Starting phenix.real_space_refine on Sun Jun 7 05:48:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qeb_53053/06_2026/9qeb_53053.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qeb_53053/06_2026/9qeb_53053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qeb_53053/06_2026/9qeb_53053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qeb_53053/06_2026/9qeb_53053.map" model { file = "/net/cci-nas-00/data/ceres_data/9qeb_53053/06_2026/9qeb_53053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qeb_53053/06_2026/9qeb_53053.cif" } resolution = 2.26 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= 0.044 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: 8 Type Number sf(0) Gaussians K 1 8.98 5 Zn 8 6.06 5 P 100 5.49 5 Mg 2 5.21 5 S 182 5.16 5 C 20562 2.51 5 N 5767 2.21 5 O 7185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33807 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 10942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 10942 Classifications: {'peptide': 1390} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1327} Chain breaks: 6 Chain: "B" Number of atoms: 9155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9155 Classifications: {'peptide': 1150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1100} Chain breaks: 6 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 2 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 909 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} 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: {'TRANS': 44} Chain: "N" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 914 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "R" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 197 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 879 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 36 Unusual residues: {' K': 1, ' MG': 2, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: "A" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 275 Classifications: {'water': 275} Link IDs: {None: 274} Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 229 Classifications: {'water': 229} Link IDs: {None: 228} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "H" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "J" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "L" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "T" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 49.906 79.625 91.286 1.00180.91 S ATOM 479 SG CYS A 70 50.288 83.334 89.707 1.00174.36 S ATOM 532 SG CYS A 77 53.241 80.968 89.552 1.00184.37 S ATOM 762 SG CYS A 107 72.978 78.977 133.264 1.00267.65 S ATOM 786 SG CYS A 110 71.046 82.193 133.706 1.00243.47 S ATOM 1091 SG CYS A 148 74.404 81.563 135.533 1.00281.24 S ATOM 1105 SG CYS A 167 71.270 79.621 136.554 1.00264.27 S ATOM 19603 SG CYS B1163 56.195 93.437 100.934 1.00186.97 S ATOM 19621 SG CYS B1166 58.184 90.501 102.160 1.00158.18 S ATOM 19746 SG CYS B1182 54.504 90.148 100.988 1.00161.71 S ATOM 19765 SG CYS B1185 55.377 91.762 104.356 1.00185.38 S ATOM 20753 SG CYS C 86 68.852 73.202 23.841 1.00240.31 S ATOM 20770 SG CYS C 88 67.144 71.039 26.393 1.00230.53 S ATOM 20803 SG CYS C 92 68.078 69.545 23.161 1.00218.78 S ATOM 20826 SG CYS C 95 70.822 70.413 25.721 1.00211.15 S ATOM 28411 SG CYS I 7 120.292 34.426 130.327 1.00315.11 S ATOM 28436 SG CYS I 10 116.476 34.151 129.994 1.00300.32 S ATOM 28602 SG CYS I 29 117.916 37.004 132.238 1.00337.95 S ATOM 28626 SG CYS I 32 118.842 33.879 133.855 1.00321.21 S ATOM 28953 SG CYS I 75 144.928 44.351 93.111 1.00311.41 S ATOM 28975 SG CYS I 78 145.391 41.134 91.925 1.00283.55 S ATOM 29191 SG CYS I 103 141.918 41.051 91.830 1.00279.94 S ATOM 29211 SG CYS I 106 143.416 40.565 95.274 1.00282.20 S ATOM 29313 SG CYS J 7 98.654 61.707 38.267 1.00123.95 S ATOM 29336 SG CYS J 10 99.101 63.836 35.097 1.00130.17 S ATOM 29616 SG CYS J 45 102.004 63.394 37.759 1.00136.03 S ATOM 29622 SG CYS J 46 100.966 60.761 35.307 1.00140.55 S ATOM 30745 SG CYS L 31 66.998 35.378 53.879 1.00232.64 S ATOM 30765 SG CYS L 34 67.153 33.296 51.129 1.00213.15 S ATOM 30869 SG CYS L 48 63.284 34.195 52.693 1.00227.98 S ATOM 30892 SG CYS L 51 66.920 31.738 53.959 1.00230.58 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O HOH C 518 " occ=0.78 Time building chain proxies: 7.78, per 1000 atoms: 0.23 Number of scatterers: 33807 At special positions: 0 Unit cell: (158.339, 150.049, 180.722, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 8 29.99 K 1 19.00 S 182 16.00 P 100 15.00 Mg 2 11.99 O 7185 8.00 N 5767 7.00 C 20562 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: 3.47 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1805 " pdb="ZN ZN A1805 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 67 " pdb=" ZN A1806 " pdb="ZN ZN A1806 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1806 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1806 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1806 " - pdb=" SG CYS A 110 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " Number of angles added : 45 7706 Ramachandran restraints generated. 3853 Oldfield, 0 Emsley, 3853 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7340 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 47 sheets defined 39.5% alpha, 20.0% beta 39 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 5.64 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.608A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 305 removed outlier: 3.622A pdb=" N MET A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 removed outlier: 3.520A pdb=" N GLY A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.692A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.918A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.965A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 661 removed outlier: 3.529A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 removed outlier: 3.566A pdb=" N ALA A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 699 " --> pdb=" O LYS A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 809 through 830 removed outlier: 3.995A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 846 removed outlier: 3.718A pdb=" N THR A 834 " --> pdb=" O LYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.566A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.598A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1057 removed outlier: 3.852A pdb=" N VAL A1045 " --> pdb=" O ALA A1041 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1082 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1083 through 1087 removed outlier: 3.634A pdb=" N ALA A1087 " --> pdb=" O PHE A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1096 Processing helix chain 'A' and resid 1096 through 1107 Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1166 through 1173 Processing helix chain 'A' and resid 1198 through 1206 removed outlier: 3.510A pdb=" N ASP A1204 " --> pdb=" O ALA A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1257 through 1270 Processing helix chain 'A' and resid 1312 through 1317 Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1364 through 1375 removed outlier: 3.986A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1430 removed outlier: 3.521A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1452 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.761A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 4.674A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 156 through 164 removed outlier: 5.536A pdb=" N GLU B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER B 162 " --> pdb=" O ASP B 159 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 163 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS B 164 " --> pdb=" O GLU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.662A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 337 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 removed outlier: 3.638A pdb=" N GLU B 437 " --> pdb=" O GLN B 433 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.569A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 495 Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.744A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.529A pdb=" N ILE B 748 " --> pdb=" O PRO B 745 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 removed outlier: 3.504A pdb=" N ILE B 755 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.215A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 788 Processing helix chain 'B' and resid 808 through 813 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.730A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.759A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.683A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 80 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 204 through 210 removed outlier: 3.900A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR C 209 " --> pdb=" O ASN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 removed outlier: 3.542A pdb=" N ASP C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 135 removed outlier: 3.851A pdb=" N THR D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY D 135 " --> pdb=" O GLU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 169 Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 5 through 26 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 44 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.654A pdb=" N MET E 57 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER E 59 " --> pdb=" O LYS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 91 through 104 removed outlier: 3.526A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.534A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 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 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.639A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 65 removed outlier: 3.584A pdb=" N ASP I 65 " --> pdb=" O ILE I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.562A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR J 52 " --> pdb=" O ARG J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 4.044A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 10.180A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.368A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 removed outlier: 4.809A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.597A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1104 through 1106 Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.690A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.515A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.948A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB2, first strand: chain 'A' and resid 769 through 770 Processing sheet with