a 67 TRP 0.013 0.001 TRP B 554 HIS 0.012 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (44959) covalent geometry : angle 0.60031 / 0.32 (61731) hydrogen bonds : bond 0.04856 / 3.21 ( 1825) hydrogen bonds : angle 4.99407 / 3.52 ( 5003) metal coordination : bond 0.00447 / 0.26 ( 34) metal coordination : angle 3.85436 / 2.48 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9588 Ramachandran restraints generated. 4794 Oldfield, 0 Emsley, 4794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9588 Ramachandran restraints generated. 4794 Oldfield, 0 Emsley, 4794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 307 time to evaluate : 1.538 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 41 MET cc_start: 0.4719 (OUTLIER) cc_final: 0.4244 (mmm) REVERT: A 54 ASN cc_start: 0.9113 (m-40) cc_final: 0.8075 (p0) REVERT: A 122 MET cc_start: 0.9156 (tpp) cc_final: 0.8736 (tpp) REVERT: A 306 ASP cc_start: 0.8050 (t0) cc_final: 0.7554 (t0) REVERT: A 470 ARG cc_start: 0.8623 (mmt-90) cc_final: 0.8373 (mmt90) REVERT: A 473 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8767 (mm) REVERT: A 635 MET cc_start: 0.9156 (tpt) cc_final: 0.8653 (tpt) REVERT: A 677 MET cc_start: 0.9341 (tpp) cc_final: 0.9034 (tpp) REVERT: A 770 MET cc_start: 0.8431 (mmp) cc_final: 0.8127 (mmm) REVERT: A 839 GLN cc_start: 0.8944 (tt0) cc_final: 0.8727 (tm-30) REVERT: A 979 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6693 (ptpp) REVERT: A 1064 GLU cc_start: 0.8425 (tp30) cc_final: 0.8164 (tp30) REVERT: A 1211 MET cc_start: 0.8930 (tpp) cc_final: 0.8648 (tpp) REVERT: A 1270 MET cc_start: 0.9134 (ttp) cc_final: 0.8868 (tmm) REVERT: A 1274 ILE cc_start: 0.8957 (mm) cc_final: 0.8698 (mm) REVERT: A 1401 MET cc_start: 0.8887 (ttp) cc_final: 0.7996 (mtm) REVERT: B 89 MET cc_start: 0.8135 (tpp) cc_final: 0.7898 (tpp) REVERT: B 302 MET cc_start: 0.7044 (ttt) cc_final: 0.6641 (ttt) REVERT: B 510 THR cc_start: 0.9491 (p) cc_final: 0.9070 (t) REVERT: B 593 MET cc_start: 0.9323 (tpp) cc_final: 0.9109 (tpp) REVERT: B 699 MET cc_start: 0.8563 (tpp) cc_final: 0.8303 (tpp) REVERT: B 944 THR cc_start: 0.9277 (p) cc_final: 0.8972 (t) REVERT: B 1134 GLU cc_start: 0.8566 (mp0) cc_final: 0.7740 (mp0) REVERT: C 20 MET cc_start: 0.7620 (tmm) cc_final: 0.7247 (tmm) REVERT: F 110 ASP cc_start: 0.8452 (p0) cc_final: 0.8042 (p0) REVERT: G 50 ASP cc_start: 0.8929 (t0) cc_final: 0.8641 (t70) REVERT: G 142 LYS cc_start: 0.7361 (mttp) cc_final: 0.6892 (tttt) REVERT: G 156 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6685 (tm-30) REVERT: H 104 GLU cc_start: 0.6887 (tm-30) cc_final: 0.6493 (tm-30) REVERT: H 145 ARG cc_start: 0.6715 (tpt90) cc_final: 0.6431 (tpt90) REVERT: I 5 ARG cc_start: 0.7527 (ptp90) cc_final: 0.6596 (ptp90) REVERT: I 14 LEU cc_start: 0.7738 (mp) cc_final: 0.7425 (mp) REVERT: I 36 GLU cc_start: 0.7393 (pm20) cc_final: 0.7056 (pm20) REVERT: I 68 LEU cc_start: 0.8127 (mt) cc_final: 0.7909 (mt) REVERT: I 81 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7612 (mmm160) REVERT: J 1 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8833 (mtt) REVERT: K 33 ILE cc_start: 0.9396 (mt) cc_final: 0.9146 (mp) REVERT: M 39 ASP cc_start: 0.8269 (t0) cc_final: 0.7290 (p0) REVERT: W 214 GLN cc_start: 0.0443 (tp40) cc_final: -0.1421 (mp10) REVERT: W 266 ASP cc_start: 0.8468 (p0) cc_final: 0.8078 (m-30) REVERT: f 58 LEU cc_start: 0.8411 (tp) cc_final: 0.7865 (pp) outliers start: 62 outliers final: 26 residues processed: 354 average time/residue: 0.2573 time to fit residues: 153.6680 Evaluate side-chains 307 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 276 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 979 LYS Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 244 PHE Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain d residue 59 MET Chi-restraints excluded: chain f residue 46 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 221 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 315 optimal weight: 5.9990 chunk 273 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 244 optimal weight: 0.9980 chunk 323 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 chunk 461 optimal weight: 0.9990 chunk 471 optimal weight: 30.0000 chunk 203 optimal weight: 0.1980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN C 242 GLN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN H 44 ASN c 108 GLN ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** 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 = 0.4147 r_free = 0.4147 target = 0.099682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.062794 restraints weight = 182291.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.064646 restraints weight = 73719.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.065799 restraints weight = 43386.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.066454 restraints weight = 32037.