Starting phenix.real_space_refine on Mon Jul 6 11:11:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qeb_53053/07_2026/9qeb_53053.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qeb_53053/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9qeb_53053/07_2026/9qeb_53053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qeb_53053/07_2026/9qeb_53053.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qeb_53053/07_2026/9qeb_53053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qeb_53053/07_2026/9qeb_53053.map" } 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-6108/lib/python3.11/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, 35 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 2, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 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: 6.86, per 1000 atoms: 0.20 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: 3.14 Conformation dependent library (CDL) restraints added in 1.5 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: 4.83 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: 10.70 Time building geometry restraints manager: 4.06 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: 5069 0.126 - 0.253: 95 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: 5.280 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: 0.700 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 43.290 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 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= 0.675 Angle : 0.978 44.228 46203 Z= 0.591 Chirality : 0.059 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 0.00926 / 0.65 (33876) covalent geometry : angle 0.91032 / 0.59 (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 : 1.194 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: 0.8094 time to fit residues: 644.6467 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 : 1.186 ------------------------------------------------------------------------------- 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: 30.0000 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: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 118 HIS A 209 ASN A 213 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 686 ASN B 706 GLN B 740 HIS B 776 GLN B 951 GLN B 984 HIS B1025 HIS B1104 HIS B1117 GLN B1178 ASN C 17 ASN C 252 GLN D 34 GLN E 99 HIS G 122 ASN H 33 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.192571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117209 restraints weight = 32642.788| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.75 r_work: 0.3337 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 33908 Z= 0.165 Angle : 0.681 13.160 46203 Z= 0.356 Chirality : 0.048 0.237 5190 Planarity : 0.005 0.056 5630 Dihedral : 17.302 163.689 5374 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.45 % Favored : 96.45 % Rotamer: Outliers : 2.13 % Allowed : 7.43 % Favored : 90.45 % 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: -0.04 (0.13), residues: 3854 helix: 0.82 (0.14), residues: 1373 sheet: -0.07 (0.20), residues: 603 loop : -0.57 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 A 556 HIS 0.011 0.002 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (33876) covalent geometry : angle 0.66508 / 0.36 (46158) hydrogen bonds : bond 0.04755 / 3.21 ( 1435) hydrogen bonds : angle 5.08373 / 3.67 ( 3994) metal coordination : bond 0.01166 / 0.70 ( 32) metal coordination : angle 4.80802 / 3.21 ( 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 515 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 442 time to evaluate : 1.289 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: 0.7874 (mmt-90) REVERT: A 205 GLU cc_start: 0.7162 (tt0) cc_final: 0.6823 (tp30) REVERT: A 293 GLU cc_start: 0.6740 (tt0) cc_final: 0.6487 (pt0) REVERT: A 393 ARG cc_start: 0.7551 (ttm110) cc_final: 0.7261 (mpt180) REVERT: A 407 ARG cc_start: 0.7018 (mtp-110) cc_final: 0.6714 (mtt180) REVERT: A 437 MET cc_start: 0.8502 (ptt) cc_final: 0.7391 (mtp) REVERT: A 461 LYS cc_start: 0.8630 (tptm) cc_final: 0.8429 (tmtt) REVERT: A 549 MET cc_start: 0.8896 (mtp) cc_final: 0.8462 (mtp) REVERT: A 696 GLU cc_start: 0.5183 (tt0) cc_final: 0.4556 (tt0) REVERT: A 801 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8054 (tt0) REVERT: A 873 MET cc_start: 0.9027 (mmp) cc_final: 0.8313 (mmt) REVERT: A 992 ASP cc_start: 0.7479 (m-30) cc_final: 0.7151 (t70) REVERT: A 1079 MET cc_start: 0.8029 (ttp) cc_final: 0.7825 (ttp) REVERT: A 1092 LYS cc_start: 0.7229 (mptt) cc_final: 0.6678 (tppt) REVERT: A 1299 VAL cc_start: 0.8002 (p) cc_final: 0.7775 (m) REVERT: A 1307 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: A 1314 SER cc_start: 0.8467 (t) cc_final: 0.8208 (p) REVERT: A 1315 GLU cc_start: 0.7721 (tt0) cc_final: 0.7275 (mm-30) REVERT: A 1366 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7631 (ptm160) REVERT: A 1420 ASP cc_start: 0.7707 (t0) cc_final: 0.7098 (p0) REVERT: A 1424 VAL cc_start: 0.8406 (m) cc_final: 0.8192 (p) REVERT: B 21 GLU cc_start: 0.7347 (pt0) cc_final: 0.6980 (mp0) REVERT: B 26 THR cc_start: 0.8285 (p) cc_final: 0.7893 (t) REVERT: B 94 LYS cc_start: 0.7465 (tttm) cc_final: 0.7239 (tttp) REVERT: B 239 GLU cc_start: 0.7459 (pt0) cc_final: 0.6722 (mp0) REVERT: B 255 GLN cc_start: 0.7276 (pt0) cc_final: 0.6880 (pt0) REVERT: B 257 LYS cc_start: 0.7015 (mtmt) cc_final: 0.6415 (mtmm) REVERT: B 378 LEU cc_start: 0.7242 (tp) cc_final: 0.7026 (tp) REVERT: B 398 ARG cc_start: 0.7482 (mpt-90) cc_final: 0.6879 (mtt-85) REVERT: B 473 MET cc_start: 0.6386 (mmp) cc_final: 0.6032 (mpp) REVERT: B 542 MET cc_start: 0.9154 (mtm) cc_final: 0.8896 (mtt) REVERT: B 552 MET cc_start: 0.7918 (tpp) cc_final: 0.7706 (mmm) REVERT: B 564 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7055 (mm-30) REVERT: B 567 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.5931 (pm20) REVERT: B 595 ARG cc_start: 0.7781 (ttt180) cc_final: 0.7072 (ttp80) REVERT: B 953 LEU cc_start: 0.8213 (tt) cc_final: 0.8001 (tm) REVERT: B 1004 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8144 (pt0) REVERT: B 1181 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7058 (tp30) REVERT: C 50 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7411 (mp0) REVERT: C 78 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7074 (pm20) REVERT: C 94 LYS cc_start: 0.8246 (mtmt) cc_final: 0.7950 (mtmt) REVERT: C 106 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7828 (mm-30) REVERT: C 136 ASP cc_start: 0.6514 (t70) cc_final: 0.6208 (t70) REVERT: C 138 GLU cc_start: 0.7103 (mp0) cc_final: 0.6613 (mp0) REVERT: C 179 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8765 (tt0) REVERT: C 264 GLN cc_start: 0.5944 (tp-100) cc_final: 0.5623 (mt0) REVERT: D 1 MET cc_start: 0.1280 (ttt) cc_final: 0.0521 (tpt) REVERT: D 117 GLU cc_start: 0.2471 (mp0) cc_final: 0.1923 (tp30) REVERT: D 187 THR cc_start: 0.3153 (OUTLIER) cc_final: 0.2901 (p) REVERT: E 4 GLU cc_start: 0.6414 (mm-30) cc_final: 0.6211 (tp30) REVERT: E 81 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7367 (tp30) REVERT: E 90 VAL cc_start: 0.6990 (t) cc_final: 0.6598 (m) REVERT: E 103 LYS cc_start: 0.7695 (mtpp) cc_final: 0.7313 (mttp) REVERT: E 106 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7115 (mp10) REVERT: G 29 LYS cc_start: 0.4069 (tppt) cc_final: 0.3676 (ttmt) REVERT: H 14 GLU cc_start: 0.8259 (tt0) cc_final: 0.7699 (mt-10) REVERT: H 27 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8359 (mm-30) REVERT: I 97 MET cc_start: 0.4776 (mtp) cc_final: 0.3783 (tmt) REVERT: J 64 ASN cc_start: 0.7431 (t0) cc_final: 0.6808 (m-40) REVERT: K 1 MET cc_start: 0.7126 (ttt) cc_final: 0.6742 (ttm) REVERT: K 20 LYS cc_start: 0.8407 (tttp) cc_final: 0.8137 (tttm) REVERT: K 54 ARG cc_start: 0.7925 (mtm180) cc_final: 0.7504 (mmp-170) outliers start: 73 outliers final: 26 residues processed: 487 average time/residue: 0.8062 time to fit residues: 460.6467 Evaluate side-chains 424 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 388 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 801 GLU Chi-restraints excluded: chain A residue 938 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 455 SER Chi-restraints excluded: chain B residue 567 GLU Chi-restraints excluded: chain B residue 570 VAL 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 