id=AB3, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AB4, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1282 through 1292 removed outlier: 3.566A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 3.511A pdb=" N ARG A1241 " --> pdb=" O PHE A1225 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A1149 " --> pdb=" O GLU A1196 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1441 through 1445 Processing sheet with id=AB8, first strand: chain 'B' and resid 69 through 73 removed outlier: 4.829A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LYS B 134 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU B 154 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N THR B 136 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 152 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 69 through 73 removed outlier: 4.829A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC2, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC3, first strand: chain 'B' and resid 404 through 407 removed outlier: 5.892A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.947A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC6, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.503A pdb=" N CYS B 741 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.412A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.513A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.422A 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: 3.513A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (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: 7.210A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 910 through 912 removed outlier: 6.949A pdb=" N THR B 939 " --> pdb=" O ILE B 911 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD5, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD6, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD7, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.304A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.727A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE1, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE2, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.594A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.594A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.327A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.736A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.577A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AE8, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.768A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF1, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.548A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE I 100 " --> pdb=" O PHE I 86 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.569A pdb=" N LYS K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR K 61 " --> pdb=" O LYS K 72 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) 1379 hydrogen bonds defined for protein. 3792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 101 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 11.79 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.39: 13313 1.39 - 1.64: 20264 1.64 - 1.88: 298 1.88 - 2.13: 0 2.13 - 2.38: 1 Bond restraints: 33876 Sorted by residual: bond pdb=" C MET I 1 " pdb=" N THR I 2 " ideal model delta sigma weight residual 1.332 2.377 -1.045 1.40e-02 5.10e+03 5.57e+03 bond pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.374 1.183 0.191 1.00e-02 1.00e+04 3.66e+02 bond pdb=" C8 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.370 1.208 0.162 1.20e-02 6.94e+03 1.82e+02 bond pdb=" C LEU A 710 " pdb=" N ARG A 711 " ideal model delta sigma weight residual 1.332 1.198 0.135 1.40e-02 5.10e+03 9.25e+01 bond pdb=" C6 ATP A1801 " pdb=" N6 ATP A1801 " ideal model delta sigma weight residual 1.337 1.442 -0.105 1.10e-02 8.26e+03 9.17e+01 ... (remaining 33871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.89: 46133 7.89 - 15.78: 22 15.78 - 23.66: 0 23.66 - 31.55: 1 31.55 - 39.44: 2 Bond angle restraints: 46158 Sorted by residual: angle pdb=" C MET I 1 " pdb=" N THR I 2 " pdb=" CA THR I 2 " ideal model delta sigma weight residual 121.54 82.10 39.44 1.91e+00 2.74e-01 4.26e+02 angle pdb=" O MET I 1 " pdb=" C MET I 1 " pdb=" N THR I 2 " ideal model delta sigma weight residual 123.00 154.19 -31.19 1.60e+00 3.91e-01 3.80e+02 angle pdb=" CA MET I 1 " pdb=" C MET I 1 " pdb=" N THR I 2 " ideal model delta sigma weight residual 116.20 79.03 37.17 2.00e+00 2.50e-01 3.45e+02 angle pdb=" PB ATP A1801 " pdb=" O3B ATP A1801 " pdb=" PG ATP A1801 " ideal model delta sigma weight residual 139.87 125.12 14.75 1.00e+00 1.00e+00 2.18e+02 angle pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " pdb=" C8 ATP A1801 " ideal model delta sigma weight residual 105.72 119.64 -13.92 1.00e+00 1.00e+00 1.94e+02 ... (remaining 46153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.33: 19594 32.33 - 64.66: 782 64.66 - 96.99: 89 96.99 - 129.32: 1 129.32 - 161.65: 5 Dihedral angle restraints: 20471 sinusoidal: 9136 harmonic: 11335 Sorted by residual: dihedral pdb=" C LYS A1221 " pdb=" N LYS A1221 " pdb=" CA LYS A1221 " pdb=" CB LYS A1221 " ideal model delta harmonic sigma weight residual -122.60 -137.51 14.91 0 2.50e+00 1.60e-01 3.56e+01 dihedral pdb=" CA HIS A 286 " pdb=" C HIS A 286 " pdb=" N HIS A 287 " pdb=" CA HIS A 287 " ideal model delta harmonic sigma weight residual -180.00 -150.61 -29.39 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" N HIS A 286 " pdb=" C HIS A 286 " pdb=" CA HIS A 286 " pdb=" CB HIS A 286 " ideal model delta harmonic sigma weight residual 122.80 108.54 14.26 0 2.50e+00 1.60e-01 3.26e+01 ... (remaining 20468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 5067 0.126 - 0.253: 97 0.253 - 0.379: 9 0.379 - 0.506: 11 0.506 - 0.632: 6 Chirality restraints: 5190 Sorted by residual: chirality pdb=" CA CYS A 67 " pdb=" N CYS A 67 " pdb=" C CYS A 67 " pdb=" CB CYS A 67 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CB THR B 944 " pdb=" CA THR B 944 " pdb=" OG1 THR B 944 " pdb=" CG2 THR B 944 " both_signs ideal model delta sigma weight residual False 2.55 1.94 0.61 2.00e-01 2.50e+01 9.22e+00 chirality pdb=" CA LYS A1221 " pdb=" N LYS A1221 " pdb=" C LYS A1221 " pdb=" CB LYS A1221 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.03e+00 ... (remaining 5187 not shown) Planarity restraints: 5630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 250 " 0.040 2.00e-02 2.50e+03 6.29e-02 6.92e+01 pdb=" CG PHE B 250 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 PHE B 250 " -0.095 2.00e-02 2.50e+03 pdb=" CD2 PHE B 250 " -0.067 2.00e-02 2.50e+03 pdb=" CE1 PHE B 250 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 250 " -0.031 2.00e-02 2.50e+03 pdb=" CZ PHE B 250 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 287 " 0.058 2.00e-02 2.50e+03 6.74e-02 6.81e+01 pdb=" CG HIS A 287 " 0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS A 287 " -0.092 2.00e-02 2.50e+03 pdb=" CD2 HIS A 287 " -0.093 2.00e-02 2.50e+03 pdb=" CE1 HIS A 287 " 0.050 2.00e-02 2.50e+03 pdb=" NE2 HIS A 287 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET I 1 " 0.023 2.00e-02 2.50e+03 7.86e-02 6.17e+01 pdb=" C MET I 1 " -0.132 2.00e-02 2.50e+03 pdb=" O MET I 1 " 0.076 2.00e-02 2.50e+03 pdb=" N THR I 2 " 0.033 2.00e-02 2.50e+03 ... (remaining 5627 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.25: 33 2.25 - 2.97: 15996 2.97 - 3.69: 62699 3.69 - 4.42: 106378 4.42 - 5.14: 169392 Nonbonded interactions: 354498 Sorted by model distance: nonbonded pdb=" C MET I 1 " pdb=" O THR I 2 " model vdw 1.523 3.270 nonbonded pdb=" OD1 ASP A 481 " pdb="MG MG A1803 " model vdw 1.807 2.170 nonbonded pdb=" OD2 ASP A 481 " pdb="MG MG A1802 " model vdw 1.850 2.170 nonbonded pdb=" NH1 ARG B 617 " pdb=" OD2 ASP I 61 " model vdw 1.896 3.120 nonbonded pdb=" O2G ATP A1801 " pdb="MG MG A1802 " model vdw 1.920 2.170 ... (remaining 354493 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.78 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.560 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: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 45.420 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 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:8.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5477 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 1.045 33908 Z= 0.653 Angle : 0.964 44.228 46203 Z= 0.553 Chirality : 0.058 0.632 5190 Planarity : 0.007 0.097 5630 Dihedral : 16.029 161.652 13131 Min Nonbonded Distance : 1.523 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.09 % Favored : 96.73 % Rotamer: Outliers : 1.31 % Allowed : 0.79 % Favored : 97.90 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 2.41 % 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: -0.06 (0.13), residues: 3853 helix: 0.85 (0.14), residues: 1326 sheet: -0.14 (0.21), residues: 600 loop : -0.58 (0.14), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.047 0.001 ARG I 30 TYR 0.061 0.002 TYR B 994 PHE 0.095 0.003 PHE B 250 TRP 0.029 0.002 TRP A 556 HIS 0.080 0.002 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00913 / 0.62 (33876) covalent geometry : angle 0.89568 / 0.55 (46158) hydrogen bonds : bond 0.17942 / 12.30 ( 1435) hydrogen bonds : angle 6.79289 / 4.94 ( 3994) metal coordination : bond 0.18573 / 9.14 ( 32) metal coordination : angle 11.47116 / 7.22 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7706 Ramachandran restraints generated. 3853 Oldfield, 0 Emsley, 3853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7706 Ramachandran restraints generated. 