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.066731 restraints weight = 27231.483| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 44993 Z= 0.139 Angle : 0.578 13.859 61758 Z= 0.308 Chirality : 0.042 0.334 6931 Planarity : 0.004 0.083 7138 Dihedral : 19.487 171.122 8004 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.36 % Favored : 97.58 % Rotamer: Outliers : 1.38 % Allowed : 9.32 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.12), residues: 4794 helix: 1.23 (0.13), residues: 1753 sheet: -0.14 (0.18), residues: 751 loop : -0.02 (0.13), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG I 24 TYR 0.030 0.001 TYR I 27 PHE 0.027 0.001 PHE G 2 TRP 0.030 0.002 TRP V 71 HIS 0.008 0.001 HIS d 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (44959) covalent geometry : angle 0.57344 / 0.31 (61731) hydrogen bonds : bond 0.04246 / 2.80 ( 1825) hydrogen bonds : angle 4.72954 / 3.35 ( 5003) metal coordination : bond 0.00464 / 0.21 ( 34) metal coordination : angle 3.58590 / 2.24 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9588 Ramachandran restraints generated. 4794 Oldfield, 0 Emsley, 4794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9588 Ramachandran restraints generated. 4794 Oldfield, 0 Emsley, 4794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 293 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.4150 (OUTLIER) cc_final: 0.3914 (mmm) REVERT: A 54 ASN cc_start: 0.9254 (m-40) cc_final: 0.8099 (p0) REVERT: A 122 MET cc_start: 0.9169 (tpp) cc_final: 0.8767 (tpp) REVERT: A 306 ASP cc_start: 0.8116 (t0) cc_final: 0.7693 (t0) REVERT: A 470 ARG cc_start: 0.8642 (mmt-90) cc_final: 0.8343 (mmt90) REVERT: A 473 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8682 (mm) REVERT: A 527 ASP cc_start: 0.8605 (m-30) cc_final: 0.8380 (m-30) REVERT: A 635 MET cc_start: 0.9140 (tpt) cc_final: 0.8503 (tpt) REVERT: A 770 MET cc_start: 0.8444 (mmp) cc_final: 0.8163 (mmm) REVERT: A 839 GLN cc_start: 0.8940 (tt0) cc_final: 0.8647 (tm-30) REVERT: A 843 VAL cc_start: 0.8936 (t) cc_final: 0.8559 (p) REVERT: A 979 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.7004 (ptpp) REVERT: A 1211 MET cc_start: 0.8859 (tpp) cc_final: 0.8607 (tpp) REVERT: A 1270 MET cc_start: 0.9184 (ttp) cc_final: 0.8900 (tmm) REVERT: A 1274 ILE cc_start: 0.9035 (mm) cc_final: 0.8731 (mm) REVERT: A 1401 MET cc_start: 0.9067 (ttp) cc_final: 0.8135 (mtm) REVERT: B 89 MET cc_start: 0.8117 (tpp) cc_final: 0.7808 (tpp) REVERT: B 302 MET cc_start: 0.7160 (ttt) cc_final: 0.6543 (ttt) REVERT: B 593 MET cc_start: 0.9428 (tpp) cc_final: 0.9157 (tpp) REVERT: B 699 MET cc_start: 0.8410 (tpp) cc_final: 0.8078 (tpp) REVERT: B 702 MET cc_start: 0.9248 (tpp) cc_final: 0.8648 (tpp) REVERT: B 944 THR cc_start: 0.9381 (p) cc_final: 0.9096 (t) REVERT: F 110 ASP cc_start: 0.8758 (p0) cc_final: 0.8363 (p0) REVERT: G 50 ASP cc_start: 0.8940 (t0) cc_final: 0.8713 (t70) REVERT: G 142 LYS cc_start: 0.7507 (mttp) cc_final: 0.7070 (tttt) REVERT: G 156 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6634 (tm-30) REVERT: H 104 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6915 (tm-30) REVERT: I 68 LEU cc_start: 0.8000 (mt) cc_final: 0.7705 (mt) REVERT: M 39 ASP cc_start: 0.8299 (t0) cc_final: 0.7773 (p0) REVERT: W 214 GLN cc_start: 0.1088 (tp40) cc_final: -0.1133 (mp10) REVERT: W 266 ASP cc_start: 0.8698 (p0) cc_final: 0.8363 (m-30) REVERT: f 58 LEU cc_start: 0.8357 (tp) cc_final: 0.7804 (pp) outliers start: 59 outliers final: 31 residues processed: 331 average time/residue: 0.2579 time to fit residues: 144.6245 Evaluate side-chains 310 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 276 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 979 LYS Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain M residue 36 CYS Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain d residue 59 MET Chi-restraints excluded: chain d residue 80 LEU Chi-restraints excluded: chain e residue 118 THR Chi-restraints excluded: chain f residue 46 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 289 optimal weight: 40.0000 chunk 390 optimal weight: 8.9990 chunk 326 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 145 optimal weight: 0.0570 chunk 69 optimal weight: 5.9990 chunk 335 optimal weight: 9.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN ** e 113 HIS ** 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 = 0.4132 r_free = 0.4132 target = 0.098997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.061892 restraints weight = 182074.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.063767 restraints weight = 72440.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.064915 restraints weight = 42447.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.065555 restraints weight = 31317.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 72)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.065943 restraints weight = 26734.772| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 44993 Z= 0.142 Angle : 0.566 13.514 61758 Z= 0.300 Chirality : 0.042 0.326 6931 Planarity : 0.004 0.055 7138 Dihedral : 19.472 171.148 8004 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.40 % Favored : 97.54 % Rotamer: Outliers : 1.48 % Allowed : 9.49 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.12), residues: 4794 helix: 1.35 (0.13), residues: 1757 sheet: -0.12 (0.18), residues: 741 loop : 0.07 (0.13), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG f 45 TYR 0.026 0.001 TYR M 70 PHE 0.031 0.001 PHE G 3 TRP 0.011 0.001 TRP B 554 HIS 0.004 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (44959) covalent geometry : angle 0.56144 / 0.30 (61731) hydrogen bonds : bond 0.03911 / 2.57 ( 1825) hydrogen bonds : angle 4.56139 / 3.23 ( 5003) metal coordination : bond 0.00585 / 0.27 ( 34) metal coordination : angle 3.48199 / 2.15 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9588 Ramachandran restraints generated. 