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 108 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 54 SER 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: 0.9990 chunk 239 optimal weight: 1.9990 chunk 203 optimal weight: 7.9990 chunk 327 optimal weight: 7.9990 chunk 160 optimal weight: 30.0000 chunk 85 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 584 ASN A 626 ASN ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN B 531 GLN B 572 HIS B 686 ASN B 957 ASN B1178 ASN C 102 GLN C 252 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.188401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112354 restraints weight = 32359.146| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.70 r_work: 0.3267 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 33908 Z= 0.209 Angle : 0.683 11.686 46203 Z= 0.358 Chirality : 0.049 0.238 5190 Planarity : 0.005 0.061 5630 Dihedral : 17.299 161.911 5360 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.57 % Rotamer: Outliers : 2.53 % Allowed : 9.41 % Favored : 88.06 % 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: 0.74 (0.14), residues: 1372 sheet: -0.12 (0.20), residues: 611 loop : -0.62 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 857 TYR 0.021 0.002 TYR B 692 PHE 0.038 0.002 PHE A 219 TRP 0.014 0.002 TRP B 31 HIS 0.017 0.002 HIS B1076 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (33876) covalent geometry : angle 0.66565 / 0.36 (46158) hydrogen bonds : bond 0.05052 / 3.44 ( 1435) hydrogen bonds : angle 4.93459 / 3.56 ( 3994) metal coordination : bond 0.00686 / 0.43 ( 32) metal coordination : angle 4.97847 / 3.17 ( 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 496 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 409 time to evaluate : 1.347 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: 0.8375 (mmt90) cc_final: 0.7832 (mmt-90) REVERT: A 205 GLU cc_start: 0.7281 (tt0) cc_final: 0.6901 (tp30) REVERT: A 293 GLU cc_start: 0.6746 (tt0) cc_final: 0.6474 (pt0) REVERT: A 385 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7089 (mt) REVERT: A 393 ARG cc_start: 0.7656 (ttm110) cc_final: 0.7286 (mpt180) REVERT: A 407 ARG cc_start: 0.7099 (mtp-110) cc_final: 0.6716 (mtt180) REVERT: A 416 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.8001 (mtm180) REVERT: A 437 MET cc_start: 0.8460 (ptt) cc_final: 0.7391 (mtp) REVERT: A 461 LYS cc_start: 0.8651 (tptm) cc_final: 0.8409 (tmtt) REVERT: A 685 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6243 (pt0) REVERT: A 992 ASP cc_start: 0.7432 (m-30) cc_final: 0.7089 (OUTLIER) REVERT: A 1079 MET cc_start: 0.8060 (ttp) cc_final: 0.7839 (ttp) REVERT: A 1092 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6718 (tppt) REVERT: A 1307 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: A 1315 GLU cc_start: 0.7848 (tt0) cc_final: 0.7238 (mm-30) REVERT: A 1420 ASP cc_start: 0.7732 (t0) cc_final: 0.6992 (p0) REVERT: A 1424 VAL cc_start: 0.8418 (m) cc_final: 0.8164 (p) REVERT: B 21 GLU cc_start: 0.7352 (pt0) cc_final: 0.7082 (mt-10) REVERT: B 26 THR cc_start: 0.8300 (p) cc_final: 0.7896 (t) REVERT: B 101 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8085 (mtt) REVERT: B 239 GLU cc_start: 0.7451 (pt0) cc_final: 0.6684 (mp0) REVERT: B 255 GLN cc_start: 0.7386 (pt0) cc_final: 0.6980 (pt0) REVERT: B 257 LYS cc_start: 0.7085 (mtmt) cc_final: 0.6533 (mtmm) REVERT: B 422 LYS cc_start: 0.6402 (mmtm) cc_final: 0.5780 (mmtm) REVERT: B 473 MET cc_start: 0.6430 (mmp) cc_final: 0.6062 (mpp) REVERT: B 542 MET cc_start: 0.9249 (mtm) cc_final: 0.9044 (mtt) REVERT: B 557 PHE cc_start: 0.8088 (m-10) cc_final: 0.7869 (m-10) REVERT: B 564 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7098 (mm-30) REVERT: B 567 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6071 (pm20) REVERT: B 595 ARG cc_start: 0.7750 (ttt180) cc_final: 0.6949 (ttp80) REVERT: B 650 GLU cc_start: 0.7557 (pt0) cc_final: 0.7080 (pm20) REVERT: B 953 LEU cc_start: 0.8144 (tt) cc_final: 0.7761 (tm) REVERT: B 1181 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7209 (tp30) REVERT: C 50 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7345 (mp0) REVERT: C 78 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7097 (pm20) REVERT: C 102 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: C 106 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7835 (mm-30) REVERT: C 138 GLU cc_start: 0.7197 (mp0) cc_final: 0.6888 (mp0) REVERT: C 152 GLU cc_start: 0.8279 (tt0) cc_final: 0.7750 (tm-30) REVERT: C 179 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8810 (tt0) REVERT: C 264 GLN cc_start: 0.6039 (tp-100) cc_final: 0.5687 (mt0) REVERT: D 1 MET cc_start: 0.1266 (ttt) cc_final: 0.0291 (tpt) REVERT: D 117 GLU cc_start: 0.2672 (mp0) cc_final: 0.2150 (tp30) REVERT: D 187 THR cc_start: 0.3327 (OUTLIER) cc_final: 0.3122 (p) REVERT: E 90 VAL cc_start: 0.7286 (t) cc_final: 0.6967 (m) REVERT: E 103 LYS cc_start: 0.7733 (mtpp) cc_final: 0.7228 (mttp) REVERT: E 106 GLN cc_start: 0.7550 (mm-40) cc_final: 0.7121 (mp10) REVERT: E 121 MET cc_start: 0.7634 (mmm) cc_final: 0.7269 (mmm) REVERT: F 72 LYS cc_start: 0.6788 (mmpt) cc_final: 0.6376 (mttt) REVERT: F 103 MET cc_start: 0.7637 (mtt) cc_final: 0.7410 (mtp) REVERT: G 14 HIS cc_start: 0.6785 (t-90) cc_final: 0.6512 (t-90) REVERT: H 14 GLU cc_start: 0.8242 (tt0) cc_final: 0.7652 (mt-10) REVERT: H 37 LYS cc_start: 0.8208 (ptpt) cc_final: 0.7896 (pttt) REVERT: H 91 ASP cc_start: 0.8136 (m-30) cc_final: 0.7785 (m-30) REVERT: I 1 MET cc_start: 0.3908 (mmm) cc_final: 0.3512 (mmt) REVERT: I 97 MET cc_start: 0.4862 (mtp) cc_final: 0.4020 (tmt) REVERT: J 64 ASN cc_start: 0.7514 (t0) cc_final: 0.6888 (m-40) REVERT: K 1 MET cc_start: 0.7169 (ttt) cc_final: 0.6785 (ttm) REVERT: K 20 LYS cc_start: 0.8379 (tttp) cc_final: 0.8070 (tttm) REVERT: K 54 ARG cc_start: 0.7967 (mtm180) cc_final: 0.7533 (mmp-170) outliers start: 87 outliers final: 38 residues processed: 461 average time/residue: 0.7808 time to fit residues: 423.4917 Evaluate side-chains 443 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 396 time to evaluate : 1.286 ------------------------------------------------------------------------------- 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 455 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 756 ILE 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 1136 SER Chi-restraints excluded: chain A residue 1307 GLU Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain B residue 101 MET 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 475 SER 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 1050 ILE 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 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 D residue 187 THR 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 G residue 108 VAL Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 54 SER 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 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: 10.0000 chunk 96 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 chunk 336 optimal weight: 20.0000 chunk 80 optimal weight: 0.7980 chunk 341 optimal weight: 7.9990 chunk 305 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 297 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 GLN A 626 ASN A 965 GLN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 ASN B1076 HIS B1178 ASN C 102 GLN D 146 GLN 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 = 0.4333 r_free = 0.4333 target = 0.192493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.112390 restraints weight = 32159.795| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.86 r_work: 0.3342 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 33908 Z= 0.265 Angle : 0.722 12.123 46203 Z= 0.378 Chirality : 0.051 0.339 5190 Planarity : 0.006 0.074 5630 Dihedral : 17.303 160.858 5353 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.50 % Rotamer: Outliers : 2.97 % Allowed : 9.96 % Favored : 87.07 % 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: -0.24 (0.13), residues: 3854 helix: 0.62 (0.14), residues: 1358 sheet: -0.12 (0.21), residues: 597 loop : -0.68 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 512 TYR 0.020 0.002 TYR B 486 PHE 0.035 0.003 PHE A 219 TRP 0.023 0.003 TRP A1228 HIS 0.020 0.002 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.26 (33876) covalent geometry : angle 0.70760 / 0.38 (46158) hydrogen bonds : bond 0.05260 / 3.57 ( 1435) hydrogen bonds : angle 4.96873 / 3.57 ( 3994) metal coordination : bond 0.00739 / 0.47 ( 32) metal coordination : angle 4.72020 / 3.03 ( 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 499 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 397 time to evaluate : 1.243 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: 0.8422 (mmt90) cc_final: 0.7874 (mmt-90) REVERT: A 175 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7210 (ttp-110) REVERT: A 205 GLU cc_start: 0.7460 (tt0) cc_final: 0.6991 (tp30) REVERT: A 293 GLU cc_start: 0.6835 (tt0) cc_final: 0.6563 (pt0) REVERT: A 393 ARG cc_start: 0.7700 (ttm110) cc_final: 0.7356 (mpt180) REVERT: A 407 ARG cc_start: 0.7090 (mtp-110) cc_final: 0.6737 (mtt180) REVERT: A 416 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7961 (mtm180) REVERT: A 437 MET cc_start: 0.8526 (ptt) cc_final: 0.7443 (mtp) REVERT: A 542 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8529 (mt-10) REVERT: A 618 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7281 (pp20) REVERT: A 685 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6196 (pt0) REVERT: A 702 LEU cc_start: 0.4042 (OUTLIER) cc_final: 0.3443 (pp) REVERT: A 724 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6225 (pt0) REVERT: A 873 MET cc_start: 0.9025 (mmp) cc_final: 0.8688 (mmt) REVERT: A 992 ASP cc_start: 0.7503 (m-30) cc_final: 0.7163 (t70) REVERT: A 1092 LYS cc_start: 0.7385 (mptt) cc_final: 0.6855 (tppt) REVERT: A 1307 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: A 1315 GLU cc_start: 0.7915 (tt0) cc_final: 0.7394 (mm-30) REVERT: A 1420 ASP cc_start: 0.7768 (t0) cc_final: 0.6900 (p0) REVERT: A 1424 VAL cc_start: 0.8439 (m) cc_final: 0.8181 (p) REVERT: B 21 GLU cc_start: 0.7487 (pt0) cc_final: 0.7177 (mt-10) REVERT: B 239 GLU cc_start: 0.7539 (pt0) cc_final: 0.6796 (mp0) REVERT: B 257 LYS cc_start: 0.7126 (mtmt) cc_final: 0.6614 (mtmm) REVERT: B 387 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6416 (mp) REVERT: B 422 LYS cc_start: 0.6514 (mmtm) cc_final: 0.5897 (mmtm) REVERT: B 473 MET cc_start: 0.6599 (mmp) cc_final: 0.6277 (mpp) REVERT: B 557 PHE cc_start: 0.8316 (m-10) cc_final: 0.8037 (m-10) REVERT: B 564 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7213 (mm-30) REVERT: B 567 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6159 (pm20) REVERT: B 595 ARG cc_start: 0.7786 (ttt180) cc_final: 0.6943 (ttp80) REVERT: B 623 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7204 (mt-10) REVERT: B 650 GLU cc_start: 0.7589 (pt0) cc_final: 0.7078 (pm20) REVERT: B 896 ASP cc_start: 0.6363 (t0) cc_final: 0.5952 (p0) REVERT: B 953 LEU cc_start: 0.8232 (tt) cc_final: 0.7793 (tm) REVERT: B 1007 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8353 (m) REVERT: B 1181 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7310 (tp30) REVERT: C 50 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7466 (mp0) REVERT: C 78 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7145 (pm20) REVERT: C 102 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: C 106 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7961 (mm-30) REVERT: C 138 GLU cc_start: 0.7296 (mp0) cc_final: 0.6979 (mp0) REVERT: C 152 GLU cc_start: 0.8338 (tt0) cc_final: 0.7767 (tm-30) REVERT: C 154 LYS cc_start: 0.8743 (mttm) cc_final: 0.8459 (mmtt) REVERT: C 179 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8879 (tt0) REVERT: C 264 GLN cc_start: 0.6186 (tp-100) cc_final: 0.5834 (mt0) REVERT: D 1 MET cc_start: 0.1255 (ttt) cc_final: 0.0083 (tpt) REVERT: E 81 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7323 (tp30) REVERT: E 90 VAL cc_start: 0.7523 (t) cc_final: 0.7186 (m) REVERT: E 103 LYS cc_start: 0.7819 (mtpp) cc_final: 0.7422 (mttp) REVERT: E 106 GLN cc_start: 0.7535 (mm-40) cc_final: 0.7141 (mp10) REVERT: E 121 MET cc_start: 0.7666 (mmm) cc_final: 0.7294 (mmm) REVERT: F 72 LYS cc_start: 0.6893 (mmpt) cc_final: 0.6545 (mttt) REVERT: F 149 GLU cc_start: 0.8284 (tt0) cc_final: 0.8034 (tt0) REVERT: G 69 GLU cc_start: 0.7267 (tt0) cc_final: 0.6829 (tm-30) REVERT: H 14 GLU cc_start: 0.8373 (tt0) cc_final: 0.7765 (mt-10) REVERT: H 37 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7998 (pttt) REVERT: I 97 MET cc_start: 0.5075 (mtp) cc_final: 0.4099 (tmt) REVERT: J 64 ASN cc_start: 0.7502 (t0) cc_final: 0.6934 (m-40) REVERT: K 1 MET cc_start: 0.7273 (ttt) cc_final: 0.6929 (ttm) REVERT: K 20 LYS cc_start: 0.8413 (tttp) cc_final: 0.8158 (tttm) REVERT: K 54 ARG cc_start: 0.8123 (mtm180) cc_final: 0.7643 (mmp-170) outliers start: 102 outliers final: 43 residues processed: 461 average time/residue: 0.7863 time to fit residues: 427.3817 Evaluate side-chains 443 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 385 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 175 ARG Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 278 THR 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 542 GLU 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 756 ILE 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 387 LEU 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 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 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 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 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 11 GLN Chi-restraints excluded: chain H residue 37 LYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 34 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 298 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 272 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 345 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN A 965 GLN ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN B 957 ASN B1178 ASN C 214 ASN E 179 GLN G 14 HIS 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 = 0.4349 r_free = 0.4349 target = 0.194136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.114651 restraints weight = 32396.004| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.87 r_work: 0.3372 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2511 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= 0.154 Angle : 0.612 12.790 46203 Z= 0.322 Chirality : 0.045 0.234 5190 Planarity : 0.004 0.053 5630 Dihedral : 17.190 161.063 5353 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.78 % Rotamer: Outliers : 2.50 % Allowed : 10.95 % Favored : 86.55 % 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: -0.07 (0.13), residues: 3854 helix: 0.81 (0.14), residues: 1374 sheet: 0.02 (0.21), residues: 600 loop : -0.66 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 904 TYR 0.015 0.001 TYR B 486 PHE 0.030 0.002 PHE A 219 TRP 0.014 0.002 TRP C 192 HIS 0.011 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (33876) covalent geometry : angle 0.59852 / 0.32 (46158) hydrogen bonds : bond 0.04358 / 2.94 ( 1435) hydrogen bonds : angle 4.75829 / 3.42 ( 3994) metal coordination : bond 0.00528 / 0.33 ( 32) metal coordination : angle 4.13870 / 2.62 ( 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 482 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 396 time to evaluate : 1.307 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 5 GLN cc_start: 0.7982 (mt0) cc_final: 0.7579 (tt0) REVERT: A 12 ARG cc_start: 0.8438 (mmt90) cc_final: 0.7843 (mmt-90) REVERT: A 175 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.6672 (ttp-110) REVERT: A 205 GLU cc_start: 0.7432 (tt0) cc_final: 0.6939 (tp30) REVERT: A 293 GLU cc_start: 0.6775 (tt0) cc_final: 0.6499 (pt0) REVERT: A 393 ARG cc_start: 0.7687 (ttm110) cc_final: 0.7411 (mpt180) REVERT: A 407 ARG cc_start: 0.7094 (mtp-110) cc_final: 0.6725 (mtt180) REVERT: A 416 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7927 (mtm180) REVERT: A 437 MET cc_start: 0.8548 (ptt) cc_final: 0.7444 (mtp) REVERT: A 542 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8491 (mt-10) REVERT: A 618 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7261 (pp20) REVERT: A 685 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6194 (pt0) REVERT: A 708 MET cc_start: 0.5180 (mtt) cc_final: 0.4671 (ttm) REVERT: A 724 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6258 (pt0) REVERT: A 873 MET cc_start: 0.9001 (mmp) cc_final: 0.8691 (mmt) REVERT: A 992 ASP cc_start: 0.7464 (m-30) cc_final: 0.7089 (t70) REVERT: A 1092 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6840 (tppt) REVERT: A 1297 GLU cc_start: 0.8298 (pm20) cc_final: 0.8057 (pm20) REVERT: A 1307 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: A 1315 GLU cc_start: 0.7939 (tt0) cc_final: 0.7394 (mm-30) REVERT: A 1420 ASP cc_start: 0.7727 (t0) cc_final: 0.6909 (p0) REVERT: A 1424 VAL cc_start: 0.8426 (m) cc_final: 0.8194 (p) REVERT: B 21 GLU cc_start: 0.7469 (pt0) cc_final: 0.7152 (mt-10) REVERT: B 239 GLU cc_start: 0.7505 (pt0) cc_final: 0.6764 (mp0) REVERT: B 257 LYS cc_start: 0.7118 (mtmt) cc_final: 0.6443 (mttp) REVERT: B 422 LYS cc_start: 0.6499 (mmtm) cc_final: 0.5867 (mmtm) REVERT: B 473 MET cc_start: 0.6581 (mmp) cc_final: 0.6244 (mpp) REVERT: B 531 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6631 (mm-40) REVERT: B 557 PHE cc_start: 0.8297 (m-10) cc_final: 0.7994 (m-10) REVERT: B 564 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7183 (mm-30) REVERT: B 567 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6150 (pm20) REVERT: B 595 ARG cc_start: 0.7755 (ttt180) cc_final: 0.6993 (ttp80) REVERT: B 622 LYS cc_start: 0.7028 (mttm) cc_final: 0.6826 (mtmp) REVERT: B 650 GLU cc_start: 0.7480 (pt0) cc_final: 0.6966 (pm20) REVERT: B 896 ASP cc_start: 0.6388 (t0) cc_final: 0.6053 (p0) REVERT: B 1181 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7217 (tp30) REVERT: C 50 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7408 (mp0) REVERT: C 78 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7138 (pm20) REVERT: C 106 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7967 (mm-30) REVERT: C 135 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8361 (mt0) REVERT: C 138 GLU cc_start: 0.7172 (mp0) cc_final: 0.6851 (mp0) REVERT: C 152 GLU cc_start: 0.8316 (tt0) cc_final: 0.7811 (tm-30) REVERT: C 179 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8828 (tt0) REVERT: C 264 GLN cc_start: 0.6082 (tp-100) cc_final: 0.5707 (mt0) REVERT: D 1 MET cc_start: 0.1104 (ttt) cc_final: -0.0049 (tpt) REVERT: D 32 GLU cc_start: 0.2965 (mm-30) cc_final: 0.2338 (tt0) REVERT: E 81 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7298 (tp30) REVERT: E 90 VAL cc_start: 0.7523 (t) cc_final: 0.7203 (m) REVERT: E 103 LYS cc_start: 0.7737 (mtpp) cc_final: 0.7256 (mttp) REVERT: E 106 GLN cc_start: 0.7535 (mm-40) cc_final: 0.7139 (mp10) REVERT: E 121 MET cc_start: 0.7705 (mmm) cc_final: 0.7365 (mmm) REVERT: F 72 LYS cc_start: 0.6925 (mmpt) cc_final: 0.6570 (mttt) REVERT: F 149 GLU cc_start: 0.8216 (tt0) cc_final: 0.7951 (tt0) REVERT: G 69 GLU cc_start: 0.7209 (tt0) cc_final: 0.6736 (tm-30) REVERT: H 14 GLU cc_start: 0.8370 (tt0) cc_final: 0.7796 (mt-10) REVERT: I 1 MET cc_start: 0.4712 (mmm) cc_final: 0.3952 (mmt) REVERT: I 97 MET cc_start: 0.5204 (mtp) cc_final: 0.4169 (tmt) REVERT: J 64 ASN cc_start: 0.7502 (t0) cc_final: 0.6933 (m-40) REVERT: K 1 MET cc_start: 0.7239 (ttt) cc_final: 0.6887 (ttm) REVERT: K 20 LYS cc_start: 0.8391 (tttp) cc_final: 0.8133 (tttm) REVERT: K 54 ARG cc_start: 0.7972 (mtm180) cc_final: 0.7503 (mmp-170) outliers start: 86 outliers final: 40 residues processed: 451 average time/residue: 0.8165 time to fit residues: 433.5839 Evaluate side-chains 440 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 388 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 175 ARG 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 542 GLU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 756 ILE 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 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 531 GLN 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 780 VAL 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 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 149 THR Chi-restraints excluded: chain D residue 187 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 300 optimal weight: 8.9990 chunk 264 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 294 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 287 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 359 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN A 965 GLN ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 ASN B1178 ASN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN 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 = 0.4333 r_free = 0.4333 target = 0.192519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.112702 restraints weight = 32074.248| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.87 r_work: 0.3347 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 33908 Z= 0.215 Angle : 0.661 11.473 46203 Z= 0.347 Chirality : 0.048 0.300 5190 Planarity : 0.005 0.061 5630 Dihedral : 17.194 160.235 5353 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.53 % Favored : 96.39 % Rotamer: Outliers : 2.68 % Allowed : 11.33 % Favored : 85.99 % 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: -0.10 (0.13), residues: 3854 helix: 0.79 (0.14), residues: 1362 sheet: 0.01 (0.21), residues: 601 loop : -0.67 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 904 TYR 0.018 0.002 TYR B 486 PHE 0.032 0.002 PHE A 219 TRP 0.014 0.002 TRP B 31 HIS 0.018 0.002 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.21 (33876) covalent geometry : angle 0.64816 / 0.35 (46158) hydrogen bonds : bond 0.04792 / 3.24 ( 1435) hydrogen bonds : angle 4.78538 / 3.44 ( 3994) metal coordination : bond 0.00605 / 0.39 ( 32) metal coordination : angle 4.20964 / 2.69 ( 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 478 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 386 time to evaluate : 1.288 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: 0.7831 (mmt-90) REVERT: A 175 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7183 (ttp-110) REVERT: A 205 GLU cc_start: 0.7468 (tt0) cc_final: 0.6945 (tp30) REVERT: A 293 GLU cc_start: 0.6807 (tt0) cc_final: 0.6498 (pt0) REVERT: A 368 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8431 (ttmp) REVERT: A 393 ARG cc_start: 0.7755 (ttm110) cc_final: 0.7451 (mpt180) REVERT: A 407 ARG cc_start: 0.7131 (mtp-110) cc_final: 0.6727 (mtt180) REVERT: A 416 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7989 (mtm180) REVERT: A 437 MET cc_start: 0.8561 (ptt) cc_final: 0.7449 (mtp) REVERT: A 542 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8537 (mt-10) REVERT: A 618 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7276 (pp20) REVERT: A 685 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6282 (pt0) REVERT: A 702 LEU cc_start: 0.4076 (OUTLIER) cc_final: 0.3459 (pp) REVERT: A 708 MET cc_start: 0.5270 (mtt) cc_final: 0.4766 (ttm) REVERT: A 724 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6231 (pt0) REVERT: A 873 MET cc_start: 0.9020 (mmp) cc_final: 0.8694 (mmt) REVERT: A 992 ASP cc_start: 0.7497 (m-30) cc_final: 0.7157 (t70) REVERT: A 1079 MET cc_start: 0.8189 (ttp) cc_final: 0.7827 (tmm) REVERT: A 1092 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6781 (tppt) REVERT: A 1297 GLU cc_start: 0.8356 (pm20) cc_final: 0.7835 (pm20) REVERT: A 1307 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: A 1420 ASP cc_start: 0.7720 (t0) cc_final: 0.6811 (p0) REVERT: A 1424 VAL cc_start: 0.8458 (m) cc_final: 0.8198 (p) REVERT: B 21 GLU cc_start: 0.7520 (pt0) cc_final: 0.7212 (mt-10) REVERT: B 239 GLU cc_start: 0.7534 (pt0) cc_final: 0.6783 (mp0) REVERT: B 257 LYS cc_start: 0.7104 (mtmt) cc_final: 0.6421 (mttp) REVERT: B 422 LYS cc_start: 0.6509 (mmtm) cc_final: 0.5862 (mmtm) REVERT: B 473 MET cc_start: 0.6573 (mmp) cc_final: 0.6233 (mpp) REVERT: B 557 PHE cc_start: 0.8279 (m-10) cc_final: 0.8077 (m-10) REVERT: B 563 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8007 (ttt) REVERT: B 564 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7151 (mm-30) REVERT: B 567 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6173 (pm20) REVERT: B 595 ARG cc_start: 0.7769 (ttt180) cc_final: 0.6993 (ttp80) REVERT: B 623 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7209 (mt-10) REVERT: B 650 GLU cc_start: 0.7535 (pt0) cc_final: 0.6975 (pm20) REVERT: B 896 ASP cc_start: 0.6536 (t0) cc_final: 0.6031 (p0) REVERT: B 1007 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8318 (m) REVERT: B 1181 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7254 (tp30) REVERT: C 50 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7394 (mp0) REVERT: C 55 THR cc_start: 0.8645 (m) cc_final: 0.8423 (p) REVERT: C 78 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7109 (pm20) REVERT: C 106 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7935 (mm-30) REVERT: C 135 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8381 (mt0) REVERT: C 138 GLU cc_start: 0.7200 (mp0) cc_final: 0.6870 (mp0) REVERT: C 152 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7569 (tm-30) REVERT: C 179 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8844 (tt0) REVERT: C 264 GLN cc_start: 0.6173 (tp-100) cc_final: 0.5805 (mt0) REVERT: D 1 MET cc_start: 0.1204 (ttt) cc_final: 0.0044 (tpt) REVERT: D 32 GLU cc_start: 0.3323 (mm-30) cc_final: 0.2441 (tt0) REVERT: E 81 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7299 (tp30) REVERT: E 90 VAL cc_start: 0.7601 (t) cc_final: 0.7293 (m) REVERT: E 103 LYS cc_start: 0.7738 (mtpp) cc_final: 0.7248 (mttp) REVERT: E 106 GLN cc_start: 0.7503 (mm-40) cc_final: 0.7115 (mp10) REVERT: E 121 MET cc_start: 0.7700 (mmm) cc_final: 0.7347 (mmm) REVERT: F 72 LYS cc_start: 0.6888 (mmpt) cc_final: 0.6529 (mttt) REVERT: F 149 GLU cc_start: 0.8215 (tt0) cc_final: 0.7975 (tt0) REVERT: G 69 GLU cc_start: 0.7357 (tt0) cc_final: 0.6871 (tm-30) REVERT: H 14 GLU cc_start: 0.8387 (tt0) cc_final: 0.7822 (mt-10) REVERT: H 80 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7908 (mtt90) REVERT: I 1 MET cc_start: 0.4492 (mmm) cc_final: 0.3651 (mmt) REVERT: I 97 MET cc_start: 0.5341 (mtp) cc_final: 0.4150 (tmt) REVERT: J 64 ASN cc_start: 0.7482 (t0) cc_final: 0.6918 (m-40) REVERT: K 1 MET cc_start: 0.7243 (ttt) cc_final: 0.6896 (ttm) REVERT: K 20 LYS cc_start: 0.8365 (tttp) cc_final: 0.8114 (tttm) REVERT: K 54 ARG cc_start: 0.8065 (mtm180) cc_final: 0.7590 (mmp-170) outliers start: 92 outliers final: 51 residues processed: 450 average time/residue: 0.7931 time to fit residues: 420.4328 Evaluate side-chains 452 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 383 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 175 ARG Chi-restraints excluded: chain A residue 278 THR 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 542 GLU 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 756 ILE Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 901 LEU 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 1136 SER Chi-restraints excluded: chain A residue 1307 GLU 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 547 VAL Chi-restraints excluded: chain B residue 563 MET 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 751 VAL 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 72 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 152 GLU 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 118 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 187 THR 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 H residue 80 ARG Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 59 VAL 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 Chi-restraints excluded: chain L residue 39 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 323 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 chunk 225 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 302 optimal weight: 4.9990 chunk 384 optimal weight: 0.4980 chunk 272 optimal weight: 0.6980 chunk 337 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 chunk 288 optimal weight: 10.0000 chunk 364 optimal weight: 8.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 GLN A 626 ASN A 965 GLN ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 ASN B1178 ASN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN E 179 GLN G 14 HIS 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 = 0.4339 r_free = 0.4339 target = 0.193115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.113585 restraints weight = 32285.630| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.87 r_work: 0.3358 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 33908 Z= 0.177 Angle : 0.620 11.433 46203 Z= 0.326 Chirality : 0.046 0.255 5190 Planarity : 0.005 0.053 5630 Dihedral : 17.116 160.396 5353 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.06 % Favored : 96.86 % Rotamer: Outliers : 2.39 % Allowed : 12.41 % Favored : 85.21 % 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: -0.01 (0.13), residues: 3854 helix: 0.88 (0.14), residues: 1364 sheet: 0.06 (0.21), residues: 581 loop : -0.62 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 904 TYR 0.015 0.002 TYR B 486 PHE 0.029 0.002 PHE A 219 TRP 0.014 0.002 TRP C 192 HIS 0.014 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (33876) covalent geometry : angle 0.60810 / 0.33 (46158) hydrogen bonds : bond 0.04403 / 2.98 ( 1435) hydrogen bonds : angle 4.68730 / 3.37 ( 3994) metal coordination : bond 0.00543 / 0.34 ( 32) metal coordination : angle 3.93802 / 2.53 ( 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 470 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 388 time to evaluate : 1.355 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: 0.8403 (mmt90) cc_final: 0.7788 (mmt-90) REVERT: A 175 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7197 (ttp-110) REVERT: A 205 GLU cc_start: 0.7493 (tt0) cc_final: 0.6952 (tp30) REVERT: A 293 GLU cc_start: 0.6735 (tt0) cc_final: 0.6460 (pt0) REVERT: A 368 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8417 (ttmp) REVERT: A 393 ARG cc_start: 0.7767 (ttm110) cc_final: 0.7526 (mpt-90) REVERT: A 407 ARG cc_start: 0.7120 (mtp-110) cc_final: 0.6717 (mtt180) REVERT: A 416 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7932 (mtm180) REVERT: A 437 MET cc_start: 0.8551 (ptt) cc_final: 0.7426 (mtp) REVERT: A 542 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8507 (mt-10) REVERT: A 618 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7282 (pp20) REVERT: A 676 MET cc_start: 0.7183 (mmm) cc_final: 0.6749 (mmm) REVERT: A 685 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6303 (pt0) REVERT: A 702 LEU cc_start: 0.3973 (OUTLIER) cc_final: 0.3392 (pp) REVERT: A 708 MET cc_start: 0.5158 (mtt) cc_final: 0.4616 (ttm) REVERT: A 724 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6243 (pt0) REVERT: A 873 MET cc_start: 0.9008 (mmp) cc_final: 0.8624 (mmt) REVERT: A 984 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7800 (tppp) REVERT: A 992 ASP cc_start: 0.7468 (m-30) cc_final: 0.7137 (t70) REVERT: A 1079 MET cc_start: 0.8130 (ttp) cc_final: 0.7566 (tmm) REVERT: A 1092 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6870 (tppp) REVERT: A 1297 GLU cc_start: 0.8323 (pm20) cc_final: 0.7763 (pm20) REVERT: A 1420 ASP cc_start: 0.7759 (t0) cc_final: 0.6844 (p0) REVERT: A 1424 VAL cc_start: 0.8457 (m) cc_final: 0.8215 (p) REVERT: B 21 GLU cc_start: 0.7562 (pt0) cc_final: 0.7250 (mt-10) REVERT: B 239 GLU cc_start: 0.7587 (pt0) cc_final: 0.6826 (mp0) REVERT: B 257 LYS cc_start: 0.7107 (mtmt) cc_final: 0.6442 (mttp) REVERT: B 422 LYS cc_start: 0.6508 (mmtm) cc_final: 0.5849 (mmtm) REVERT: B 473 MET cc_start: 0.6572 (mmp) cc_final: 0.6231 (mpp) REVERT: B 557 PHE cc_start: 0.8285 (m-10) cc_final: 0.8063 (m-10) REVERT: B 563 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7855 (ttt) REVERT: B 564 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7139 (mm-30) REVERT: B 595 ARG cc_start: 0.7677 (ttt180) cc_final: 0.6809 (ttp80) REVERT: B 623 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7076 (mt-10) REVERT: B 662 MET cc_start: 0.8016 (mmm) cc_final: 0.7597 (mmm) REVERT: B 896 ASP cc_start: 0.6513 (t0) cc_final: 0.6067 (p0) REVERT: B 953 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7683 (tm) REVERT: B 1181 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7222 (tp30) REVERT: C 50 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7380 (mp0) REVERT: C 55 THR cc_start: 0.8627 (m) cc_final: 0.8421 (p) REVERT: C 78 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7075 (pm20) REVERT: C 106 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7917 (mm-30) REVERT: C 135 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8408 (mt0) REVERT: C 138 GLU cc_start: 0.7178 (mp0) cc_final: 0.6844 (mp0) REVERT: C 152 GLU cc_start: 0.8314 (tt0) cc_final: 0.7611 (tm-30) REVERT: C 179 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8841 (tt0) REVERT: C 264 GLN cc_start: 0.6171 (tp-100) cc_final: 0.5804 (mt0) REVERT: D 1 MET cc_start: 0.1251 (ttt) cc_final: -0.0036 (tpt) REVERT: D 32 GLU cc_start: 0.3335 (mm-30) cc_final: 0.2570 (tt0) REVERT: E 50 MET cc_start: 0.6544 (tmm) cc_final: 0.6336 (tmt) REVERT: E 81 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7295 (tp30) REVERT: E 90 VAL cc_start: 0.7648 (t) cc_final: 0.7359 (m) REVERT: E 103 LYS cc_start: 0.7707 (mtpp) cc_final: 0.7206 (mttp) REVERT: E 106 GLN cc_start: 0.7527 (mm-40) cc_final: 0.7160 (mp10) REVERT: E 121 MET cc_start: 0.7687 (mmm) cc_final: 0.7360 (mmm) REVERT: F 72 LYS cc_start: 0.6883 (mmpt) cc_final: 0.6554 (mttt) REVERT: F 149 GLU cc_start: 0.8223 (tt0) cc_final: 0.7983 (tt0) REVERT: G 69 GLU cc_start: 0.7466 (tt0) cc_final: 0.6946 (tm-30) REVERT: H 14 GLU cc_start: 0.8378 (tt0) cc_final: 0.7855 (mt-10) REVERT: H 80 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7918 (mtt90) REVERT: I 1 MET cc_start: 0.4588 (mmm) cc_final: 0.3767 (mmt) REVERT: I 97 MET cc_start: 0.5476 (mtp) cc_final: 0.4185 (tmt) REVERT: J 64 ASN cc_start: 0.7484 (t0) cc_final: 0.6911 (m-40) REVERT: K 1 MET cc_start: 0.7267 (ttt) cc_final: 0.6993 (ttm) REVERT: K 20 LYS cc_start: 0.8367 (tttp) cc_final: 0.8119 (tttm) REVERT: K 54 ARG cc_start: 0.7976 (mtm180) cc_final: 0.7484 (mmp-170) outliers start: 82 outliers final: 47 residues processed: 449 average time/residue: 0.8075 time to fit residues: 427.0845 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 : 1.392 ------------------------------------------------------------------------------- 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 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 542 GLU 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 756 ILE Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 938 LYS Chi-restraints excluded: chain A residue 984 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 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 475 SER Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 563 MET 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 915 THR Chi-restraints excluded: chain B residue 953 LEU 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 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 118 THR Chi-restraints excluded: chain D residue 149 THR 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 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 Chi-restraints excluded: chain L residue 39 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 221 optimal weight: 0.0970 chunk 74 optimal weight: 0.9980 chunk 252 optimal weight: 0.0070 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 393 optimal weight: 10.0000 chunk 268 optimal weight: 4.9990 chunk 370 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 626 ASN A 706 HIS A 965 GLN ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 ASN C 214 ASN E 179 GLN H 35 GLN H 128 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.188109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.112791 restraints weight = 32394.074| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.72 r_work: 0.3254 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33908 Z= 0.120 Angle : 0.559 11.683 46203 Z= 0.296 Chirality : 0.044 0.218 5190 Planarity : 0.004 0.053 5630 Dihedral : 16.994 160.590 5353 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.22 % Favored : 96.70 % Rotamer: Outliers : 2.15 % Allowed : 12.84 % Favored : 85.00 % 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: 0.21 (0.13), residues: 3854 helix: 1.10 (0.14), residues: 1358 sheet: 0.12 (0.21), residues: 579 loop : -0.49 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 904 TYR 0.011 0.001 TYR B 486 PHE 0.026 0.001 PHE A 219 TRP 0.014 0.001 TRP C 192 HIS 0.009 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (33876) covalent geometry : angle 0.54838 / 0.30 (46158) hydrogen bonds : bond 0.03803 / 2.56 ( 1435) hydrogen bonds : angle 4.52002 / 3.25 ( 3994) metal coordination : bond 0.00432 / 0.27 ( 32) metal coordination : angle 3.54662 / 2.25 ( 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 464 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 390 time to evaluate : 1.227 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: 0.8362 (mmt90) cc_final: 0.7761 (mmt-90) REVERT: A 205 GLU cc_start: 0.7452 (tt0) cc_final: 0.6927 (tp30) REVERT: A 280 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6851 (mt-10) REVERT: A 293 GLU cc_start: 0.6677 (tt0) cc_final: 0.6425 (pt0) REVERT: A 407 ARG cc_start: 0.7160 (mtp-110) cc_final: 0.6789 (mtt180) REVERT: A 416 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.8016 (mtm180) REVERT: A 437 MET cc_start: 0.8581 (ptt) cc_final: 0.7464 (mtp) REVERT: A 494 SER cc_start: 0.8790 (t) cc_final: 0.8556 (p) REVERT: A 618 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7246 (pp20) REVERT: A 685 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6412 (pt0) REVERT: A 702 LEU cc_start: 0.4131 (OUTLIER) cc_final: 0.3537 (pp) REVERT: A 708 MET cc_start: 0.4811 (mtt) cc_final: 0.4375 (ttm) REVERT: A 724 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6295 (pt0) REVERT: A 822 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6694 (mm-30) REVERT: A 873 MET cc_start: 0.8992 (mmp) cc_final: 0.8673 (mmt) REVERT: A 984 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7817 (tppp) REVERT: A 992 ASP cc_start: 0.7497 (m-30) cc_final: 0.7129 (t70) REVERT: A 1092 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6854 (tppp) REVERT: A 1297 GLU cc_start: 0.8216 (pm20) cc_final: 0.7648 (pm20) REVERT: A 1420 ASP cc_start: 0.7708 (t0) cc_final: 0.6948 (p0) REVERT: A 1424 VAL cc_start: 0.8482 (m) cc_final: 0.8257 (p) REVERT: B 21 GLU cc_start: 0.7482 (pt0) cc_final: 0.7069 (mp0) REVERT: B 239 GLU cc_start: 0.7519 (pt0) cc_final: 0.6794 (mp0) REVERT: B 257 LYS cc_start: 0.7093 (mtmt) cc_final: 0.6452 (mttp) REVERT: B 422 LYS cc_start: 0.6553 (mmtm) cc_final: 0.5827 (mmtm) REVERT: B 473 MET cc_start: 0.6512 (mmp) cc_final: 0.6160 (mpp) REVERT: B 557 PHE cc_start: 0.8260 (m-10) cc_final: 0.8026 (m-10) REVERT: B 564 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7167 (mm-30) REVERT: B 595 ARG cc_start: 0.7609 (ttt180) cc_final: 0.6782 (ttp80) REVERT: B 896 ASP cc_start: 0.6552 (t0) cc_final: 0.6194 (p0) REVERT: B 953 LEU cc_start: 0.8138 (tt) cc_final: 0.7728 (tm) REVERT: B 1181 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7207 (tp30) REVERT: C 50 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7312 (mp0) REVERT: C 72 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8221 (mp) REVERT: C 78 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7156 (pm20) REVERT: C 106 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7877 (mm-30) REVERT: C 138 GLU cc_start: 0.7171 (mp0) cc_final: 0.6852 (mp0) REVERT: C 152 GLU cc_start: 0.8245 (tt0) cc_final: 0.7587 (tm-30) REVERT: C 179 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8754 (tt0) REVERT: C 264 GLN cc_start: 0.6093 (tp-100) cc_final: 0.5746 (mt0) REVERT: D 1 MET cc_start: 0.1094 (ttt) cc_final: -0.0148 (tpt) REVERT: E 81 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7212 (tp30) REVERT: E 90 VAL cc_start: 0.7664 (t) cc_final: 0.7402 (m) REVERT: E 103 LYS cc_start: 0.7678 (mtpp) cc_final: 0.7373 (mppt) REVERT: E 106 GLN cc_start: 0.7475 (mm-40) cc_final: 0.7122 (mp10) REVERT: E 121 MET cc_start: 0.7751 (mmm) cc_final: 0.7464 (mmm) REVERT: F 72 LYS cc_start: 0.6862 (mmpt) cc_final: 0.6543 (mttt) REVERT: F 149 GLU cc_start: 0.8191 (tt0) cc_final: 0.7839 (tt0) REVERT: G 26 LEU cc_start: 0.5993 (tt) cc_final: 0.5543 (mp) REVERT: G 69 GLU cc_start: 0.7404 (tt0) cc_final: 0.6843 (tm-30) REVERT: H 14 GLU cc_start: 0.8313 (tt0) cc_final: 0.7857 (mt-10) REVERT: H 80 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7872 (mtt90) REVERT: I 97 MET cc_start: 0.5512 (mtp) cc_final: 0.4253 (tmt) REVERT: J 64 ASN cc_start: 0.7441 (t0) cc_final: 0.6869 (m-40) REVERT: K 1 MET cc_start: 0.7305 (ttt) cc_final: 0.6966 (ttm) REVERT: K 20 LYS cc_start: 0.8387 (tttp) cc_final: 0.8052 (tttm) REVERT: K 54 ARG cc_start: 0.7959 (mtm180) cc_final: 0.7514 (mmp-170) outliers start: 74 outliers final: 45 residues processed: 442 average time/residue: 0.7428 time to fit residues: 388.1427 Evaluate side-chains 432 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 376 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 