3853 Oldfield, 0 Emsley, 3853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 641 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.5611 (mmt90) cc_final: 0.4886 (mmt-90) REVERT: A 75 ASN cc_start: 0.6508 (t0) cc_final: 0.6222 (t0) REVERT: A 175 ARG cc_start: 0.4937 (ttp80) cc_final: 0.4675 (ttp-110) REVERT: A 177 ASP cc_start: 0.5446 (t0) cc_final: 0.5245 (t0) REVERT: A 205 GLU cc_start: 0.5471 (tt0) cc_final: 0.4987 (tp30) REVERT: A 215 SER cc_start: 0.5694 (t) cc_final: 0.5266 (p) REVERT: A 293 GLU cc_start: 0.5160 (tt0) cc_final: 0.4849 (pt0) REVERT: A 368 LYS cc_start: 0.6878 (ttmt) cc_final: 0.6633 (ttmp) REVERT: A 393 ARG cc_start: 0.6034 (ttm110) cc_final: 0.5636 (mpt180) REVERT: A 407 ARG cc_start: 0.5522 (mtp-110) cc_final: 0.5297 (mtt180) REVERT: A 437 MET cc_start: 0.6491 (ptt) cc_final: 0.5432 (mtp) REVERT: A 453 MET cc_start: 0.7230 (mpp) cc_final: 0.6957 (mpp) REVERT: A 461 LYS cc_start: 0.7047 (tptm) cc_final: 0.6582 (tmtt) REVERT: A 542 GLU cc_start: 0.5750 (mt-10) cc_final: 0.5297 (mt-10) REVERT: A 591 PHE cc_start: 0.7330 (m-80) cc_final: 0.6847 (m-80) REVERT: A 605 MET cc_start: 0.6573 (tpt) cc_final: 0.6236 (tpp) REVERT: A 696 GLU cc_start: 0.3308 (tt0) cc_final: 0.3062 (tt0) REVERT: A 771 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6741 (mt-10) REVERT: A 854 ASN cc_start: 0.7135 (OUTLIER) cc_final: 0.6849 (m-40) REVERT: A 873 MET cc_start: 0.6983 (mmp) cc_final: 0.6000 (mmt) REVERT: A 894 GLU cc_start: 0.5904 (tp30) cc_final: 0.5573 (mm-30) REVERT: A 992 ASP cc_start: 0.5724 (m-30) cc_final: 0.5327 (t70) REVERT: A 1005 GLU cc_start: 0.5987 (mm-30) cc_final: 0.5770 (tp30) REVERT: A 1133 LEU cc_start: 0.5487 (mt) cc_final: 0.5234 (mp) REVERT: A 1278 ASN cc_start: 0.7396 (m-40) cc_final: 0.7066 (m-40) REVERT: A 1314 SER cc_start: 0.7027 (t) cc_final: 0.6439 (p) REVERT: A 1315 GLU cc_start: 0.5933 (tt0) cc_final: 0.5161 (mm-30) REVERT: A 1366 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.5204 (ptm160) REVERT: A 1420 ASP cc_start: 0.6345 (t0) cc_final: 0.5107 (p0) REVERT: A 1424 VAL cc_start: 0.6395 (m) cc_final: 0.6117 (p) REVERT: B 21 GLU cc_start: 0.6300 (pt0) cc_final: 0.5893 (mt-10) REVERT: B 26 THR cc_start: 0.6650 (p) cc_final: 0.6253 (t) REVERT: B 29 ASP cc_start: 0.6710 (m-30) cc_final: 0.6489 (m-30) REVERT: B 239 GLU cc_start: 0.5388 (pt0) cc_final: 0.4727 (mp0) REVERT: B 257 LYS cc_start: 0.4895 (mtmt) cc_final: 0.4605 (mtmm) REVERT: B 393 LYS cc_start: 0.6587 (ttpt) cc_final: 0.6068 (pttp) REVERT: B 473 MET cc_start: 0.5461 (mmp) cc_final: 0.4934 (mpp) REVERT: B 529 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7155 (pt0) REVERT: B 542 MET cc_start: 0.6929 (mtm) cc_final: 0.6639 (mtt) REVERT: B 564 GLU cc_start: 0.6186 (mt-10) cc_final: 0.5804 (mm-30) REVERT: B 591 ARG cc_start: 0.7094 (mtp-110) cc_final: 0.6767 (mtt90) REVERT: B 595 ARG cc_start: 0.6128 (ttt180) cc_final: 0.5459 (ttp80) REVERT: B 650 GLU cc_start: 0.6340 (pt0) cc_final: 0.5740 (pm20) REVERT: B 792 MET cc_start: 0.7481 (mtm) cc_final: 0.7238 (mtt) REVERT: B 953 LEU cc_start: 0.5656 (tt) cc_final: 0.5391 (tm) REVERT: B 1004 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6192 (pt0) REVERT: B 1021 MET cc_start: 0.7517 (mtm) cc_final: 0.7268 (mtp) REVERT: B 1057 LYS cc_start: 0.5851 (mttt) cc_final: 0.5292 (ttpt) REVERT: B 1183 LYS cc_start: 0.5804 (pttm) cc_final: 0.5402 (mmtp) REVERT: C 19 ASP cc_start: 0.5431 (t0) cc_final: 0.5211 (t0) REVERT: C 50 GLU cc_start: 0.5566 (mt-10) cc_final: 0.5145 (mp0) REVERT: C 56 THR cc_start: 0.5190 (m) cc_final: 0.4956 (p) REVERT: C 75 MET cc_start: 0.6384 (mmm) cc_final: 0.6045 (tpt) REVERT: C 78 GLU cc_start: 0.6457 (mt-10) cc_final: 0.5326 (pm20) REVERT: C 94 LYS cc_start: 0.5547 (mtmt) cc_final: 0.5300 (mtmt) REVERT: C 102 GLN cc_start: 0.6829 (mt0) cc_final: 0.6601 (tt0) REVERT: C 106 GLU cc_start: 0.5776 (mt-10) cc_final: 0.5393 (mm-30) REVERT: C 121 VAL cc_start: 0.5955 (t) cc_final: 0.5684 (m) REVERT: C 123 ASN cc_start: 0.5873 (t0) cc_final: 0.5661 (t0) REVERT: C 125 MET cc_start: 0.6261 (mtp) cc_final: 0.5980 (mtt) REVERT: C 129 ILE cc_start: 0.5354 (tt) cc_final: 0.5093 (pt) REVERT: C 131 HIS cc_start: 0.4782 (m-70) cc_final: 0.4439 (m90) REVERT: C 136 ASP cc_start: 0.3424 (t70) cc_final: 0.3003 (t70) REVERT: C 137 LYS cc_start: 0.5983 (tttm) cc_final: 0.5767 (tttp) REVERT: C 138 GLU cc_start: 0.4537 (mp0) cc_final: 0.4129 (mp0) REVERT: C 152 GLU cc_start: 0.5631 (tt0) cc_final: 0.4535 (tm-30) REVERT: C 214 ASN cc_start: 0.6310 (m110) cc_final: 0.6084 (m110) REVERT: C 224 GLN cc_start: 0.5802 (mt0) cc_final: 0.5512 (mm-40) REVERT: E 4 GLU cc_start: 0.5758 (mm-30) cc_final: 0.5450 (tp30) REVERT: E 32 GLN cc_start: 0.6042 (tt0) cc_final: 0.5714 (tp40) REVERT: E 36 GLU cc_start: 0.6429 (mt-10) cc_final: 0.6192 (mt-10) REVERT: E 56 LYS cc_start: 0.6992 (tmmt) cc_final: 0.6731 (ttmm) REVERT: E 103 LYS cc_start: 0.6633 (mtpp) cc_final: 0.6368 (mttp) REVERT: E 106 GLN cc_start: 0.5816 (mm-40) cc_final: 0.5284 (mp10) REVERT: E 152 LYS cc_start: 0.6617 (tttp) cc_final: 0.6391 (tptt) REVERT: E 192 ARG cc_start: 0.6862 (ttt180) cc_final: 0.6346 (mpt-90) REVERT: E 201 LYS cc_start: 0.6766 (mtmt) cc_final: 0.6536 (ptpp) REVERT: F 129 LYS cc_start: 0.4833 (mmtm) cc_final: 0.4516 (mmtp) REVERT: F 149 GLU cc_start: 0.6430 (tt0) cc_final: 0.6075 (tt0) REVERT: H 14 GLU cc_start: 0.5673 (tt0) cc_final: 0.5059 (mt-10) REVERT: H 92 ASP cc_start: 0.5324 (m-30) cc_final: 0.5002 (p0) REVERT: H 138 GLU cc_start: 0.5719 (pt0) cc_final: 0.5438 (pt0) REVERT: I 13 MET cc_start: 0.0544 (ptt) cc_final: -0.0045 (OUTLIER) REVERT: I 97 MET cc_start: 0.4214 (mtp) cc_final: 0.3376 (tmt) REVERT: J 26 GLN cc_start: 0.5893 (tt0) cc_final: 0.5616 (mp10) REVERT: J 64 ASN cc_start: 0.5859 (t0) cc_final: 0.5176 (m110) REVERT: K 1 MET cc_start: 0.5387 (ttt) cc_final: 0.4978 (ttm) REVERT: K 17 SER cc_start: 0.6403 (m) cc_final: 0.6077 (t) REVERT: K 20 LYS cc_start: 0.5321 (tttp) cc_final: 0.5103 (tttm) REVERT: K 54 ARG cc_start: 0.6527 (mtm180) cc_final: 0.5571 (mmp-170) REVERT: K 79 GLU cc_start: 0.7250 (tt0) cc_final: 0.6680 (tp30) outliers start: 45 outliers final: 7 residues processed: 678 average time/residue: 0.8758 time to fit residues: 692.1948 Evaluate side-chains 443 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 433 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 854 ASN Chi-restraints excluded: chain A residue 1366 ARG Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain E residue 207 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain L residue 34 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 118 HIS A 209 ASN A 213 HIS A 287 HIS A 358 ASN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN A 611 GLN A 626 ASN A 854 ASN A1052 GLN A1082 ASN ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1390 ASN B 46 GLN B 325 GLN B 484 ASN ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 HIS B 686 ASN B 740 HIS B 951 GLN B 984 HIS B1025 HIS B1104 HIS ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1178 ASN C 17 ASN C 252 GLN D 34 GLN E 99 HIS H 33 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.192208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116747 restraints weight = 32581.819| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.76 r_work: 0.3323 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 33908 Z= 0.166 Angle : 0.658 12.220 46203 Z= 0.342 Chirality : 0.046 0.199 5190 Planarity : 0.005 0.055 5630 Dihedral : 17.154 160.434 5374 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.32 % Favored : 96.57 % Rotamer: Outliers : 2.04 % Allowed : 7.48 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.02 (0.13), residues: 3854 helix: 0.90 (0.14), residues: 1367 sheet: -0.14 (0.21), residues: 607 loop : -0.52 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 857 TYR 0.023 0.002 TYR B 797 PHE 0.037 0.002 PHE A 219 TRP 0.016 0.002 TRP E 13 HIS 0.011 0.002 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (33876) covalent geometry : angle 0.64049 / 0.34 (46158) hydrogen bonds : bond 0.04659 / 3.16 ( 1435) hydrogen bonds : angle 5.02947 / 3.63 ( 3994) metal coordination : bond 0.00886 / 0.49 ( 32) metal coordination : angle 4.84750 / 3.20 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 438 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8312 (mmt90) cc_final: 0.7871 (mmt-90) REVERT: A 36 ARG cc_start: 0.7819 (mtt-85) cc_final: 0.7549 (mtt-85) REVERT: A 205 GLU cc_start: 0.7169 (tt0) cc_final: 0.6808 (tp30) REVERT: A 293 GLU cc_start: 0.6733 (tt0) cc_final: 0.6478 (pt0) REVERT: A 393 ARG cc_start: 0.7605 (ttm110) cc_final: 0.7298 (mpt180) REVERT: A 407 ARG cc_start: 0.6992 (mtp-110) cc_final: 0.6694 (mtt180) REVERT: A 437 MET cc_start: 0.8495 (ptt) cc_final: 0.7367 (mtp) REVERT: A 535 THR cc_start: 0.8613 (m) cc_final: 0.8410 (p) REVERT: A 549 MET cc_start: 0.8945 (mtp) cc_final: 0.8679 (mtp) REVERT: A 685 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6264 (pt0) REVERT: A 696 GLU cc_start: 0.5238 (tt0) cc_final: 0.4621 (tt0) REVERT: A 873 MET cc_start: 0.9016 (mmp) cc_final: 0.8343 (mmt) REVERT: A 894 GLU cc_start: 0.8098 (tp30) cc_final: 0.7850 (mm-30) REVERT: A 992 ASP cc_start: 0.7465 (m-30) cc_final: 0.7135 (t70) REVERT: A 1079 MET cc_start: 0.8012 (ttp) cc_final: 0.7804 (ttp) REVERT: A 1092 LYS cc_start: 0.7239 (mptt) cc_final: 0.6698 (tppt) REVERT: A 1267 MET cc_start: 0.5433 (mtt) cc_final: 0.4753 (pp-130) REVERT: A 1307 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: A 1314 SER cc_start: 0.8451 (t) cc_final: 0.8149 (p) REVERT: A 1315 GLU cc_start: 0.7693 (tt0) cc_final: 0.7186 (mm-30) REVERT: A 1366 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7790 (ptm160) REVERT: A 1420 ASP cc_start: 0.7703 (t0) cc_final: 0.7114 (p0) REVERT: A 1424 VAL cc_start: 0.8398 (m) cc_final: 0.8195 (p) REVERT: B 21 GLU cc_start: 0.7360 (pt0) cc_final: 0.7094 (mt-10) REVERT: B 26 THR cc_start: 0.8285 (p) cc_final: 0.7892 (t) REVERT: B 94 LYS cc_start: 0.7451 (tttm) cc_final: 0.7209 (tttp) REVERT: B 239 GLU cc_start: 0.7397 (pt0) cc_final: 0.6654 (mp0) REVERT: B 255 GLN cc_start: 0.7313 (pt0) cc_final: 0.7031 (pt0) REVERT: B 257 LYS cc_start: 0.7026 (mtmt) cc_final: 0.6435 (mtmm) REVERT: B 357 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.6706 (tp-100) REVERT: B 378 LEU cc_start: 0.7336 (tp) cc_final: 0.7134 (tp) REVERT: B 393 LYS cc_start: 0.7550 (ttpt) cc_final: 0.7052 (pttp) REVERT: B 473 MET cc_start: 0.6359 (mmp) cc_final: 0.6007 (mpp) REVERT: B 542 MET cc_start: 0.9161 (mtm) cc_final: 0.8913 (mtt) REVERT: B 552 MET cc_start: 0.7914 (tpp) cc_final: 0.7704 (mmm) REVERT: B 564 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7091 (mm-30) REVERT: B 567 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.5976 (pm20) REVERT: B 595 ARG cc_start: 0.7798 (ttt180) cc_final: 0.7030 (ttp80) REVERT: B 622 LYS cc_start: 0.6783 (OUTLIER) cc_final: 0.6548 (tttt) REVERT: B 650 GLU cc_start: 0.7662 (pt0) cc_final: 0.7074 (pm20) REVERT: B 1004 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8117 (pt0) REVERT: B 1181 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7098 (tp30) REVERT: C 50 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7347 (mp0) REVERT: C 78 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7068 (pm20) REVERT: C 106 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7797 (mm-30) REVERT: C 135 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8455 (mt0) REVERT: C 138 GLU cc_start: 0.7082 (mp0) cc_final: 0.6807 (mp0) REVERT: C 179 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8738 (tt0) REVERT: C 264 GLN cc_start: 0.5969 (tp-100) cc_final: 0.5641 (mt0) REVERT: D 1 MET cc_start: 0.1301 (ttt) cc_final: 0.0416 (tpt) REVERT: D 117 GLU cc_start: 0.2487 (mp0) cc_final: 0.1994 (tp30) REVERT: D 187 THR cc_start: 0.3104 (OUTLIER) cc_final: 0.2848 (p) REVERT: E 4 GLU cc_start: 0.6439 (mm-30) cc_final: 0.6222 (tp30) REVERT: E 75 MET cc_start: 0.8445 (ptm) cc_final: 0.8243 (ptm) REVERT: E 81 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7327 (tp30) REVERT: E 90 VAL cc_start: 0.7025 (t) cc_final: 0.6643 (m) REVERT: E 103 LYS cc_start: 0.7669 (mtpp) cc_final: 