4794 Oldfield, 0 Emsley, 4794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9588 Ramachandran restraints generated. 4794 Oldfield, 0 Emsley, 4794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 284 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.4200 (OUTLIER) cc_final: 0.3808 (mmm) REVERT: A 54 ASN cc_start: 0.9384 (m-40) cc_final: 0.8287 (p0) REVERT: A 122 MET cc_start: 0.9194 (tpp) cc_final: 0.8834 (tpp) REVERT: A 233 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: A 296 LEU cc_start: 0.9218 (tp) cc_final: 0.8919 (tt) REVERT: A 306 ASP cc_start: 0.8130 (t0) cc_final: 0.7736 (t0) REVERT: A 470 ARG cc_start: 0.8679 (mmt-90) cc_final: 0.8202 (mmt90) REVERT: A 487 GLU cc_start: 0.8473 (mp0) cc_final: 0.8264 (pm20) REVERT: A 635 MET cc_start: 0.9113 (tpt) cc_final: 0.8760 (tpt) REVERT: A 770 MET cc_start: 0.8481 (mmp) cc_final: 0.8172 (mmm) REVERT: A 839 GLN cc_start: 0.8943 (tt0) cc_final: 0.8668 (tm-30) REVERT: A 979 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7275 (ptpp) REVERT: A 1107 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8959 (mm) REVERT: A 1204 MET cc_start: 0.8808 (ptm) cc_final: 0.8588 (ptp) REVERT: A 1209 LEU cc_start: 0.8828 (pp) cc_final: 0.8462 (mm) REVERT: A 1211 MET cc_start: 0.8902 (tpp) cc_final: 0.8499 (tpp) REVERT: A 1270 MET cc_start: 0.9223 (ttp) cc_final: 0.8962 (tmm) REVERT: A 1396 ASP cc_start: 0.8556 (t0) cc_final: 0.8323 (t0) REVERT: A 1401 MET cc_start: 0.9104 (ttp) cc_final: 0.8099 (mtm) REVERT: A 1410 GLU cc_start: 0.8723 (mp0) cc_final: 0.8481 (mp0) REVERT: B 89 MET cc_start: 0.8325 (tpp) cc_final: 0.8116 (tpp) REVERT: B 164 MET cc_start: 0.7649 (ttp) cc_final: 0.7388 (ttm) REVERT: B 302 MET cc_start: 0.7199 (ttt) cc_final: 0.6582 (ttt) REVERT: B 699 MET cc_start: 0.8464 (tpp) cc_final: 0.8039 (tpp) REVERT: B 792 MET cc_start: 0.8929 (ttm) cc_final: 0.8532 (ttm) REVERT: B 944 THR cc_start: 0.9384 (p) cc_final: 0.9096 (t) REVERT: B 999 MET cc_start: 0.9212 (mmm) cc_final: 0.8480 (tpp) REVERT: B 1134 GLU cc_start: 0.8580 (mp0) cc_final: 0.7611 (mp0) REVERT: F 110 ASP cc_start: 0.8823 (p0) cc_final: 0.8408 (p0) REVERT: G 1 MET cc_start: 0.8869 (ttt) cc_final: 0.8632 (tmm) REVERT: G 50 ASP cc_start: 0.8943 (t0) cc_final: 0.8723 (t0) REVERT: G 55 ASP cc_start: 0.9221 (t0) cc_final: 0.8973 (p0) REVERT: G 142 LYS cc_start: 0.7496 (mttp) cc_final: 0.7027 (tttt) REVERT: G 156 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6636 (tm-30) REVERT: I 65 ASP cc_start: 0.8393 (t0) cc_final: 0.8087 (t0) REVERT: J 1 MET cc_start: 0.9092 (mtt) cc_final: 0.8817 (mtp) REVERT: K 39 ASP cc_start: 0.8384 (t0) cc_final: 0.8179 (t0) REVERT: M 39 ASP cc_start: 0.8379 (t0) cc_final: 0.7709 (p0) REVERT: V 25 MET cc_start: 0.3226 (mpp) cc_final: 0.2347 (mtp) REVERT: W 266 ASP cc_start: 0.8695 (p0) cc_final: 0.8361 (m-30) REVERT: f 58 LEU cc_start: 0.8362 (tp) cc_final: 0.7817 (pp) outliers start: 63 outliers final: 35 residues processed: 331 average time/residue: 0.2475 time to fit residues: 140.2908 Evaluate side-chains 303 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 264 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 979 LYS Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 908 ASP Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain M residue 36 CYS Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain d residue 59 MET Chi-restraints excluded: chain d residue 80 LEU Chi-restraints excluded: chain e residue 118 THR Chi-restraints excluded: chain f residue 46 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 406 optimal weight: 50.0000 chunk 306 optimal weight: 10.0000 chunk 336 optimal weight: 30.0000 chunk 460 optimal weight: 50.0000 chunk 396 optimal weight: 50.0000 chunk 361 optimal weight: 20.0000 chunk 416 optimal weight: 20.0000 chunk 495 optimal weight: 30.0000 chunk 463 optimal weight: 10.0000 chunk 123 optimal weight: 0.4980 chunk 89 optimal weight: 7.9990 overall best weight: 9.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 GLN A 446 ASN ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 GLN A 967 GLN B 97 HIS B 215 GLN B 227 HIS B 356 HIS B 776 GLN ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 GLN G 107 ASN H 44 ASN d 47 GLN ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.092371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.053923 restraints weight = 183543.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.055566 restraints weight = 75968.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.056570 restraints weight = 46152.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.057111 restraints weight = 34953.