287 HIS 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 618 GLU 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 901 LEU Chi-restraints excluded: chain A residue 938 LYS Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 1092 LYS Chi-restraints excluded: chain A residue 1283 VAL 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 547 VAL Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 36 VAL 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 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 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 H residue 9 ILE 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 Chi-restraints excluded: chain L residue 39 SER 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: 0.9990 chunk 35 optimal weight: 3.9990 chunk 199 optimal weight: 0.7980 chunk 327 optimal weight: 0.8980 chunk 182 optimal weight: 8.9990 chunk 321 optimal weight: 6.9990 chunk 297 optimal weight: 1.9990 chunk 392 optimal weight: 40.0000 chunk 157 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 626 ASN A 965 GLN ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 ASN C 214 ASN E 179 GLN H 35 GLN H 128 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.186488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.110779 restraints weight = 32286.078| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.71 r_work: 0.3223 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (15 function evaluations) r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 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 0.068 33908 Z= 0.170 Angle : 0.609 13.041 46203 Z= 0.319 Chirality : 0.046 0.237 5190 Planarity : 0.005 0.053 5630 Dihedral : 17.021 160.117 5353 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.78 % Rotamer: Outliers : 2.15 % Allowed : 13.16 % 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: 0.15 (0.13), residues: 3854 helix: 1.03 (0.14), residues: 1365 sheet: 0.08 (0.21), residues: 586 loop : -0.51 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 904 TYR 0.015 0.002 TYR B 486 PHE 0.029 0.002 PHE A 219 TRP 0.012 0.002 TRP B 31 HIS 0.012 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (33876) covalent geometry : angle 0.59834 / 0.32 (46158) hydrogen bonds : bond 0.04263 / 2.88 ( 1435) hydrogen bonds : angle 4.59721 / 3.30 ( 3994) metal coordination : bond 0.00483 / 0.31 ( 32) metal coordination : angle 3.66140 / 2.36 ( 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 451 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 377 time to evaluate : 1.321 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: 0.8425 (mmt90) cc_final: 0.7781 (mmt-90) REVERT: A 205 GLU cc_start: 0.7461 (tt0) cc_final: 0.6931 (tp30) REVERT: A 280 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6838 (mt-10) REVERT: A 293 GLU cc_start: 0.6725 (tt0) cc_final: 0.6464 (pt0) REVERT: A 407 ARG cc_start: 0.7112 (mtp-110) cc_final: 0.6738 (mtt180) REVERT: A 416 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.8005 (mtm180) REVERT: A 437 MET cc_start: 0.8546 (ptt) cc_final: 0.7435 (mtp) REVERT: A 611 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7308 (mp10) REVERT: A 618 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7234 (pp20) REVERT: A 676 MET cc_start: 0.7220 (mmm) cc_final: 0.6836 (mmm) REVERT: A 685 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6440 (pt0) REVERT: A 702 LEU cc_start: 0.4194 (OUTLIER) cc_final: 0.3693 (pp) REVERT: A 708 MET cc_start: 0.4805 (mtt) cc_final: 0.4376 (ttm) REVERT: A 724 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6247 (pt0) REVERT: A 873 MET cc_start: 0.9016 (mmp) cc_final: 0.8637 (mmt) REVERT: A 984 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7824 (tppp) REVERT: A 992 ASP cc_start: 0.7484 (m-30) cc_final: 0.7170 (t70) REVERT: A 1079 MET cc_start: 0.8096 (ttp) cc_final: 0.7725 (tmm) REVERT: A 1092 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6775 (tppp) REVERT: A 1297 GLU cc_start: 0.8307 (pm20) cc_final: 0.7723 (pm20) REVERT: A 1420 ASP cc_start: 0.7716 (t0) cc_final: 0.6926 (p0) REVERT: A 1424 VAL cc_start: 0.8496 (m) cc_final: 0.8240 (p) REVERT: B 21 GLU cc_start: 0.7492 (pt0) cc_final: 0.7240 (mt-10) REVERT: B 239 GLU cc_start: 0.7528 (pt0) cc_final: 0.6801 (mp0) REVERT: B 257 LYS cc_start: 0.7119 (mtmt) cc_final: 0.6488 (mttp) REVERT: B 357 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.6607 (tp-100) REVERT: B 422 LYS cc_start: 0.6570 (mmtm) cc_final: 0.5840 (mmtm) REVERT: B 473 MET cc_start: 0.6550 (mmp) cc_final: 0.6210 (mpp) REVERT: B 557 PHE cc_start: 0.8306 (m-10) cc_final: 0.8077 (m-10) REVERT: B 564 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7190 (mm-30) REVERT: B 595 ARG cc_start: 0.7659 (ttt180) cc_final: 0.6816 (ttp80) REVERT: B 896 ASP cc_start: 0.6544 (t0) cc_final: 0.6224 (p0) REVERT: B 1181 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7287 (tp30) REVERT: B 1189 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8375 (pp) REVERT: C 50 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7354 (mp0) REVERT: C 72 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8009 (mp) REVERT: C 78 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7122 (pm20) REVERT: C 106 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7870 (mm-30) REVERT: C 135 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8356 (mt0) REVERT: C 138 GLU cc_start: 0.7191 (mp0) cc_final: 0.6856 (mp0) REVERT: C 152 GLU cc_start: 0.8274 (tt0) cc_final: 0.7760 (tm-30) REVERT: C 179 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8785 (tt0) REVERT: C 264 GLN cc_start: 0.6140 (tp-100) cc_final: 0.5791 (mt0) REVERT: D 1 MET cc_start: 0.1220 (ttt) cc_final: -0.0337 (tpt) REVERT: E 50 MET cc_start: 0.6533 (tmm) cc_final: 0.6314 (tmt) REVERT: E 81 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7264 (tp30) REVERT: E 90 VAL cc_start: 0.7726 (t) cc_final: 0.7467 (m) REVERT: E 103 LYS cc_start: 0.7690 (mtpp) cc_final: 0.7376 (mppt) REVERT: E 106 GLN cc_start: 0.7512 (mm-40) cc_final: 0.7142 (mp10) REVERT: E 121 MET cc_start: 0.7750 (mmm) cc_final: 0.7443 (mmm) REVERT: F 72 LYS cc_start: 0.6908 (mmpt) cc_final: 0.6584 (mttt) REVERT: F 149 GLU cc_start: 0.8196 (tt0) cc_final: 0.7941 (tt0) REVERT: G 26 LEU cc_start: 0.6095 (tt) cc_final: 0.5694 (mp) REVERT: G 69 GLU cc_start: 0.7447 (tt0) cc_final: 0.6890 (tm-30) REVERT: H 14 GLU cc_start: 0.8312 (tt0) cc_final: 0.7849 (mt-10) REVERT: H 80 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7956 (mtt90) REVERT: I 97 MET cc_start: 0.5524 (mtp) cc_final: 0.4283 (tmt) REVERT: J 64 ASN cc_start: 0.7442 (t0) cc_final: 0.6882 (m-40) REVERT: K 1 MET cc_start: 0.7313 (ttt) cc_final: 0.6968 (ttm) REVERT: K 20 LYS cc_start: 0.8389 (tttp) cc_final: 0.8144 (tttm) REVERT: K 54 ARG cc_start: 0.7981 (mtm180) cc_final: 0.7532 (mmp-170) REVERT: L 54 ARG cc_start: 0.6415 (OUTLIER) cc_final: 0.6148 (mtt-85) outliers start: 74 outliers final: 51 residues processed: 430 average time/residue: 0.8147 time to fit residues: 413.2822 Evaluate side-chains 441 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 375 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 287 HIS Chi-restraints excluded: chain A residue 360 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 611 GLN 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 822 GLU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 938 LYS Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 1092 LYS Chi-restraints excluded: chain A residue 1283 VAL 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 364 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 36 VAL 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 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 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 F residue 103 MET 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 Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 54 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 179 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 209 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 216 optimal weight: 1.9990 chunk 246 optimal weight: 0.9980 chunk 391 optimal weight: 50.0000 chunk 388 optimal weight: 20.0000 chunk 247 optimal weight: 10.0000 chunk 87 optimal weight: 0.0570 chunk 191 optimal weight: 0.7980 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 