0.7180 (mttp) REVERT: E 106 GLN cc_start: 0.7548 (mm-40) cc_final: 0.7143 (mp10) REVERT: E 121 MET cc_start: 0.7614 (mmm) cc_final: 0.7257 (mmm) REVERT: F 103 MET cc_start: 0.7672 (mtt) cc_final: 0.7461 (mtp) REVERT: G 29 LYS cc_start: 0.4183 (tppt) cc_final: 0.3794 (ttmt) REVERT: H 14 GLU cc_start: 0.8175 (tt0) cc_final: 0.7654 (mt-10) REVERT: H 37 LYS cc_start: 0.8150 (ptmt) cc_final: 0.7848 (pttt) REVERT: I 97 MET cc_start: 0.4775 (mtp) cc_final: 0.3801 (tmt) REVERT: J 64 ASN cc_start: 0.7444 (t0) cc_final: 0.6823 (m-40) REVERT: K 1 MET cc_start: 0.7088 (ttt) cc_final: 0.6707 (ttm) REVERT: K 20 LYS cc_start: 0.8398 (tttp) cc_final: 0.8129 (tttm) REVERT: K 54 ARG cc_start: 0.7951 (mtm180) cc_final: 0.7512 (mmp-170) outliers start: 70 outliers final: 26 residues processed: 478 average time/residue: 0.8941 time to fit residues: 497.5078 Evaluate side-chains 427 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 390 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 938 LYS Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 1307 GLU Chi-restraints excluded: chain A residue 1366 ARG Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 567 GLU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1150 ARG Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain L residue 33 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 336 optimal weight: 20.0000 chunk 246 optimal weight: 0.6980 chunk 239 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 327 optimal weight: 0.9980 chunk 160 optimal weight: 40.0000 chunk 85 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 ASN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN B 776 GLN B 957 ASN B1178 ASN C 102 GLN C 123 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.191230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115881 restraints weight = 32576.804| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.73 r_work: 0.3319 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33908 Z= 0.141 Angle : 0.590 10.937 46203 Z= 0.309 Chirality : 0.044 0.183 5190 Planarity : 0.005 0.055 5630 Dihedral : 16.985 159.287 5360 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.96 % Favored : 96.96 % Rotamer: Outliers : 2.33 % Allowed : 9.44 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.12 (0.13), residues: 3854 helix: 1.01 (0.14), residues: 1367 sheet: 0.04 (0.21), residues: 593 loop : -0.54 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 591 TYR 0.013 0.001 TYR B 486 PHE 0.033 0.002 PHE A 219 TRP 0.012 0.002 TRP E 13 HIS 0.011 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (33876) covalent geometry : angle 0.57602 / 0.31 (46158) hydrogen bonds : bond 0.04129 / 2.80 ( 1435) hydrogen bonds : angle 4.69978 / 3.39 ( 3994) metal coordination : bond 0.00592 / 0.36 ( 32) metal coordination : angle 4.06662 / 2.59 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 405 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8304 (mmt90) cc_final: 0.7804 (mmt-90) REVERT: A 205 GLU cc_start: 0.7232 (tt0) cc_final: 0.6820 (tp30) REVERT: A 293 GLU cc_start: 0.6652 (tt0) cc_final: 0.6411 (pt0) REVERT: A 385 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.6956 (mt) REVERT: A 393 ARG cc_start: 0.7584 (ttm110) cc_final: 0.7328 (mpt180) REVERT: A 398 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6872 (tm-30) REVERT: A 407 ARG cc_start: 0.7011 (mtp-110) cc_final: 0.6684 (mtt180) REVERT: A 437 MET cc_start: 0.8433 (ptt) cc_final: 0.7383 (mtp) REVERT: A 494 SER cc_start: 0.8689 (t) cc_final: 0.8373 (p) REVERT: A 549 MET cc_start: 0.8948 (mtp) cc_final: 0.8663 (mtp) REVERT: A 618 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7160 (pp20) REVERT: A 685 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6272 (pt0) REVERT: A 708 MET cc_start: 0.4936 (mtt) cc_final: 0.4399 (ttm) REVERT: A 894 GLU cc_start: 0.8067 (tp30) cc_final: 0.7789 (mm-30) REVERT: A 992 ASP cc_start: 0.7410 (m-30) cc_final: 0.7099 (OUTLIER) REVERT: A 1092 LYS cc_start: 0.7310 (mptt) cc_final: 0.6776 (tppt) REVERT: A 1267 MET cc_start: 0.5408 (mtt) cc_final: 0.4805 (pp-130) REVERT: A 1297 GLU cc_start: 0.8222 (pm20) cc_final: 0.7732 (pm20) REVERT: A 1307 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: A 1315 GLU cc_start: 0.7779 (tt0) cc_final: 0.7198 (mm-30) REVERT: A 1420 ASP cc_start: 0.7663 (t0) cc_final: 0.7104 (p0) REVERT: A 1424 VAL cc_start: 0.8430 (m) cc_final: 0.8202 (p) REVERT: B 21 GLU cc_start: 0.7335 (pt0) cc_final: 0.7058 (mt-10) REVERT: B 26 THR cc_start: 0.8296 (p) cc_final: 0.7858 (t) REVERT: B 239 GLU cc_start: 0.7423 (pt0) cc_final: 0.6703 (mp0) REVERT: B 257 LYS cc_start: 0.7109 (mtmt) cc_final: 0.6566 (mtmm) REVERT: B 422 LYS cc_start: 0.6368 (mmtm) cc_final: 0.5746 (mmtm) REVERT: B 432 MET cc_start: 0.5944 (OUTLIER) cc_final: 0.4690 (ptp) REVERT: B 451 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7233 (ttmm) REVERT: B 473 MET cc_start: 0.6335 (mmp) cc_final: 0.6000 (mpp) REVERT: B 542 MET cc_start: 0.9194 (mtm) cc_final: 0.8938 (mtt) REVERT: B 557 PHE cc_start: 0.8047 (m-10) cc_final: 0.7831 (m-10) REVERT: B 564 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7119 (mm-30) REVERT: B 567 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6058 (pm20) REVERT: B 595 ARG cc_start: 0.7767 (ttt180) cc_final: 0.6922 (ttp80) REVERT: B 650 GLU cc_start: 0.7638 (pt0) cc_final: 0.7228 (pm20) REVERT: B 662 MET cc_start: 0.7932 (mmm) cc_final: 0.7409 (mmm) REVERT: B 1004 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8148 (pt0) REVERT: B 1181 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7120 (tp30) REVERT: C 50 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7303 (mp0) REVERT: C 72 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8117 (mp) REVERT: C 78 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7120 (pm20) REVERT: C 102 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7908 (mp10) REVERT: C 106 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7834 (mm-30) REVERT: C 138 GLU cc_start: 0.7175 (mp0) cc_final: 0.6769 (mp0) REVERT: C 152 GLU cc_start: 0.8254 (tt0) cc_final: 0.7835 (tm-30) REVERT: C 179 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8741 (tt0) REVERT: C 264 GLN cc_start: 0.5990 (tp-100) cc_final: 0.5659 (mt0) REVERT: D 1 MET cc_start: 0.1063 (ttt) cc_final: 0.0129 (tpt) REVERT: D 117 GLU cc_start: 0.2710 (mp0) cc_final: 0.2137 (tp30) REVERT: D 145 MET cc_start: 0.4919 (mmm) cc_final: 0.3972 (ttp) REVERT: D 187 THR cc_start: 0.3220 (t) cc_final: 0.3013 (p) REVERT: E 4 GLU cc_start: 0.6481 (mm-30) cc_final: 0.6260 (tp30) REVERT: E 90 VAL cc_start: 0.7185 (t) cc_final: 0.6869 (m) REVERT: E 103 LYS cc_start: 0.7681 (mtpp) cc_final: 0.7194 (mttp) REVERT: E 106 GLN cc_start: 0.7483 (mm-40) cc_final: 0.7094 (mp10) REVERT: E 121 MET cc_start: 0.7696 (mmm) cc_final: 0.7420 (mmm) REVERT: F 72 LYS cc_start: 0.6816 (mmpt) cc_final: 0.6394 (mttt) REVERT: F 103 MET cc_start: 0.7601 (mtt) cc_final: 0.7386 (mtp) REVERT: G 14 HIS cc_start: 0.6724 (t-90) cc_final: 0.6396 (t-90) REVERT: G 29 LYS cc_start: 0.4521 (tppt) cc_final: 0.4087 (ttmt) REVERT: H 14 GLU cc_start: 0.8178 (tt0) cc_final: 0.7628 (mt-10) REVERT: I 97 MET cc_start: 0.4876 (mtp) cc_final: 0.4026 (tmt) REVERT: J 64 ASN cc_start: 0.7424 (t0) cc_final: 0.6803 (m-40) REVERT: K 1 MET cc_start: 0.7137 (ttt) cc_final: 0.6789 (ttm) REVERT: K 20 LYS cc_start: 0.8380 (tttp) cc_final: 0.8118 (tttm) REVERT: K 54 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7508 (mmp-170) outliers start: 80 outliers final: 29 residues processed: 455 average time/residue: 0.8837 time to fit residues: 469.7647 Evaluate side-chains 419 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 379 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 938 LYS Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1307 GLU Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 567 GLU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain L residue 55 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 16 optimal weight: 9.9990 chunk 355 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 225 optimal weight: 10.0000 chunk 336 optimal weight: 20.0000 chunk 80 optimal weight: 0.5980 chunk 341 optimal weight: 7.9990 chunk 305 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 297 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 626 ASN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 ASN A 965 GLN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN B 957 ASN ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN C 252 GLN D 146 GLN G 122 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.194620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.114787 restraints weight = 32287.741| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.89 r_work: 0.3374 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 33908 Z= 0.188 Angle : 0.632 13.314 46203 Z= 0.330 Chirality : 0.046 0.244 5190 Planarity : 0.005 0.057 5630 Dihedral : 16.979 157.889 5356 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.37 % Favored : 96.55 % Rotamer: Outliers : 2.36 % Allowed : 10.16 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.05 (0.13), residues: 3854 helix: 0.89 (0.14), residues: 1377 sheet: 0.10 (0.21), residues: 571 loop : -0.56 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1366 TYR 0.018 0.002 TYR B 486 PHE 0.034 0.002 PHE A 219 TRP 0.014 0.002 TRP B 31 HIS 0.014 0.002 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (33876) covalent geometry : angle 0.61946 / 0.33 (46158) hydrogen bonds : bond 0.04479 / 3.03 ( 1435) hydrogen bonds : angle 4.73762 / 3.41 ( 3994) metal coordination : bond 0.00545 / 0.35 ( 32) metal coordination : angle 4.05477 / 2.61 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 400 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8379 (mmt90) cc_final: 0.7824 (mmt-90) REVERT: A 205 GLU cc_start: 0.7348 (tt0) cc_final: 0.6912 (tp30) REVERT: A 293 GLU cc_start: 0.6724 (tt0) cc_final: 0.6465 (pt0) REVERT: A 385 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7141 (mt) REVERT: A 393 ARG cc_start: 0.7709 (ttm110) cc_final: 0.7503 (mpt-90) REVERT: A 398 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.7080 (tm-30) REVERT: A 407 ARG cc_start: 0.7089 (mtp-110) cc_final: 0.6675 (mtt180) REVERT: A 437 MET cc_start: 0.8488 (ptt) cc_final: 0.7406 (mtp) REVERT: A 549 MET cc_start: 0.9039 (mtp) cc_final: 0.8709 (mtp) REVERT: A 618 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7297 (pp20) REVERT: A 685 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6230 (pt0) REVERT: A 708 MET cc_start: 0.5041 (mtt) cc_final: 0.4459 (ttm) REVERT: A 894 GLU cc_start: 0.8069 (tp30) cc_final: 0.7826 (mm-30) REVERT: A 992 ASP cc_start: 0.7503 (m-30) cc_final: 0.7167 (t70) REVERT: A 1079 MET cc_start: 0.8158 (ttp) cc_final: 0.7870 (ttp) REVERT: A 1092 LYS