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.057448 restraints weight = 30227.060| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.212 44993 Z= 0.575 Angle : 1.014 26.584 61758 Z= 0.512 Chirality : 0.054 0.287 6931 Planarity : 0.006 0.064 7138 Dihedral : 19.777 171.963 8004 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.78 % Favored : 96.16 % Rotamer: Outliers : 2.25 % Allowed : 9.79 % Favored : 87.96 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.12), residues: 4794 helix: 0.51 (0.12), residues: 1761 sheet: -0.59 (0.18), residues: 742 loop : -0.32 (0.13), residues: 2291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1129 TYR 0.041 0.003 TYR M 70 PHE 0.046 0.003 PHE A1227 TRP 0.026 0.003 TRP A1230 HIS 0.017 0.003 HIS K 40 Details of bonding type rmsd/Z covalent geometry : bond 0.01271 / 0.57 (44959) covalent geometry : angle 0.99786 / 0.51 (61731) hydrogen bonds : bond 0.05598 / 3.68 ( 1825) hydrogen bonds : angle 5.47258 / 3.85 ( 5003) metal coordination : bond 0.04425 / 2.24 ( 34) metal coordination : angle 8.74210 / 5.05 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9588 Ramachandran restraints generated. 4794 Oldfield, 0 Emsley, 4794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9588 Ramachandran restraints generated. 4794 Oldfield, 0 Emsley, 4794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 258 time to evaluate : 1.648 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 41 MET cc_start: 0.5309 (OUTLIER) cc_final: 0.4796 (mmm) REVERT: A 239 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8958 (p) REVERT: A 253 MET cc_start: 0.0968 (tpt) cc_final: 0.0668 (tpt) REVERT: A 282 MET cc_start: 0.9358 (OUTLIER) cc_final: 0.8940 (ptp) REVERT: A 296 LEU cc_start: 0.9340 (tp) cc_final: 0.9107 (tt) REVERT: A 305 MET cc_start: 0.9253 (mmm) cc_final: 0.8556 (mmm) REVERT: A 487 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8502 (pm20) REVERT: A 505 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8909 (mp) REVERT: A 635 MET cc_start: 0.9205 (tpt) cc_final: 0.8716 (tpt) REVERT: A 709 MET cc_start: 0.8025 (mmp) cc_final: 0.7236 (mtp) REVERT: A 1396 ASP cc_start: 0.8930 (t0) cc_final: 0.8654 (t0) REVERT: B 89 MET cc_start: 0.8555 (tpp) cc_final: 0.8317 (tpp) REVERT: B 302 MET cc_start: 0.7581 (ttt) cc_final: 0.7268 (ttt) REVERT: B 524 GLN cc_start: 0.8951 (mp10) cc_final: 0.8695 (pm20) REVERT: B 563 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7196 (p0) REVERT: B 944 THR cc_start: 0.9448 (p) cc_final: 0.9155 (t) REVERT: B 1122 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.7992 (tmt90) REVERT: B 1210 MET cc_start: 0.9129 (tpp) cc_final: 0.8286 (tpp) REVERT: F 116 ASP cc_start: 0.8846 (t0) cc_final: 0.8615 (t0) REVERT: G 41 GLN cc_start: 0.8486 (tp-100) cc_final: 0.8189 (tp40) REVERT: G 50 ASP cc_start: 0.8940 (t0) cc_final: 0.8724 (t0) REVERT: G 55 ASP cc_start: 0.9103 (t0) cc_final: 0.8824 (p0) REVERT: G 156 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6325 (tm-30) REVERT: H 104 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7960 (tm-30) REVERT: H 144 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.7862 (ttm-80) REVERT: J 48 MET cc_start: 0.8210 (tpp) cc_final: 0.7915 (mpp) REVERT: K 39 ASP cc_start: 0.8740 (t0) cc_final: 0.8369 (t0) REVERT: M 55 SER cc_start: 0.7027 (m) cc_final: 0.6749 (t) outliers start: 96 outliers final: 53 residues processed: 328 average time/residue: 0.2565 time to fit residues: 143.4578 Evaluate side-chains 295 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 234 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 979 LYS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1274 ILE Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 1122 ARG Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain E residue 71 TYR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 144 ARG Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain d residue 59 MET Chi-restraints excluded: chain e residue 119 ILE Chi-restraints excluded: chain f residue 46 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 191 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 299 optimal weight: 2.9990 chunk 333 optimal weight: 2.9990 chunk 338 optimal weight: 20.0000 chunk 27 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 chunk 443 optimal weight: 30.0000 chunk 183 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 GLN ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 GLN A 967 GLN C 13 GLN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN G 107 ASN ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.095366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.057038 restraints weight = 178511.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.058825 restraints weight = 71145.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.059915 restraints weight = 42319.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.060536 restraints weight = 31601.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.060842 restraints weight = 27133.472| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 44993 Z= 0.141 Angle : 0.618 21.776 61758 Z= 0.320 Chirality : 0.043 0.400 6931 Planarity : 0.004 0.049 7138 Dihedral : 19.719 169.689 8004 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.67 % Favored : 97.29 % Rotamer: Outliers : 1.41 % Allowed : 11.24 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.12), residues: 4794 helix: 1.14 (0.12), residues: 1754 sheet: -0.45 (0.19), residues: 743 loop : -0.04 (0.13), residues: 2297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 180 TYR 0.031 0.001 TYR M 70 PHE 0.027 0.001 PHE M 23 TRP 0.018 0.001 TRP C 209 HIS 0.005 0.001 HIS A 660 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (44959) covalent geometry : angle 0.60472 / 0.32 (61731) hydrogen bonds : bond 0.04055 / 2.67 ( 1825) hydrogen bonds : angle 4.74057 / 3.36 ( 5003) metal coordination : bond 0.01050 / 0.50 ( 34) metal coordination : angle 6.06978 / 3.53 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9588 Ramachandran restraints generated. 