626 ASN A 965 GLN ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 ASN C 214 ASN H 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.187778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.112610 restraints weight = 32479.352| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.70 r_work: 0.3250 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33908 Z= 0.127 Angle : 0.564 11.975 46203 Z= 0.298 Chirality : 0.044 0.220 5190 Planarity : 0.004 0.053 5630 Dihedral : 16.935 160.330 5353 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.78 % Rotamer: Outliers : 1.95 % Allowed : 13.45 % 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: 0.25 (0.13), residues: 3854 helix: 1.15 (0.14), residues: 1368 sheet: 0.12 (0.21), residues: 586 loop : -0.49 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 579 TYR 0.011 0.001 TYR A1349 PHE 0.027 0.001 PHE A 219 TRP 0.013 0.001 TRP C 192 HIS 0.009 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (33876) covalent geometry : angle 0.55400 / 0.30 (46158) hydrogen bonds : bond 0.03845 / 2.59 ( 1435) hydrogen bonds : angle 4.49622 / 3.23 ( 3994) metal coordination : bond 0.00426 / 0.27 ( 32) metal coordination : angle 3.42079 / 2.20 ( 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 451 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 384 time to evaluate : 1.341 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: 0.8395 (mmt90) cc_final: 0.7767 (mmt-90) REVERT: A 205 GLU cc_start: 0.7454 (tt0) cc_final: 0.6921 (tp30) REVERT: A 280 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6786 (mt-10) REVERT: A 293 GLU cc_start: 0.6651 (tt0) cc_final: 0.6410 (pt0) REVERT: A 407 ARG cc_start: 0.7189 (mtp-110) cc_final: 0.6827 (mtt180) REVERT: A 437 MET cc_start: 0.8575 (ptt) cc_final: 0.7462 (mtp) REVERT: A 611 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.7303 (mp10) REVERT: A 618 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7251 (pp20) REVERT: A 676 MET cc_start: 0.7200 (mmm) cc_final: 0.6800 (mmm) REVERT: A 685 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6365 (pt0) REVERT: A 702 LEU cc_start: 0.4195 (OUTLIER) cc_final: 0.3600 (pp) REVERT: A 708 MET cc_start: 0.4697 (mtt) cc_final: 0.4246 (ttm) REVERT: A 873 MET cc_start: 0.8997 (mmp) cc_final: 0.8678 (mmt) REVERT: A 984 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7848 (tppp) REVERT: A 1079 MET cc_start: 0.8079 (ttp) cc_final: 0.7791 (tmm) REVERT: A 1092 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6901 (tppp) REVERT: A 1281 ARG cc_start: 0.7816 (ttt180) cc_final: 0.7594 (ttt90) REVERT: A 1297 GLU cc_start: 0.8210 (pm20) cc_final: 0.7719 (pm20) REVERT: A 1420 ASP cc_start: 0.7688 (t0) cc_final: 0.6943 (p0) REVERT: A 1424 VAL cc_start: 0.8493 (m) cc_final: 0.8253 (p) REVERT: B 21 GLU cc_start: 0.7473 (pt0) cc_final: 0.7095 (mp0) REVERT: B 239 GLU cc_start: 0.7562 (pt0) cc_final: 0.6832 (mp0) REVERT: B 257 LYS cc_start: 0.7086 (mtmt) cc_final: 0.6460 (mttp) REVERT: B 422 LYS cc_start: 0.6548 (mmtm) cc_final: 0.5815 (mmtm) REVERT: B 473 MET cc_start: 0.6476 (mmp) cc_final: 0.6135 (mpp) REVERT: B 564 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7113 (mm-30) REVERT: B 595 ARG cc_start: 0.7603 (ttt180) cc_final: 0.6767 (ttp80) REVERT: B 662 MET cc_start: 0.7911 (mmm) cc_final: 0.7569 (mmm) REVERT: B 896 ASP cc_start: 0.6544 (t0) cc_final: 0.6185 (p0) REVERT: B 953 LEU cc_start: 0.8181 (tt) cc_final: 0.7740 (tm) REVERT: B 1181 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7184 (tp30) REVERT: C 50 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7327 (mp0) REVERT: C 78 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7152 (pm20) REVERT: C 106 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7827 (mm-30) REVERT: C 135 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8380 (mt0) REVERT: C 138 GLU cc_start: 0.7180 (mp0) cc_final: 0.6852 (mp0) REVERT: C 152 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: C 179 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8853 (tt0) REVERT: C 264 GLN cc_start: 0.6128 (tp-100) cc_final: 0.5781 (mt0) REVERT: D 1 MET cc_start: 0.1143 (ttt) cc_final: -0.0420 (tpt) REVERT: D 149 THR cc_start: 0.3771 (OUTLIER) cc_final: 0.3436 (p) REVERT: E 50 MET cc_start: 0.6609 (tmm) cc_final: 0.6383 (tmt) REVERT: E 81 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7212 (tp30) REVERT: E 90 VAL cc_start: 0.7710 (t) cc_final: 0.7461 (m) REVERT: E 103 LYS cc_start: 0.7659 (mtpp) cc_final: 0.7351 (mppt) REVERT: E 106 GLN cc_start: 0.7516 (mm-40) cc_final: 0.7171 (mp10) REVERT: E 121 MET cc_start: 0.7762 (mmm) cc_final: 0.7481 (mmm) REVERT: F 72 LYS cc_start: 0.6906 (mmpt) cc_final: 0.6588 (mttt) REVERT: F 149 GLU cc_start: 0.8181 (tt0) cc_final: 0.7932 (tt0) REVERT: G 26 LEU cc_start: 0.6078 (tt) cc_final: 0.5811 (mt) REVERT: G 69 GLU cc_start: 0.7376 (tt0) cc_final: 0.6803 (tm-30) REVERT: G 106 MET cc_start: 0.1995 (ttm) cc_final: 0.1753 (ttp) REVERT: H 14 GLU cc_start: 0.8325 (tt0) cc_final: 0.7871 (mt-10) REVERT: H 80 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7905 (mtt90) REVERT: I 97 MET cc_start: 0.5468 (mtp) cc_final: 0.4284 (tmt) REVERT: J 64 ASN cc_start: 0.7428 (t0) cc_final: 0.6858 (m-40) REVERT: K 1 MET cc_start: 0.7286 (ttt) cc_final: 0.6951 (ttm) REVERT: K 54 ARG cc_start: 0.7965 (mtm180) cc_final: 0.7512 (mmp-170) REVERT: L 54 ARG cc_start: 0.6445 (OUTLIER) cc_final: 0.6157 (mtt-85) outliers start: 67 outliers final: 46 residues processed: 432 average time/residue: 0.8320 time to fit residues: 423.1544 Evaluate side-chains 438 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 379 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 360 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 472 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 611 GLN 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 822 GLU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 938 LYS Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 1092 LYS Chi-restraints excluded: chain A residue 1283 VAL 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 475 SER Chi-restraints excluded: chain B residue 547 VAL 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 1181 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 152 GLU 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 149 THR Chi-restraints excluded: chain D residue 187 THR 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 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 Chi-restraints excluded: chain L residue 54 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 347 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 281 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 345 optimal weight: 8.9990 chunk 359 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 75 optimal weight: 0.4980 chunk 106 optimal weight: 0.8980 chunk 351 optimal weight: 4.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 390 GLN A 626 ASN A 965 GLN ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 ASN C 102 GLN C 214 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 = 0.4196 r_free = 0.4196 target = 0.185907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.110307 restraints weight = 32181.505| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.70 r_work: 0.3217 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 33908 Z= 0.180 Angle : 0.618 11.829 46203 Z= 0.324 Chirality : 0.046 0.252 5190 Planarity : 0.005 0.053 5630 Dihedral : 16.955 159.612 5351 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.37 % Favored : 96.55 % Rotamer: Outliers : 2.10 % Allowed : 13.34 % Favored : 84.57 % 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: 0.14 (0.13), residues: 3854 helix: 1.02 (0.14), residues: 1364 sheet: 0.03 (0.21), residues: 593 loop : -0.51 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 904 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 0.013 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (33876) covalent geometry : angle 0.60769 / 0.32 (46158) hydrogen bonds : bond 0.04390 / 2.97 ( 1435) hydrogen bonds : angle 4.61016 / 3.31 ( 3994) metal coordination : bond 0.00505 / 0.32 ( 32) metal coordination : angle 3.63505 / 2.35 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22849.75 seconds wall clock time: 386 minutes 53.60 seconds (23213.60 seconds total)