cc_start: 0.7307 (mptt) cc_final: 0.6817 (tppt) REVERT: A 1297 GLU cc_start: 0.8306 (pm20) cc_final: 0.7797 (pm20) REVERT: A 1307 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: A 1315 GLU cc_start: 0.7917 (tt0) cc_final: 0.7392 (mm-30) REVERT: A 1420 ASP cc_start: 0.7699 (t0) cc_final: 0.7016 (p0) REVERT: A 1424 VAL cc_start: 0.8457 (m) cc_final: 0.8186 (p) REVERT: B 21 GLU cc_start: 0.7444 (pt0) cc_final: 0.7107 (mt-10) REVERT: B 239 GLU cc_start: 0.7468 (pt0) cc_final: 0.6747 (mp0) REVERT: B 257 LYS cc_start: 0.7092 (mtmt) cc_final: 0.6394 (mttp) REVERT: B 422 LYS cc_start: 0.6497 (mmtm) cc_final: 0.5837 (mmtm) REVERT: B 451 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7237 (ttmm) REVERT: B 473 MET cc_start: 0.6488 (mmp) cc_final: 0.6117 (mpp) REVERT: B 542 MET cc_start: 0.9264 (mtm) cc_final: 0.9044 (mtt) REVERT: B 564 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7198 (mm-30) REVERT: B 567 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6145 (pm20) REVERT: B 595 ARG cc_start: 0.7764 (ttt180) cc_final: 0.6928 (ttp80) REVERT: B 623 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7039 (mt-10) REVERT: B 896 ASP cc_start: 0.6422 (t0) cc_final: 0.5930 (p0) REVERT: B 1181 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7222 (tp30) REVERT: C 50 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7422 (mp0) REVERT: C 78 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7138 (pm20) REVERT: C 106 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7918 (mm-30) REVERT: C 138 GLU cc_start: 0.7219 (mp0) cc_final: 0.6903 (mp0) REVERT: C 152 GLU cc_start: 0.8290 (tt0) cc_final: 0.7716 (tm-30) REVERT: C 179 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8833 (tt0) REVERT: C 264 GLN cc_start: 0.6116 (tp-100) cc_final: 0.5726 (mt0) REVERT: D 1 MET cc_start: 0.1236 (ttt) cc_final: -0.0001 (tpt) REVERT: D 44 GLU cc_start: 0.2552 (OUTLIER) cc_final: 0.1779 (tt0) REVERT: D 117 GLU cc_start: 0.2743 (mp0) cc_final: 0.2230 (tp30) REVERT: E 81 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7303 (tp30) REVERT: E 90 VAL cc_start: 0.7369 (t) cc_final: 0.7020 (m) REVERT: E 103 LYS cc_start: 0.7697 (mtpp) cc_final: 0.7246 (mttp) REVERT: E 106 GLN cc_start: 0.7555 (mm-40) cc_final: 0.7134 (mp10) REVERT: E 121 MET cc_start: 0.7656 (mmm) cc_final: 0.7364 (mmm) REVERT: F 72 LYS cc_start: 0.6863 (mmpt) cc_final: 0.6517 (mttt) REVERT: H 14 GLU cc_start: 0.8307 (tt0) cc_final: 0.7697 (mt-10) REVERT: H 91 ASP cc_start: 0.8091 (m-30) cc_final: 0.7731 (m-30) REVERT: I 1 MET cc_start: 0.4146 (mmm) cc_final: 0.2004 (ptp) REVERT: I 97 MET cc_start: 0.5178 (mtp) cc_final: 0.4115 (tmt) REVERT: J 64 ASN cc_start: 0.7561 (t0) cc_final: 0.6939 (m-40) REVERT: K 1 MET cc_start: 0.7118 (ttt) cc_final: 0.6770 (ttm) REVERT: K 20 LYS cc_start: 0.8376 (tttp) cc_final: 0.8094 (tttm) REVERT: K 54 ARG cc_start: 0.7978 (mtm180) cc_final: 0.7463 (mmp-170) REVERT: L 54 ARG cc_start: 0.6218 (OUTLIER) cc_final: 0.5973 (mtt-85) outliers start: 81 outliers final: 40 residues processed: 455 average time/residue: 0.8828 time to fit residues: 468.6583 Evaluate side-chains 430 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 378 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 938 LYS Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1307 GLU Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 567 GLU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1050 ILE Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain L residue 54 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 34 optimal weight: 0.3980 chunk 138 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 175 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 272 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 345 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN B 957 ASN B1076 HIS ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1178 ASN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN G 14 HIS G 122 ASN H 35 GLN H 128 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.188795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.112899 restraints weight = 32553.621| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.72 r_work: 0.3254 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33908 Z= 0.143 Angle : 0.573 10.871 46203 Z= 0.301 Chirality : 0.044 0.207 5190 Planarity : 0.004 0.054 5630 Dihedral : 16.867 157.271 5356 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.98 % Favored : 96.94 % Rotamer: Outliers : 2.21 % Allowed : 11.21 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.16 (0.13), residues: 3854 helix: 1.02 (0.14), residues: 1379 sheet: 0.15 (0.21), residues: 572 loop : -0.54 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 579 TYR 0.013 0.001 TYR B 486 PHE 0.030 0.002 PHE A 219 TRP 0.015 0.002 TRP A1228 HIS 0.010 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (33876) covalent geometry : angle 0.56132 / 0.30 (46158) hydrogen bonds : bond 0.03952 / 2.67 ( 1435) hydrogen bonds : angle 4.56188 / 3.29 ( 3994) metal coordination : bond 0.00474 / 0.30 ( 32) metal coordination : angle 3.68531 / 2.36 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 395 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8354 (mmt90) cc_final: 0.7796 (mmt-90) REVERT: A 205 GLU cc_start: 0.7338 (tt0) cc_final: 0.6892 (tp30) REVERT: A 293 GLU cc_start: 0.6752 (tt0) cc_final: 0.6506 (pt0) REVERT: A 385 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7104 (mt) REVERT: A 407 ARG cc_start: 0.7074 (mtp-110) cc_final: 0.6703 (mtt180) REVERT: A 437 MET cc_start: 0.8523 (ptt) cc_final: 0.7464 (mtp) REVERT: A 618 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7285 (pp20) REVERT: A 685 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6335 (pt0) REVERT: A 702 LEU cc_start: 0.3996 (OUTLIER) cc_final: 0.3438 (pp) REVERT: A 708 MET cc_start: 0.4814 (mtt) cc_final: 0.4322 (ttm) REVERT: A 894 GLU cc_start: 0.8117 (tp30) cc_final: 0.7838 (mm-30) REVERT: A 992 ASP cc_start: 0.7461 (m-30) cc_final: 0.7110 (t70) REVERT: A 1092 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6853 (tppp) REVERT: A 1297 GLU cc_start: 0.8259 (pm20) cc_final: 0.7675 (pm20) REVERT: A 1315 GLU cc_start: 0.7914 (tt0) cc_final: 0.7378 (mm-30) REVERT: A 1420 ASP cc_start: 0.7720 (t0) cc_final: 0.7101 (p0) REVERT: A 1424 VAL cc_start: 0.8481 (m) cc_final: 0.8235 (p) REVERT: B 21 GLU cc_start: 0.7408 (pt0) cc_final: 0.7141 (mt-10) REVERT: B 239 GLU cc_start: 0.7435 (pt0) cc_final: 0.6740 (mp0) REVERT: B 257 LYS cc_start: 0.7097 (mtmt) cc_final: 0.6435 (mttp) REVERT: B 357 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.6726 (tp-100) REVERT: B 422 LYS cc_start: 0.6554 (mmtm) cc_final: 0.5860 (mmtm) REVERT: B 451 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7219 (ttmm) REVERT: B 473 MET cc_start: 0.6526 (mmp) cc_final: 0.6170 (mpp) REVERT: B 557 PHE cc_start: 0.8136 (m-10) cc_final: 0.7880 (m-10) REVERT: B 564 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7127 (mm-30) REVERT: B 567 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6162 (pm20) REVERT: B 595 ARG cc_start: 0.7697 (ttt180) cc_final: 0.6887 (ttp80) REVERT: B 623 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7021 (mt-10) REVERT: B 650 GLU cc_start: 0.7554 (pt0) cc_final: 0.7029 (pm20) REVERT: B 662 MET cc_start: 0.7888 (mmm) cc_final: 0.7432 (mmm) REVERT: B 896 ASP cc_start: 0.6429 (t0) cc_final: 0.6061 (p0) REVERT: B 1181 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7253 (tp30) REVERT: C 50 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7355 (mp0) REVERT: C 72 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8198 (mp) REVERT: C 78 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7161 (pm20) REVERT: C 106 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7894 (mm-30) REVERT: C 135 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8337 (mt0) REVERT: C 138 GLU cc_start: 0.7214 (mp0) cc_final: 0.6903 (mp0) REVERT: C 152 GLU cc_start: 0.8219 (tt0) cc_final: 0.7771 (tm-30) REVERT: C 179 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8760 (tt0) REVERT: C 264 GLN cc_start: 0.6094 (tp-100) cc_final: 0.5745 (mt0) REVERT: D 1 MET cc_start: 0.1208 (ttt) cc_final: -0.0021 (tpt) REVERT: D 32 GLU cc_start: 0.3129 (mm-30) cc_final: 0.2424 (tt0) REVERT: D 44 GLU cc_start: 0.2359 (OUTLIER) cc_final: 0.1777 (tt0) REVERT: D 145 MET cc_start: 0.4753 (mmm) cc_final: 0.3722 (ttp) REVERT: E 81 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7256 (tp30) REVERT: E 90 VAL cc_start: 0.7431 (t) cc_final: 0.7110 (m) REVERT: E 103 LYS cc_start: 0.7698 (mtpp) cc_final: 0.7409 (mppt) REVERT: E 106 GLN cc_start: 0.7512 (mm-40) cc_final: 0.7136 (mp10) REVERT: E 121 MET cc_start: 0.7705 (mmm) cc_final: 0.7444 (mmm) REVERT: F 72 LYS cc_start: 0.6876 (mmpt) cc_final: 0.6525 (mttt) REVERT: H 14 GLU cc_start: 0.8327 (tt0) cc_final: 0.7715 (pt0) REVERT: H 91 ASP cc_start: 0.8101 (m-30) cc_final: 0.7756 (m-30) REVERT: I 1 MET cc_start: 0.4224 (mmm) cc_final: 0.2022 (ptp) REVERT: I 97 MET cc_start: 0.5249 (mtp) cc_final: 0.4064 (tmt) REVERT: J 64 ASN cc_start: 0.7484 (t0) cc_final: 0.6890 (m-40) REVERT: K 1 MET cc_start: 0.7180 (ttt) cc_final: 0.6864 (ttm) REVERT: K 20 LYS cc_start: 0.8419 (tttp) cc_final: 0.8149 (tttm) REVERT: K 54 ARG cc_start: 0.7949 (mtm180) cc_final: 0.7515 (mmp-170) outliers start: 76 outliers final: 36 residues processed: 449 average time/residue: 0.8737 time to fit residues: 458.4872 Evaluate side-chains 425 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 375 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 938 LYS Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1092 LYS Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 567 GLU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain L residue 33 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 300 optimal weight: 6.9990 chunk 264 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 294 optimal weight: 8.9990 chunk 70 optimal weight: 0.1980 chunk 287 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 359 optimal weight: 0.6980 chunk 248 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN A 626 ASN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 ASN ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN E 179 GLN G 14 HIS H 35 GLN H 128 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.188066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.112555 restraints weight = 32252.921| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.69 r_work: 0.3248 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33908 Z= 0.148 Angle : 0.574 11.176 46203 Z= 0.302 Chirality : 0.044 0.217 5190 Planarity : 0.004 0.053 5630 Dihedral : 16.793 155.995 5356 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.37 % Favored : 96.55 % Rotamer: Outliers : 2.53 % Allowed : 11.56 