4794 Oldfield, 0 Emsley, 4794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9588 Ramachandran restraints generated. 4794 Oldfield, 0 Emsley, 4794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 271 time to evaluate : 1.590 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 41 MET cc_start: 0.4973 (OUTLIER) cc_final: 0.4581 (mmm) REVERT: A 235 MET cc_start: 0.9378 (ttm) cc_final: 0.9024 (ttp) REVERT: A 282 MET cc_start: 0.9290 (ptp) cc_final: 0.8906 (ptp) REVERT: A 306 ASP cc_start: 0.8450 (t0) cc_final: 0.8240 (t0) REVERT: A 470 ARG cc_start: 0.8870 (mmt90) cc_final: 0.8147 (mmt90) REVERT: A 473 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8817 (mm) REVERT: A 487 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8341 (pm20) REVERT: A 505 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8906 (mp) REVERT: A 635 MET cc_start: 0.9176 (tpt) cc_final: 0.8710 (tpt) REVERT: A 770 MET cc_start: 0.8678 (mmp) cc_final: 0.8297 (mmm) REVERT: A 839 GLN cc_start: 0.8890 (tt0) cc_final: 0.8599 (tm-30) REVERT: A 1401 MET cc_start: 0.9203 (ttp) cc_final: 0.8479 (mtm) REVERT: B 89 MET cc_start: 0.8517 (tpp) cc_final: 0.8165 (tpp) REVERT: B 302 MET cc_start: 0.7511 (ttt) cc_final: 0.6923 (ttt) REVERT: B 524 GLN cc_start: 0.8882 (mp10) cc_final: 0.8622 (pm20) REVERT: B 556 MET cc_start: 0.9343 (ttt) cc_final: 0.8579 (tmm) REVERT: B 702 MET cc_start: 0.9116 (tpp) cc_final: 0.8618 (tpp) REVERT: B 792 MET cc_start: 0.8890 (ttm) cc_final: 0.8468 (ttm) REVERT: B 944 THR cc_start: 0.9442 (p) cc_final: 0.9171 (t) REVERT: B 999 MET cc_start: 0.9283 (mmm) cc_final: 0.8806 (tpp) REVERT: B 1072 MET cc_start: 0.9013 (mtp) cc_final: 0.7582 (mmm) REVERT: B 1134 GLU cc_start: 0.8861 (mp0) cc_final: 0.7642 (mp0) REVERT: B 1152 MET cc_start: 0.7808 (ttm) cc_final: 0.7438 (tpt) REVERT: E 34 MET cc_start: 0.9117 (tpp) cc_final: 0.8657 (tpp) REVERT: F 116 ASP cc_start: 0.8813 (t0) cc_final: 0.8568 (t0) REVERT: G 41 GLN cc_start: 0.8532 (tp-100) cc_final: 0.8224 (tp40) REVERT: G 50 ASP cc_start: 0.8957 (t0) cc_final: 0.8735 (t0) REVERT: G 55 ASP cc_start: 0.9116 (t0) cc_final: 0.8814 (p0) REVERT: G 106 LEU cc_start: 0.4387 (OUTLIER) cc_final: 0.3860 (pt) REVERT: G 156 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6487 (tm-30) REVERT: H 104 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7933 (tm-30) REVERT: J 48 MET cc_start: 0.8280 (tpp) cc_final: 0.7919 (mpp) REVERT: K 39 ASP cc_start: 0.8725 (t0) cc_final: 0.8327 (t0) REVERT: W 266 ASP cc_start: 0.8783 (p0) cc_final: 0.8398 (m-30) REVERT: f 58 LEU cc_start: 0.8302 (tp) cc_final: 0.7721 (pp) outliers start: 60 outliers final: 33 residues processed: 313 average time/residue: 0.2513 time to fit residues: 135.2292 Evaluate side-chains 288 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 979 LYS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain M residue 36 CYS Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain W residue 354 LEU Chi-restraints excluded: chain d residue 59 MET Chi-restraints excluded: chain f residue 46 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 181 optimal weight: 0.0050 chunk 444 optimal weight: 40.0000 chunk 4 optimal weight: 10.0000 chunk 323 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 496 optimal weight: 40.0000 chunk 133 optimal weight: 6.9990 chunk 225 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 106 optimal weight: 0.0010 chunk 20 optimal weight: 0.8980 overall best weight: 1.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 GLN B 506 GLN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.095083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.056724 restraints weight = 177898.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.058474 restraints weight = 73103.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.059522 restraints weight = 43892.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.060030 restraints weight = 32957.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.060446 restraints weight = 28617.590| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 44993 Z= 0.163 Angle : 0.598 17.592 61758 Z= 0.312 Chirality : 0.042 0.305 6931 Planarity : 0.004 0.048 7138 Dihedral : 19.661 170.232 8004 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.05 % Favored : 96.91 % Rotamer: Outliers : 1.29 % Allowed : 11.43 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.12), residues: 4794 helix: 1.32 (0.13), residues: 1758 sheet: -0.45 (0.18), residues: 748 loop : 0.02 (0.14), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 180 TYR 0.025 0.001 TYR A 544 PHE 0.026 0.001 PHE M 23 TRP 0.013 0.001 TRP B 554 HIS 0.005 0.001 HIS d 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (44959) covalent geometry : angle 0.58988 / 0.31 (61731) hydrogen bonds : bond 0.03861 / 2.54 ( 1825) hydrogen bonds : angle 4.62478 / 3.30 ( 5003) metal coordination : bond 0.01073 / 0.52 ( 34) metal coordination : angle 4.71670 / 2.82 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9588 Ramachandran restraints generated. 4794 Oldfield, 0 Emsley, 4794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9588 Ramachandran restraints generated. 4794 Oldfield, 0 Emsley, 4794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 259 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.5083 (OUTLIER) cc_final: 0.4767 (mmm) REVERT: A 235 MET cc_start: 0.9409 (ttm) cc_final: 0.9142 (ttp) REVERT: A 282 MET cc_start: 0.9286 (ptp) cc_final: 0.8917 (ptp) REVERT: A 470 ARG cc_start: 0.8814 (mmt90) cc_final: 0.8175 (mmt90) REVERT: A 487 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8339 (pm20) REVERT: A 505 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8898 (mp) REVERT: A 548 MET cc_start: 0.8421 (mtm) cc_final: 0.7879 (mpp) REVERT: A 635 MET cc_start: 0.9146 (tpt) cc_final: 0.8558 (tpt) REVERT: A 770 MET cc_start: 0.8703 (mmp) cc_final: 0.8292 (mmm) REVERT: A 839 GLN cc_start: 0.8903 (tt0) cc_final: 0.8448 (tm-30) REVERT: A 1401 MET cc_start: 0.9206 (ttp) cc_final: 0.8513 (mtm) REVERT: B 89 MET cc_start: 0.8596 (tpp) cc_final: 0.8202 (tpp) REVERT: B 302 MET cc_start: 0.7526 (ttt) cc_final: 0.6894 (ttt) REVERT: B 305 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8445 (tpt) REVERT: B 556 MET cc_start: 0.9349 (ttt) cc_final: 0.8528 (tmm) REVERT: B 702 MET cc_start: 0.9165 (tpp) cc_final: 0.8571 (tpp) REVERT: B 792 MET cc_start: 0.8908 (ttm) cc_final: 0.8483 (ttm) REVERT: B 944 THR cc_start: 0.9437 (p) cc_final: 0.9162 (t) REVERT: B 1098 MET cc_start: 0.8752 (mtm) cc_final: 0.8393 (mtm) REVERT: B 1134 GLU cc_start: 0.8854 (mp0) cc_final: 0.7617 (mp0) REVERT: B 1152 MET cc_start: 0.7778 (ttm) cc_final: 0.7555 (tpt) REVERT: E 34 MET cc_start: 0.9132 (tpp) cc_final: 0.8641 (tpp) REVERT: F 116 ASP cc_start: 0.8730 (t0) cc_final: 0.8458 (t0) REVERT: F 149 ASP cc_start: 0.9396 (p0) cc_final: 0.9182 (p0) REVERT: G 41 GLN cc_start: 0.8513 (tp-100) cc_final: 0.8235 (tp40) REVERT: G 50 ASP cc_start: 0.8957 (t0) cc_final: 0.8731 (t0) REVERT: G 55 ASP cc_start: 0.9097 (t0) cc_final: 0.8798 (p0) REVERT: G 106 LEU cc_start: 0.4342 (OUTLIER) cc_final: 0.3903 (pt) REVERT: G 156 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6412 (tm-30) REVERT: G 157 ILE cc_start: 0.2582 (OUTLIER) cc_final: 0.1586 (pt) REVERT: H 104 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8020 (tm-30) REVERT: K 39 ASP cc_start: 0.8752 (t0) cc_final: 0.8329 (t0) REVERT: V 64 GLU cc_start: 0.8092 (tp30) cc_final: 0.7833 (tm-30) REVERT: W 266 ASP cc_start: 0.8759 (p0) cc_final: 0.8384 (m-30) REVERT: b 84 MET cc_start: 0.4757 (tpp) cc_final: 0.2935 (mmt) REVERT: f 58 LEU cc_start: 0.8303 (tp) cc_final: 0.7751 (pp) outliers start: 55 outliers final: 34 residues processed: 299 average time/residue: 0.2516 time to fit residues: 130.2666 Evaluate side-chains 289 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 249 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 979 LYS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain W residue 354 LEU Chi-restraints excluded: chain d residue 59 MET Chi-restraints excluded: chain e residue 119 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 135 optimal weight: 0.6980 chunk 470 optimal weight: 40.0000 chunk 40 optimal weight: 4.9990 chunk 430 optimal weight: 20.0000 chunk 335 optimal weight: 30.0000 chunk 282 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 187 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 482 optimal weight: 10.0000 chunk 363 optimal weight: 0.1980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 ASN H 138 ASN ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.095850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.057606 restraints weight = 178392.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.059413 restraints weight = 70678.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.060528 restraints weight = 41804.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 73)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.061167 restraints weight = 31204.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.061433 restraints weight = 26698.552| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 44993 Z= 0.121 Angle : 0.570 19.716 61758 Z= 0.298 Chirality : 0.041 0.336 6931 Planarity : 0.003 0.047 7138 Dihedral : 19.634 170.888 8004 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.86 % Favored : 97.10 % Rotamer: Outliers : 1.05 % Allowed : 11.90 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.12), residues: 4794 helix: 1.44 (0.13), residues: 1761 sheet: -0.36 (0.18), residues: 743 loop : 0.10 (0.14), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 180 TYR 0.019 0.001 TYR A 544 PHE 0.026 0.001 PHE M 23 TRP 0.012 0.001 TRP C 209 HIS 0.005 0.001 HIS d 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (44959) covalent geometry : angle 0.56472 / 0.30 (61731) hydrogen bonds : bond 0.03555 / 2.34 ( 1825) hydrogen bonds : angle 4.46027 / 3.18 ( 5003) metal coordination : bond 0.00519 / 0.25 ( 34) metal coordination : angle 3.72246 / 2.40 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9588 Ramachandran restraints generated. 4794 Oldfield, 0 Emsley, 4794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9588 Ramachandran restraints generated. 