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.23 (0.13), residues: 3854 helix: 1.12 (0.14), residues: 1367 sheet: 0.18 (0.21), residues: 575 loop : -0.51 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 579 TYR 0.014 0.001 TYR B 486 PHE 0.030 0.002 PHE A 219 TRP 0.012 0.002 TRP C 192 HIS 0.012 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (33876) covalent geometry : angle 0.56352 / 0.30 (46158) hydrogen bonds : bond 0.03970 / 2.68 ( 1435) hydrogen bonds : angle 4.51719 / 3.25 ( 3994) metal coordination : bond 0.00446 / 0.28 ( 32) metal coordination : angle 3.53815 / 2.29 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 388 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8399 (mmt90) cc_final: 0.7811 (mmt-90) REVERT: A 205 GLU cc_start: 0.7427 (tt0) cc_final: 0.6943 (tp30) REVERT: A 293 GLU cc_start: 0.6762 (tt0) cc_final: 0.6518 (pt0) REVERT: A 385 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7191 (mt) REVERT: A 407 ARG cc_start: 0.7036 (mtp-110) cc_final: 0.6710 (mtt180) REVERT: A 437 MET cc_start: 0.8542 (ptt) cc_final: 0.7465 (mtp) REVERT: A 618 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7304 (pp20) REVERT: A 685 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6477 (pt0) REVERT: A 702 LEU cc_start: 0.4119 (OUTLIER) cc_final: 0.3562 (pp) REVERT: A 708 MET cc_start: 0.4771 (mtt) cc_final: 0.4303 (ttm) REVERT: A 894 GLU cc_start: 0.8115 (tp30) cc_final: 0.7853 (mm-30) REVERT: A 992 ASP cc_start: 0.7509 (m-30) cc_final: 0.7203 (t70) REVERT: A 1079 MET cc_start: 0.8160 (ttp) cc_final: 0.7802 (tmm) REVERT: A 1092 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.6900 (tppp) REVERT: A 1297 GLU cc_start: 0.8264 (pm20) cc_final: 0.7694 (pm20) REVERT: A 1307 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: A 1420 ASP cc_start: 0.7703 (t0) cc_final: 0.7052 (p0) REVERT: A 1424 VAL cc_start: 0.8502 (m) cc_final: 0.8248 (p) REVERT: A 1452 LYS cc_start: 0.6835 (OUTLIER) cc_final: 0.6614 (ttpp) REVERT: B 21 GLU cc_start: 0.7465 (pt0) cc_final: 0.7064 (mp0) REVERT: B 239 GLU cc_start: 0.7449 (pt0) cc_final: 0.6748 (mp0) REVERT: B 257 LYS cc_start: 0.7082 (mtmt) cc_final: 0.6394 (mttp) REVERT: B 422 LYS cc_start: 0.6560 (mmtm) cc_final: 0.5842 (mmtm) REVERT: B 432 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.4663 (ptm) REVERT: B 451 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7223 (ttmm) REVERT: B 473 MET cc_start: 0.6532 (mmp) cc_final: 0.6187 (mpp) REVERT: B 557 PHE cc_start: 0.8182 (m-10) cc_final: 0.7917 (m-10) REVERT: B 564 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7204 (mm-30) REVERT: B 595 ARG cc_start: 0.7661 (ttt180) cc_final: 0.6826 (ttp80) REVERT: B 623 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7053 (mm-30) REVERT: B 896 ASP cc_start: 0.6649 (t0) cc_final: 0.6147 (p0) REVERT: B 1004 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8118 (pt0) REVERT: B 1181 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7281 (tp30) REVERT: C 50 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7364 (mp0) REVERT: C 72 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8227 (mp) REVERT: C 78 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7179 (pm20) REVERT: C 102 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7140 (mp-120) REVERT: C 106 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7889 (mm-30) REVERT: C 135 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8373 (mt0) REVERT: C 138 GLU cc_start: 0.7199 (mp0) cc_final: 0.6880 (mp0) REVERT: C 152 GLU cc_start: 0.8230 (tt0) cc_final: 0.7575 (tm-30) REVERT: C 179 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8775 (tt0) REVERT: C 264 GLN cc_start: 0.6090 (tp-100) cc_final: 0.5752 (mt0) REVERT: D 1 MET cc_start: 0.1175 (ttt) cc_final: -0.0163 (tpt) REVERT: D 32 GLU cc_start: 0.3393 (mm-30) cc_final: 0.2585 (tt0) REVERT: D 44 GLU cc_start: 0.2454 (OUTLIER) cc_final: 0.1929 (tt0) REVERT: E 81 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7243 (tp30) REVERT: E 90 VAL cc_start: 0.7551 (t) cc_final: 0.7251 (m) REVERT: E 103 LYS cc_start: 0.7679 (mtpp) cc_final: 0.7406 (mppt) REVERT: E 106 GLN cc_start: 0.7477 (mm-40) cc_final: 0.7148 (mp10) REVERT: E 121 MET cc_start: 0.7750 (mmm) cc_final: 0.7500 (mmm) REVERT: F 72 LYS cc_start: 0.6876 (mmpt) cc_final: 0.6556 (mttt) REVERT: G 101 VAL cc_start: 0.0518 (OUTLIER) cc_final: 0.0305 (p) REVERT: H 14 GLU cc_start: 0.8316 (tt0) cc_final: 0.7784 (pt0) REVERT: I 1 MET cc_start: 0.4339 (mmm) cc_final: 0.2142 (ptp) REVERT: I 97 MET cc_start: 0.5462 (mtp) cc_final: 0.4220 (tmt) REVERT: J 64 ASN cc_start: 0.7407 (t0) cc_final: 0.6868 (m-40) REVERT: K 1 MET cc_start: 0.7207 (ttt) cc_final: 0.6870 (ttm) REVERT: K 20 LYS cc_start: 0.8411 (tttp) cc_final: 0.8143 (tttm) REVERT: K 54 ARG cc_start: 0.7977 (mtm180) cc_final: 0.7548 (mmp-170) outliers start: 87 outliers final: 45 residues processed: 444 average time/residue: 0.8560 time to fit residues: 446.0076 Evaluate side-chains 438 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 375 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 938 LYS Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1092 LYS Chi-restraints excluded: chain A residue 1307 GLU Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1452 LYS Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1150 ARG Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain L residue 33 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 323 optimal weight: 0.0980 chunk 319 optimal weight: 4.9990 chunk 225 optimal weight: 8.9990 chunk 118 optimal weight: 0.0870 chunk 302 optimal weight: 0.9980 chunk 384 optimal weight: 10.0000 chunk 272 optimal weight: 0.9990 chunk 337 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 288 optimal weight: 8.9990 chunk 364 optimal weight: 9.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 626 ASN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 ASN ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1179 GLN C 214 ASN G 14 HIS H 128 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.188523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.113185 restraints weight = 32500.011| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.70 r_work: 0.3255 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33908 Z= 0.131 Angle : 0.556 11.483 46203 Z= 0.293 Chirality : 0.043 0.195 5190 Planarity : 0.004 0.054 5630 Dihedral : 16.740 155.599 5356 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.11 % Favored : 96.81 % Rotamer: Outliers : 2.15 % Allowed : 12.49 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.31 (0.13), residues: 3854 helix: 1.20 (0.14), residues: 1367 sheet: 0.19 (0.21), residues: 581 loop : -0.47 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 579 TYR 0.012 0.001 TYR B 486 PHE 0.028 0.002 PHE A 219 TRP 0.012 0.001 TRP C 192 HIS 0.009 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (33876) covalent geometry : angle 0.54597 / 0.29 (46158) hydrogen bonds : bond 0.03766 / 2.55 ( 1435) hydrogen bonds : angle 4.45987 / 3.21 ( 3994) metal coordination : bond 0.00409 / 0.26 ( 32) metal coordination : angle 3.37327 / 2.18 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 379 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8386 (mmt90) cc_final: 0.7782 (mmt-90) REVERT: A 205 GLU cc_start: 0.7405 (tt0) cc_final: 0.6910 (tp30) REVERT: A 280 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6902 (mt-10) REVERT: A 293 GLU cc_start: 0.6730 (tt0) cc_final: 0.6493 (pt0) REVERT: A 385 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7129 (mt) REVERT: A 407 ARG cc_start: 0.7078 (mtp-110) cc_final: 0.6731 (mtt180) REVERT: A 437 MET cc_start: 0.8538 (ptt) cc_final: 0.7456 (mtp) REVERT: A 455 MET cc_start: 0.8843 (ttt) cc_final: 0.8640 (ttm) REVERT: A 618 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7304 (pp20) REVERT: A 685 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6394 (pt0) REVERT: A 702 LEU cc_start: 0.4072 (OUTLIER) cc_final: 0.3537 (pp) REVERT: A 708 MET cc_start: 0.4655 (mtt) cc_final: 0.4224 (ttm) REVERT: A 894 GLU cc_start: 0.8055 (tp30) cc_final: 0.7791 (mm-30) REVERT: A 992 ASP cc_start: 0.7512 (m-30) cc_final: 0.7157 (t70) REVERT: A 1079 MET cc_start: 0.8153 (ttp) cc_final: 0.7774 (tmm) REVERT: A 1092 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6928 (tppp) REVERT: A 1297 GLU cc_start: 0.8250 (pm20) cc_final: 0.7757 (pm20) REVERT: A 1420 ASP cc_start: 0.7651 (t0) cc_final: 0.7026 (p0) REVERT: A 1424 VAL cc_start: 0.8504 (m) cc_final: 0.8259 (p) REVERT: B 21 GLU cc_start: 0.7452 (pt0) cc_final: 0.7052 (mp0) REVERT: B 239 GLU cc_start: 0.7425 (pt0) cc_final: 0.6727 (mp0) REVERT: B 257 LYS cc_start: 0.7054 (mtmt) cc_final: 0.6386 (mttp) REVERT: B 357 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.6728 (tp-100) REVERT: B 422 LYS cc_start: 0.6541 (mmtm) cc_final: 0.5811 (mmtm) REVERT: B 432 MET cc_start: 0.5978 (OUTLIER) cc_final: 0.4719 (ptm) REVERT: B 451 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7173 (ttmm) REVERT: B 473 MET cc_start: 0.6519 (mmp) cc_final: 0.6176 (mpp) REVERT: B 557 PHE cc_start: 0.8166 (m-10) cc_final: 0.7907 (m-10) REVERT: B 564 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7186 (mm-30) REVERT: B 595 ARG cc_start: 0.7632 (ttt180) cc_final: 0.6804 (ttp80) REVERT: B 623 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6841 (mt-10) REVERT: B 896 ASP cc_start: 0.6555 (t0) cc_final: 0.6098 (p0) REVERT: B 1181 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7247 (tp30) REVERT: C 50 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7328 (mp0) REVERT: C 78 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7161 (pm20) REVERT: C 106 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7801 (mm-30) REVERT: C 135 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8358 (mt0) REVERT: C 138 GLU cc_start: 0.7173 (mp0) cc_final: 0.6849 (mp0) REVERT: C 152 GLU cc_start: 0.8170 (tt0) cc_final: 0.7768 (tm-30) REVERT: C 264 GLN cc_start: 0.6111 (tp-100) cc_final: 0.5771 (mt0) REVERT: D 1 MET cc_start: 0.1022 (ttt) cc_final: -0.0188 (tpt) REVERT: D 32 GLU cc_start: 0.3253 (mm-30) cc_final: 0.2565 (tt0) REVERT: D 44 GLU cc_start: 0.2452 (OUTLIER) cc_final: 0.1963 (tt0) REVERT: E 81 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7225 (tp30) REVERT: E 90 VAL cc_start: 0.7530 (t) cc_final: 0.7243 (m) REVERT: E 103 LYS cc_start: 0.7663 (mtpp) cc_final: 0.7206 (mttp) REVERT: E 106 GLN cc_start: 0.7478 (mm-40) cc_final: 0.7160 (mp10) REVERT: E 121 MET cc_start: 0.7722 (mmm) cc_final: 0.7485 (mmm) REVERT: F 72 LYS cc_start: 0.6870 (mmpt) cc_final: 0.6538 (mttt) REVERT: G 101 VAL cc_start: 0.0467 (OUTLIER) cc_final: 0.0260 (p) REVERT: H 14 GLU cc_start: 0.8295 (tt0) cc_final: 0.7777 (pt0) REVERT: H 91 ASP cc_start: 0.8055 (m-30) cc_final: 0.7846 (m-30) REVERT: I 1 MET cc_start: 0.4497 (mmm) cc_final: 