4794 Oldfield, 0 Emsley, 4794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 264 time to evaluate : 1.699 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 41 MET cc_start: 0.4936 (OUTLIER) cc_final: 0.4692 (mmm) REVERT: A 74 MET cc_start: 0.8875 (tpp) cc_final: 0.8434 (mmt) REVERT: A 242 VAL cc_start: 0.8967 (t) cc_final: 0.8557 (p) REVERT: A 282 MET cc_start: 0.9250 (ptp) cc_final: 0.8918 (ptp) REVERT: A 470 ARG cc_start: 0.8744 (mmt90) cc_final: 0.8159 (mmt90) REVERT: A 487 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8228 (pm20) REVERT: A 505 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8851 (mp) REVERT: A 548 MET cc_start: 0.8391 (mtm) cc_final: 0.7775 (mpp) REVERT: A 635 MET cc_start: 0.9128 (tpt) cc_final: 0.8559 (tpt) REVERT: A 770 MET cc_start: 0.8659 (mmp) cc_final: 0.8248 (mmm) REVERT: A 839 GLN cc_start: 0.8887 (tt0) cc_final: 0.8520 (tm-30) REVERT: A 1401 MET cc_start: 0.9156 (ttp) cc_final: 0.8458 (mtm) REVERT: B 89 MET cc_start: 0.8585 (tpp) cc_final: 0.8172 (tpp) REVERT: B 302 MET cc_start: 0.7481 (ttt) cc_final: 0.6825 (ttt) REVERT: B 305 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8466 (tpt) REVERT: B 556 MET cc_start: 0.9332 (ttt) cc_final: 0.8486 (tmm) REVERT: B 702 MET cc_start: 0.9164 (tpp) cc_final: 0.8570 (tpp) REVERT: B 792 MET cc_start: 0.8918 (ttm) cc_final: 0.8543 (ttm) REVERT: B 944 THR cc_start: 0.9431 (p) cc_final: 0.9166 (t) REVERT: B 1072 MET cc_start: 0.9049 (mtp) cc_final: 0.7669 (mmm) REVERT: B 1098 MET cc_start: 0.8759 (mtm) cc_final: 0.8410 (mtm) REVERT: B 1134 GLU cc_start: 0.8734 (mp0) cc_final: 0.7462 (mp0) REVERT: B 1152 MET cc_start: 0.7732 (ttm) cc_final: 0.7495 (tpt) REVERT: C 20 MET cc_start: 0.8527 (ttp) cc_final: 0.8118 (ttp) REVERT: E 34 MET cc_start: 0.9107 (tpp) cc_final: 0.8643 (tpp) REVERT: F 116 ASP cc_start: 0.8711 (t0) cc_final: 0.8450 (t0) REVERT: G 1 MET cc_start: 0.8553 (ptm) cc_final: 0.8286 (ppp) REVERT: G 41 GLN cc_start: 0.8580 (tp-100) cc_final: 0.8285 (tp40) REVERT: G 50 ASP cc_start: 0.8934 (t0) cc_final: 0.8706 (t0) REVERT: G 55 ASP cc_start: 0.9102 (t0) cc_final: 0.8812 (p0) REVERT: G 106 LEU cc_start: 0.4292 (OUTLIER) cc_final: 0.3809 (pt) REVERT: G 156 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6408 (tm-30) REVERT: G 157 ILE cc_start: 0.2605 (OUTLIER) cc_final: 0.1624 (pt) REVERT: H 104 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8137 (tm-30) REVERT: K 39 ASP cc_start: 0.8723 (t0) cc_final: 0.8299 (t0) REVERT: M 55 SER cc_start: 0.6928 (m) cc_final: 0.6710 (t) REVERT: V 64 GLU cc_start: 0.8113 (tp30) cc_final: 0.7865 (tm-30) REVERT: W 266 ASP cc_start: 0.8763 (p0) cc_final: 0.8377 (m-30) REVERT: f 58 LEU cc_start: 0.8360 (tp) cc_final: 0.7818 (pp) outliers start: 45 outliers final: 27 residues processed: 296 average time/residue: 0.2582 time to fit residues: 131.6834 Evaluate side-chains 284 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 251 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain M residue 36 CYS Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain W residue 354 LEU Chi-restraints excluded: chain d residue 59 MET Chi-restraints excluded: chain e residue 119 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 12 optimal weight: 6.9990 chunk 172 optimal weight: 0.3980 chunk 160 optimal weight: 10.0000 chunk 492 optimal weight: 9.9990 chunk 283 optimal weight: 0.0050 chunk 466 optimal weight: 50.0000 chunk 212 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 chunk 331 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 426 optimal weight: 0.9990 overall best weight: 1.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 ASN c 93 ASN ** e 113 HIS ** 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 = 0.4052 r_free = 0.4052 target = 0.095736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.057646 restraints weight = 180598.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.059449 restraints weight = 71182.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.060558 restraints weight = 41926.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.061197 restraints weight = 31185.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.061457 restraints weight = 26658.919| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.296 44993 Z= 0.167 Angle : 0.660 59.183 61758 Z= 0.358 Chirality : 0.043 0.524 6931 Planarity : 0.004 0.047 7138 Dihedral : 19.635 170.902 8004 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.80 % Favored : 97.16 % Rotamer: Outliers : 1.10 % Allowed : 11.90 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % 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: 0.70 (0.12), residues: 4794 helix: 1.43 (0.13), residues: 1761 sheet: -0.36 (0.18), residues: 743 loop : 0.10 (0.14), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 180 TYR 0.018 0.001 TYR A 544 PHE 0.034 0.001 PHE M 23 TRP 0.010 0.001 TRP C 209 HIS 0.007 0.001 HIS d 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (44959) covalent geometry : angle 0.65521 / 0.36 (61731) hydrogen bonds : bond 0.03564 / 2.35 ( 1825) hydrogen bonds : angle 4.46667 / 3.19 ( 5003) metal coordination : bond 0.00563 / 0.27 ( 34) metal coordination : angle 3.67720 / 2.35 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9588 Ramachandran restraints generated. 4794 Oldfield, 0 Emsley, 4794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9588 Ramachandran restraints generated. 4794 Oldfield, 0 Emsley, 4794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 251 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.4936 (OUTLIER) cc_final: 0.4694 (mmm) REVERT: A 74 MET cc_start: 0.8884 (tpp) cc_final: 0.8457 (mmt) REVERT: A 242 VAL cc_start: 0.8962 (t) cc_final: 0.8559 (p) REVERT: A 282 MET cc_start: 0.9250 (ptp) cc_final: 0.8918 (ptp) REVERT: A 470 ARG cc_start: 0.8738 (mmt90) cc_final: 0.8156 (mmt90) REVERT: A 487 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8227 (pm20) REVERT: A 505 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8851 (mp) REVERT: A 548 MET cc_start: 0.8383 (mtm) cc_final: 0.7772 (mpp) REVERT: A 606 MET cc_start: 0.8986 (tpp) cc_final: 0.8403 (tpp) REVERT: A 635 MET cc_start: 0.9130 (tpt) cc_final: 0.8554 (tpt) REVERT: A 770 MET cc_start: 0.8644 (mmp) cc_final: 0.8240 (mmm) REVERT: A 839 GLN cc_start: 0.8890 (tt0) cc_final: 0.8524 (tm-30) REVERT: A 1401 MET cc_start: 0.9155 (ttp) cc_final: 0.8458 (mtm) REVERT: B 89 MET cc_start: 0.8580 (tpp) cc_final: 0.8167 (tpp) REVERT: B 302 MET cc_start: 0.7486 (ttt) cc_final: 0.6823 (ttt) REVERT: B 305 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8466 (tpt) REVERT: B 556 MET cc_start: 0.9334 (ttt) cc_final: 0.8491 (tmm) REVERT: B 702 MET cc_start: 0.9164 (tpp) cc_final: 0.8573 (tpp) REVERT: B 792 MET cc_start: 0.8920 (ttm) cc_final: 0.8543 (ttm) REVERT: B 944 THR cc_start: 0.9431 (p) cc_final: 0.9164 (t) REVERT: B 1072 MET cc_start: 0.9043 (mtp) cc_final: 0.7655 (mmm) REVERT: B 1098 MET cc_start: 0.8767 (mtm) cc_final: 0.8423 (mtm) REVERT: B 1134 GLU cc_start: 0.8748 (mp0) cc_final: 0.7459 (mp0) REVERT: B 1152 MET cc_start: 0.7734 (ttm) cc_final: 0.7498 (tpt) REVERT: C 20 MET cc_start: 0.8531 (ttp) cc_final: 0.8114 (ttp) REVERT: E 34 MET cc_start: 0.9106 (tpp) cc_final: 0.8754 (tpp) REVERT: E 122 MET cc_start: 0.8668 (ttt) cc_final: 0.8341 (ttp) REVERT: F 116 ASP cc_start: 0.8711 (t0) cc_final: 0.8447 (t0) REVERT: G 1 MET cc_start: 0.8570 (ptm) cc_final: 0.8341 (ppp) REVERT: G 41 GLN cc_start: 0.8562 (tp-100) cc_final: 0.8284 (tp40) REVERT: G 50 ASP cc_start: 0.8931 (t0) cc_final: 0.8703 (t0) REVERT: G 55 ASP cc_start: 0.9101 (t0) cc_final: 0.8807 (p0) REVERT: G 106 LEU cc_start: 0.4091 (OUTLIER) cc_final: 0.3159 (pt) REVERT: G 156 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6389 (tm-30) REVERT: G 157 ILE cc_start: 0.2609 (OUTLIER) cc_final: 0.1616 (pt) REVERT: H 104 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8133 (tm-30) REVERT: J 48 MET cc_start: 0.7996 (mmm) cc_final: 0.7370 (mtp) REVERT: K 39 ASP cc_start: 0.8724 (t0) cc_final: 0.8297 (t0) REVERT: M 55 SER cc_start: 0.6920 (m) cc_final: 0.6699 (t) REVERT: V 64 GLU cc_start: 0.8115 (tp30) cc_final: 0.7870 (tm-30) REVERT: W 266 ASP cc_start: 0.8767 (p0) cc_final: 0.8381 (m-30) REVERT: f 58 LEU cc_start: 0.8360 (tp) cc_final: 0.7822 (pp) outliers start: 47 outliers final: 38 residues processed: 277 average time/residue: 0.2508 time to fit residues: 121.0421 Evaluate side-chains 294 residues out of total 4269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain M residue 36 CYS Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain V residue 25 MET Chi-restraints excluded: chain W residue 354 LEU Chi-restraints excluded: chain d residue 109 HIS Chi-restraints excluded: chain e residue 119 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 42 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 422 optimal weight: 9.9990 chunk 314 optimal weight: 0.9990 chunk 265 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 200 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** 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 = 0.4052 r_free = 0.4052 target = 0.095835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.057564 restraints weight = 180084.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.059382 restraints weight = 71150.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.060492 restraints weight = 41953.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.061143 restraints weight = 31236.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.061403 restraints weight = 26701.198| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.296 44993 Z= 0.167 Angle : 0.660 59.183 61758 Z= 0.358 Chirality : 0.043 0.524 6931 Planarity : 0.004 0.047 7138 Dihedral : 19.635 170.902 8004 Min Nonbonded Distance : 1.653 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.80 % Favored : 97.16 % Rotamer: Outliers : 1.03 % Allowed : 11.97 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % 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: 0.70 (0.12), residues: 4794 helix: 1.43 (0.13), residues: 1761 sheet: -0.36 (0.18), residues: 743 loop : 0.10 (0.14), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 180 TYR 0.018 0.001 TYR A 544 PHE 0.034 0.001 PHE M 23 TRP 0.010 0.001 TRP C 209 HIS 0.007 0.001 HIS d 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (44959) covalent geometry : angle 0.65521 / 0.36 (61731) hydrogen bonds : bond 0.03564 / 2.35 ( 1825) hydrogen bonds : angle 4.46667 / 3.19 ( 5003) metal coordination : bond 0.00563 / 0.27 ( 34) metal coordination : angle 3.67720 / 2.35 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11704.62 seconds wall clock time: 201 minutes 12.19 seconds (12072.19 seconds total)