0.2306 (ptp) REVERT: I 97 MET cc_start: 0.5505 (mtp) cc_final: 0.4233 (tmt) REVERT: J 64 ASN cc_start: 0.7413 (t0) cc_final: 0.6871 (m-40) REVERT: K 1 MET cc_start: 0.7193 (ttt) cc_final: 0.6873 (ttm) REVERT: K 20 LYS cc_start: 0.8388 (tttp) cc_final: 0.8123 (tttm) REVERT: K 54 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7494 (mmp-170) outliers start: 74 outliers final: 42 residues processed: 429 average time/residue: 0.8538 time to fit residues: 429.4898 Evaluate side-chains 426 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 371 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 938 LYS Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1092 LYS Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1150 ARG Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain L residue 33 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 221 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 252 optimal weight: 0.0050 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 393 optimal weight: 4.9990 chunk 268 optimal weight: 0.9990 chunk 370 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 626 ASN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 ASN B1117 GLN B1179 GLN C 102 GLN C 214 ASN E 179 GLN G 14 HIS H 128 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.186639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.110920 restraints weight = 32400.541| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.71 r_work: 0.3226 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 33908 Z= 0.180 Angle : 0.604 11.504 46203 Z= 0.317 Chirality : 0.045 0.250 5190 Planarity : 0.005 0.052 5630 Dihedral : 16.773 154.423 5350 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.48 % Favored : 96.45 % Rotamer: Outliers : 2.50 % Allowed : 12.46 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.20 (0.13), residues: 3854 helix: 1.04 (0.14), residues: 1371 sheet: 0.17 (0.21), residues: 583 loop : -0.49 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 579 TYR 0.016 0.002 TYR B 486 PHE 0.030 0.002 PHE A 219 TRP 0.012 0.002 TRP B 31 HIS 0.015 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (33876) covalent geometry : angle 0.59398 / 0.32 (46158) hydrogen bonds : bond 0.04295 / 2.91 ( 1435) hydrogen bonds : angle 4.57503 / 3.29 ( 3994) metal coordination : bond 0.00500 / 0.33 ( 32) metal coordination : angle 3.62096 / 2.34 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 382 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8427 (mmt90) cc_final: 0.7774 (mmt-90) REVERT: A 205 GLU cc_start: 0.7451 (tt0) cc_final: 0.6949 (tp30) REVERT: A 280 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6886 (mt-10) REVERT: A 293 GLU cc_start: 0.6758 (tt0) cc_final: 0.6497 (pt0) REVERT: A 368 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8410 (ttmp) REVERT: A 393 ARG cc_start: 0.7995 (mpt-90) cc_final: 0.7283 (mpt90) REVERT: A 407 ARG cc_start: 0.7075 (mtp-110) cc_final: 0.6717 (mtt180) REVERT: A 437 MET cc_start: 0.8564 (ptt) cc_final: 0.7466 (mtp) REVERT: A 618 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7350 (pp20) REVERT: A 685 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6442 (pt0) REVERT: A 702 LEU cc_start: 0.4228 (OUTLIER) cc_final: 0.3661 (pp) REVERT: A 708 MET cc_start: 0.4653 (mtt) cc_final: 0.4185 (ttm) REVERT: A 724 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6247 (pt0) REVERT: A 894 GLU cc_start: 0.8130 (tp30) cc_final: 0.7916 (mm-30) REVERT: A 992 ASP cc_start: 0.7530 (m-30) cc_final: 0.7207 (t70) REVERT: A 1079 MET cc_start: 0.8166 (ttp) cc_final: 0.7759 (tmm) REVERT: A 1092 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.6901 (tppp) REVERT: A 1297 GLU cc_start: 0.8310 (pm20) cc_final: 0.7728 (pm20) REVERT: A 1307 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: A 1420 ASP cc_start: 0.7694 (t0) cc_final: 0.6932 (p0) REVERT: A 1424 VAL cc_start: 0.8497 (m) cc_final: 0.8235 (p) REVERT: B 21 GLU cc_start: 0.7492 (pt0) cc_final: 0.7089 (mp0) REVERT: B 239 GLU cc_start: 0.7485 (pt0) cc_final: 0.6798 (mp0) REVERT: B 257 LYS cc_start: 0.7082 (mtmt) cc_final: 0.6478 (mttp) REVERT: B 313 MET cc_start: 0.6116 (mtp) cc_final: 0.5859 (ptp) REVERT: B 357 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6713 (tp-100) REVERT: B 387 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6478 (mp) REVERT: B 422 LYS cc_start: 0.6585 (mmtm) cc_final: 0.5853 (mmtm) REVERT: B 432 MET cc_start: 0.6060 (OUTLIER) cc_final: 0.4726 (ptm) REVERT: B 451 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7236 (ttmm) REVERT: B 473 MET cc_start: 0.6550 (mmp) cc_final: 0.6192 (mpp) REVERT: B 557 PHE cc_start: 0.8187 (m-10) cc_final: 0.7906 (m-10) REVERT: B 564 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7203 (mm-30) REVERT: B 595 ARG cc_start: 0.7648 (ttt180) cc_final: 0.6790 (ttp80) REVERT: B 623 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6979 (mt-10) REVERT: B 896 ASP cc_start: 0.6568 (t0) cc_final: 0.6136 (p0) REVERT: B 1050 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8499 (mt) REVERT: B 1181 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7281 (tp30) REVERT: C 50 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7352 (mp0) REVERT: C 78 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7120 (pm20) REVERT: C 106 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7888 (mm-30) REVERT: C 135 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8350 (mt0) REVERT: C 138 GLU cc_start: 0.7172 (mp0) cc_final: 0.6839 (mp0) REVERT: C 152 GLU cc_start: 0.8239 (tt0) cc_final: 0.7702 (tm-30) REVERT: C 264 GLN cc_start: 0.6179 (tp-100) cc_final: 0.5870 (mt0) REVERT: D 1 MET cc_start: 0.1085 (ttt) cc_final: -0.0497 (tpt) REVERT: D 32 GLU cc_start: 0.3433 (mm-30) cc_final: 0.2703 (mt-10) REVERT: D 44 GLU cc_start: 0.2528 (OUTLIER) cc_final: 0.2075 (tt0) REVERT: E 81 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7274 (tp30) REVERT: E 90 VAL cc_start: 0.7644 (t) cc_final: 0.7378 (m) REVERT: E 103 LYS cc_start: 0.7733 (mtpp) cc_final: 0.7431 (mppt) REVERT: E 106 GLN cc_start: 0.7421 (mm-40) cc_final: 0.7119 (mp10) REVERT: E 121 MET cc_start: 0.7725 (mmm) cc_final: 0.7460 (mmm) REVERT: F 72 LYS cc_start: 0.6924 (mmpt) cc_final: 0.6600 (mttt) REVERT: G 26 LEU cc_start: 0.6160 (tt) cc_final: 0.5567 (mp) REVERT: G 101 VAL cc_start: 0.0497 (OUTLIER) cc_final: 0.0271 (p) REVERT: H 14 GLU cc_start: 0.8337 (tt0) cc_final: 0.7782 (pt0) REVERT: H 80 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7916 (mtt90) REVERT: I 1 MET cc_start: 0.4288 (mmm) cc_final: 0.2129 (ptp) REVERT: I 97 MET cc_start: 0.5609 (mtp) cc_final: 0.4332 (tmt) REVERT: J 64 ASN cc_start: 0.7451 (t0) cc_final: 0.6894 (m-40) REVERT: K 1 MET cc_start: 0.7273 (ttt) cc_final: 0.6903 (ttm) REVERT: K 20 LYS cc_start: 0.8373 (tttp) cc_final: 0.8101 (tttm) REVERT: K 54 ARG cc_start: 0.7993 (mtm180) cc_final: 0.7535 (mmp-170) outliers start: 86 outliers final: 50 residues processed: 444 average time/residue: 0.8569 time to fit residues: 446.9596 Evaluate side-chains 447 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 379 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 938 LYS Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1092 LYS Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1307 GLU Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1050 ILE Chi-restraints excluded: chain B residue 1150 ARG Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain L residue 33 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 113 optimal weight: 30.0000 chunk 202 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 199 optimal weight: 0.9980 chunk 327 optimal weight: 7.9990 chunk 182 optimal weight: 7.9990 chunk 321 optimal weight: 5.9990 chunk 297 optimal weight: 5.9990 chunk 392 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 626 ASN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN B 957 ASN B1179 GLN C 102 GLN C 214 ASN G 122 ASN H 128 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.189960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.113629 restraints weight = 32106.822| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.75 r_work: 0.3355 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 33908 Z= 0.257 Angle : 0.691 12.097 46203 Z= 0.361 Chirality : 0.049 0.331 5190 Planarity : 0.005 0.077 5630 Dihedral : 16.902 153.243 5350 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.50 % Rotamer: Outliers : 2.50 % Allowed : 12.70 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -0.00 (0.13), residues: 3854 helix: 0.81 (0.14), residues: 1358 sheet: 0.04 (0.21), residues: 571 loop : -0.54 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 212 TYR 0.019 0.002 TYR A1349 PHE 0.033 0.003 PHE A 219 TRP 0.016 0.002 TRP A 954 HIS 0.022 0.002 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.26 (33876) covalent geometry : angle 0.68003 / 0.36 (46158) hydrogen bonds : bond 0.05011 / 3.40 ( 1435) hydrogen bonds : angle 4.77836 / 3.43 ( 3994) metal coordination : bond 0.00705 / 0.46 ( 32) metal coordination : angle 4.03722 / 2.63 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 389 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8474 (mmt90) cc_final: 0.7794 (mmt-90) REVERT: A 175 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7007 (ttp-110) REVERT: A 205 GLU cc_start: 0.7456 (tt0) cc_final: 0.6891 (tp30) REVERT: A 280 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6856 (mt-10) REVERT: A 293 GLU cc_start: 0.6841 (tt0) cc_final: 0.6544 (pt0) REVERT: A 368 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8434 (ttmp) REVERT: A 398 GLU cc_start: 0.7411 (tt0) cc_final: 0.7133 (tm-30) REVERT: A 407 ARG cc_start: 0.7138 (mtp-110) cc_final: 0.6675 (mtt180) REVERT: A 437 MET cc_start: 0.8574 (ptt) cc_final: 0.7453 (mtp) REVERT: A 685 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6297 (pt0) REVERT: A 702 LEU cc_start: 0.4194 (OUTLIER) cc_final: 0.3540 (pp) REVERT: A 708 MET cc_start: 0.4994 (mtt) cc_final: 0.4468 (ttm) REVERT: A 724 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6251 (pt0) REVERT: A 992 ASP cc_start: 0.7512 (m-30) cc_final: 0.7251 (t70) REVERT: A 1079 MET cc_start: 0.8143 (ttp) cc_final: 0.7760 (tmm) REVERT: A 1092 LYS cc_start: 0.7458 (mptt) cc_final: 0.6916 (tppt) REVERT: A 1297 GLU cc_start: 0.8369 (pm20) cc_final: 0.7781 (pm20) REVERT: A 1307 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: A 1424 VAL cc_start: 0.8466 (m) cc_final: 0.8192 (p) REVERT: B 21 GLU cc_start: 0.7587 (pt0) cc_final: 0.7047 (mp0) REVERT: B 239 GLU cc_start: 0.7556 (pt0) cc_final: 0.6833 (mp0) REVERT: B 257 LYS cc_start: 0.7117 (mtmt) cc_final: 0.6498 (mttp) REVERT: B 422 LYS cc_start: 0.6637 (mmtm) cc_final: 0.5897 (mmtm) REVERT: B 432 MET cc_start: 0.6143 (OUTLIER) cc_final: 0.4844 (ptp) REVERT: B 451 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7267 (ttmm) REVERT: B 473 MET cc_start: 0.6540 (mmp) cc_final: 0.6228 (mpp) REVERT: B 531 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6714 (mm-40) REVERT: B 564 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7218 (mm-30) REVERT: B 595 ARG cc_start: 0.7674 (ttt180) cc_final: 0.6753 (ttp80) REVERT: B 623 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7198 (mm-30) REVERT: B 896 ASP cc_start: 0.6476 (t0) cc_final: 0.6165 (p0) REVERT: B 1007 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8359 (m) REVERT: B 1050 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8546 (mt) REVERT: B 1181 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7577 (tp30) REVERT: C 50 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7372 (mp0) REVERT: C 78 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7140 (pm20) REVERT: C 102 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7643 (mt0) REVERT: C 106 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7934 (mm-30) REVERT: C 136 ASP cc_start: 0.6979 (t70) cc_final: 0.6460 (t70) REVERT: C 138 GLU cc_start: 0.7196 (mp0) cc_final: 0.6606 (mp0) REVERT: C 165 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8413 (mtmm) REVERT: C 264 GLN cc_start: 0.6252 (tp-100) cc_final: 0.5942 (mt0) REVERT: D 1 MET cc_start: 0.1120 (ttt) cc_final: -0.0368 (tpt) REVERT: D 32 GLU cc_start: 0.3658 (mm-30) cc_final: 0.2796 (mm-30) REVERT: E 90 VAL cc_start: 0.7749 (t) cc_final: 0.7500 (m) REVERT: E 103 LYS cc_start: 0.7863 (mtpp) cc_final: 0.7358 (mttp) REVERT: E 106 GLN cc_start: 0.7464 (mm-40) cc_final: 0.7060 (mp10) REVERT: E 121 MET cc_start: 0.7722 (mmm) cc_final: 0.7355 (mmm) REVERT: F 72 LYS cc_start: 0.6925 (mmpt) cc_final: 0.6622 (mttt) REVERT: F 149 GLU cc_start: 0.8266 (tt0) cc_final: 0.8022 (tt0) REVERT: G 26 LEU cc_start: 0.6368 (tt) cc_final: 0.5908 (mt) REVERT: G 101 VAL cc_start: 0.0623 (OUTLIER) cc_final: 0.0409 (p) REVERT: H 14 GLU cc_start: 0.8351 (tt0) cc_final: 0.7803 (pt0) REVERT: H 80 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7916 (mtt90) REVERT: I 97 MET cc_start: 0.5744 (mtp) cc_final: 0.4411 (tmt) REVERT: J 64 ASN cc_start: 0.7454 (t0) cc_final: 0.6917 (m-40) REVERT: K 1 MET cc_start: 0.7251 (ttt) cc_final: 0.6927 (ttm) REVERT: K 20 LYS cc_start: 0.8373 (tttp) cc_final: 0.8105 (tttm) REVERT: K 54 ARG cc_start: 0.8092 (mtm180) cc_final: 0.7619 (mmp-170) outliers start: 86 outliers final: 51 residues processed: 448 average time/residue: 0.8549 time to fit residues: 448.4137 Evaluate side-chains 445 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 378 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 938 LYS Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1307 GLU Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1050 ILE Chi-restraints excluded: chain B residue 1150 ARG Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain L residue 33 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 179 optimal weight: 1.9990 chunk 171 optimal weight: 9.9990 chunk 209 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 216 optimal weight: 0.8980 chunk 246 optimal weight: 0.8980 chunk 391 optimal weight: 20.0000 chunk 388 optimal weight: 9.9990 chunk 247 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 626 ASN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 HIS A 965 GLN ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 ASN C 102 GLN C 214 ASN G 10 ASN G 122 ASN H 128 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.186882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.111897 restraints weight = 32396.270| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.69 r_work: 0.3236 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33908 Z= 0.143 Angle : 0.583 12.013 46203 Z= 0.307 Chirality : 0.044 0.221 5190 Planarity : 0.004 0.054 5630 Dihedral : 16.725 152.944 5350 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.19 % Favored : 96.73 % Rotamer: Outliers : 1.89 % Allowed : 13.42 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.13), residues: 3854 helix: 1.04 (0.14), residues: 1358 sheet: 0.04 (0.21), residues: 580 loop : -0.47 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 579 TYR 0.013 0.001 TYR C 229 PHE 0.028 0.002 PHE A 219 TRP 0.015 0.001 TRP C 192 HIS 0.011 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (33876) covalent geometry : angle 0.57258 / 0.31 (46158) hydrogen bonds : bond 0.03998 / 2.70 ( 1435) hydrogen bonds : angle 4.56141 / 3.28 ( 3994) metal coordination : bond 0.00456 / 0.29 ( 32) metal coordination : angle 3.56361 / 2.31 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 379 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8442 (mmt90) cc_final: 0.7786 (mmt-90) REVERT: A 205 GLU cc_start: 0.7425 (tt0) cc_final: 0.6893 (tp30) REVERT: A 280 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6856 (mt-10) REVERT: A 293 GLU cc_start: 0.6688 (tt0) cc_final: 0.6400 (pt0) REVERT: A 393 ARG cc_start: 0.7972 (mpt-90) cc_final: 0.7274 (mpt90) REVERT: A 407 ARG cc_start: 0.7162 (mtp-110) cc_final: 0.6747 (mtt180) REVERT: A 416 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7962 (mtm180) REVERT: A 437 MET cc_start: 0.8601 (ptt) cc_final: 0.7490 (mtp) REVERT: A 618 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7287 (pp20) REVERT: A 685 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6403 (pt0) REVERT: A 702 LEU cc_start: 0.4137 (OUTLIER) cc_final: 0.3547 (pp) REVERT: A 708 MET cc_start: 0.4816 (mtt) cc_final: 0.4346 (ttm) REVERT: A 724 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6256 (pt0) REVERT: A 992 ASP cc_start: 0.7512 (m-30) cc_final: 0.7219 (t70) REVERT: A 1092 LYS cc_start: 0.7450 (mptt) cc_final: 0.6940 (tppp) REVERT: A 1209 MET cc_start: 0.5347 (tmm) cc_final: 0.3383 (tpp) REVERT: A 1297 GLU cc_start: 0.8270 (pm20) cc_final: 0.7728 (pm20) REVERT: A 1420 ASP cc_start: 0.7817 (t0) cc_final: 0.7012 (p0) REVERT: A 1424 VAL cc_start: 0.8497 (m) cc_final: 0.8247 (p) REVERT: B 21 GLU cc_start: 0.7464 (pt0) cc_final: 0.7168 (mt-10) REVERT: B 239 GLU cc_start: 0.7499 (pt0) cc_final: 0.6803 (mp0) REVERT: B 257 LYS cc_start: 0.7118 (mtmt) cc_final: 0.6511 (mttp) REVERT: B 357 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.6681 (tp-100) REVERT: B 422 LYS cc_start: 0.6586 (mmtm) cc_final: 0.5848 (mmtm) REVERT: B 432 MET cc_start: 0.6088 (OUTLIER) cc_final: 0.4826 (ptp) REVERT: B 451 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7172 (ttmm) REVERT: B 473 MET cc_start: 0.6599 (mmp) cc_final: 0.6251 (mpp) REVERT: B 564 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7191 (mm-30) REVERT: B 595 ARG cc_start: 0.7635 (ttt180) cc_final: 0.6794 (ttp80) REVERT: B 623 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6911 (mt-10) REVERT: B 896 ASP cc_start: 0.6538 (t0) cc_final: 0.6271 (p0) REVERT: B 1181 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7222 (tp30) REVERT: C 50 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7348 (mp0) REVERT: C 78 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7151 (pm20) REVERT: C 106 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7909 (mm-30) REVERT: C 138 GLU cc_start: 0.7172 (mp0) cc_final: 0.6853 (mp0) REVERT: C 152 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7791 (tm-30) REVERT: C 264 GLN cc_start: 0.6069 (tp-100) cc_final: 0.5742 (mt0) REVERT: D 1 MET cc_start: 0.1003 (ttt) cc_final: -0.0603 (tpt) REVERT: D 32 GLU cc_start: 0.3508 (mm-30) cc_final: 0.2653 (mm-30) REVERT: D 148 LEU cc_start: 0.6081 (mt) cc_final: 0.5795 (pt) REVERT: D 149 THR cc_start: 0.3619 (OUTLIER) cc_final: 0.3164 (p) REVERT: E 81 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7247 (tp30) REVERT: E 90 VAL cc_start: 0.7684 (t) cc_final: 0.7461 (m) REVERT: E 103 LYS cc_start: 0.7769 (mtpp) cc_final: 0.7421 (mppt) REVERT: E 106 GLN cc_start: 0.7424 (mm-40) cc_final: 0.7060 (mp10) REVERT: E 121 MET cc_start: 0.7740 (mmm) cc_final: 0.7426 (mmm) REVERT: F 72 LYS cc_start: 0.6908 (mmpt) cc_final: 0.6597 (mttt) REVERT: F 111 LEU cc_start: 0.8257 (mt) cc_final: 0.7977 (mm) REVERT: F 149 GLU cc_start: 0.8189 (tt0) cc_final: 0.7943 (tt0) REVERT: G 5 LYS cc_start: 0.3317 (OUTLIER) cc_final: 0.3072 (tptm) REVERT: G 101 VAL cc_start: 0.0561 (OUTLIER) cc_final: 0.0356 (p) REVERT: H 14 GLU cc_start: 0.8286 (tt0) cc_final: 0.7844 (pt0) REVERT: H 80 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7879 (mtt90) REVERT: I 97 MET cc_start: 0.5796 (mtp) cc_final: 0.4478 (tmt) REVERT: J 64 ASN cc_start: 0.7363 (t0) cc_final: 0.6854 (m-40) REVERT: K 1 MET cc_start: 0.7279 (ttt) cc_final: 0.6967 (ttm) REVERT: K 20 LYS cc_start: 0.8386 (tttp) cc_final: 0.8125 (tttm) REVERT: K 54 ARG cc_start: 0.7995 (mtm180) cc_final: 0.7561 (mmp-170) outliers start: 65 outliers final: 38 residues processed: 423 average time/residue: 0.8585 time to fit residues: 425.6516 Evaluate side-chains 426 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 373 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 938 LYS Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1150 ARG Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain L residue 33 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 347 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 345 optimal weight: 4.9990 chunk 359 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 351 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 ASN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN B 957 ASN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN G 10 ASN H 128 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.187337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.112427 restraints weight = 32269.921| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.70 r_work: 0.3249 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33908 Z= 0.139 Angle : 0.569 11.926 46203 Z= 0.299 Chirality : 0.043 0.202 5190 Planarity : 0.004 0.053 5630 Dihedral : 16.612 152.543 5350 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.27 % Favored : 96.65 % Rotamer: Outliers : 1.72 % Allowed : 13.69 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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 (0.13), residues: 3854 helix: 1.19 (0.14), residues: 1351 sheet: 0.11 (0.21), residues: 578 loop : -0.42 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 579 TYR 0.013 0.001 TYR A1349 PHE 0.028 0.002 PHE A 219 TRP 0.013 0.001 TRP C 192 HIS 0.012 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (33876) covalent geometry : angle 0.56042 / 0.30 (46158) hydrogen bonds : bond 0.03843 / 2.59 ( 1435) hydrogen bonds : angle 4.47001 / 3.22 ( 3994) metal coordination : bond 0.00411 / 0.26 ( 32) metal coordination : angle 3.28020 / 2.13 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24894.10 seconds wall clock time: 421 minutes 22.81 seconds (25282.81 seconds total)