Starting phenix.real_space_refine on Thu Dec 26 09:55:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s5n_19743/12_2024/8s5n_19743.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s5n_19743/12_2024/8s5n_19743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s5n_19743/12_2024/8s5n_19743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s5n_19743/12_2024/8s5n_19743.map" model { file = "/net/cci-nas-00/data/ceres_data/8s5n_19743/12_2024/8s5n_19743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s5n_19743/12_2024/8s5n_19743.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 129 5.49 5 Mg 1 5.21 5 S 250 5.16 5 C 27813 2.51 5 N 7867 2.21 5 O 8646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 44716 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 11274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1423, 11274 Classifications: {'peptide': 1423} Link IDs: {'PCIS': 2, 'PTRANS': 68, 'TRANS': 1352} Chain breaks: 4 Chain: "B" Number of atoms: 9005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1127, 9005 Classifications: {'peptide': 1127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1074} Chain breaks: 4 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1050 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 928 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2015 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 11, 'TRANS': 249} Chain breaks: 1 Chain: "N" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1117 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} Chain breaks: 1 Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1422 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "P" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 252 Classifications: {'RNA': 12} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 10} Chain: "Q" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "R" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1788 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Chain: "T" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1288 Classifications: {'DNA': 64} Link IDs: {'rna3p': 63} Chain breaks: 1 Chain: "U" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 931 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "V" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 806 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "W" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1535 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 5, 'TRANS': 181} Chain: "X" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 70.667 107.304 86.553 1.00 66.90 S ATOM 486 SG CYS A 74 67.193 106.353 87.316 1.00 66.55 S ATOM 533 SG CYS A 81 69.955 103.977 87.992 1.00 52.78 S ATOM 768 SG CYS A 111 70.911 76.094 50.213 1.00 83.98 S ATOM 796 SG CYS A 114 68.035 76.840 47.707 1.00 87.29 S ATOM 1109 SG CYS A 154 69.188 73.271 48.780 1.00106.90 S ATOM 1132 SG CYS A 184 71.039 75.727 46.300 1.00 94.01 S ATOM 19848 SG CYS B1119 56.589 95.596 79.140 1.00 71.32 S ATOM 19870 SG CYS B1122 59.779 94.376 77.425 1.00 73.52 S ATOM 19985 SG CYS B1137 59.106 98.146 78.230 1.00 82.35 S ATOM 20006 SG CYS B1140 57.564 96.175 75.303 1.00 85.98 S ATOM 20973 SG CYS C 88 86.215 108.311 152.411 1.00 67.41 S ATOM 20986 SG CYS C 90 87.560 108.831 148.895 1.00 69.94 S ATOM 21021 SG CYS C 94 89.675 109.887 151.890 1.00 58.05 S ATOM 21043 SG CYS C 97 89.031 106.196 151.266 1.00 58.61 S ATOM 28329 SG CYS I 17 127.969 44.958 55.804 1.00110.57 S ATOM 28353 SG CYS I 20 127.332 48.265 54.228 1.00104.27 S ATOM 28514 SG CYS I 39 124.441 45.836 54.356 1.00106.87 S ATOM 28539 SG CYS I 42 127.174 45.049 52.072 1.00107.60 S ATOM 28891 SG CYS I 86 134.984 30.109 96.438 1.00 78.17 S ATOM 28915 SG CYS I 89 138.499 31.191 97.493 1.00 87.99 S ATOM 29119 SG CYS I 114 135.562 33.560 97.584 1.00 61.10 S ATOM 29154 SG CYS I 119 137.166 32.578 94.280 1.00 82.86 S ATOM 29265 SG CYS J 7 105.475 80.299 142.752 1.00 32.96 S ATOM 29289 SG CYS J 10 103.992 80.231 146.287 1.00 33.36 S ATOM 29553 SG CYS J 44 105.091 77.059 144.682 1.00 36.39 S ATOM 29559 SG CYS J 45 107.600 79.518 145.964 1.00 36.59 S ATOM 30679 SG CYS L 19 118.977 112.211 117.028 1.00 58.09 S ATOM 30698 SG CYS L 22 121.381 114.179 119.240 1.00 62.23 S ATOM 30815 SG CYS L 36 119.604 115.891 116.343 1.00 65.25 S ATOM 30841 SG CYS L 39 122.255 113.282 115.642 1.00 64.89 S ATOM 31023 SG CYS M 15 66.987 115.411 109.377 1.00122.73 S ATOM 31170 SG CYS M 34 69.550 116.008 111.965 1.00113.02 S ATOM 31192 SG CYS M 37 66.023 114.890 113.045 1.00118.55 S ATOM 42765 SG CYS W 129 59.254 130.024 78.478 1.00268.02 S ATOM 42957 SG CYS W 154 59.199 127.673 82.037 1.00170.05 S ATOM 42981 SG CYS W 157 61.143 130.925 81.472 1.00178.56 S Time building chain proxies: 22.20, per 1000 atoms: 0.50 Number of scatterers: 44716 At special positions: 0 Unit cell: (179.55, 176.4, 185.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 10 29.99 S 250 16.00 P 129 15.00 Mg 1 11.99 O 8646 8.00 N 7867 7.00 C 27813 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: 11.27 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " 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 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" ND1 HIS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 15 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 34 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 37 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 129 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 157 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 154 " Number of angles added : 48 10366 Ramachandran restraints generated. 5183 Oldfield, 0 Emsley, 5183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9904 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 61 sheets defined 39.8% alpha, 16.5% beta 55 base pairs and 108 stacking pairs defined. Time for finding SS restraints: 15.17 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 removed outlier: 3.672A pdb=" N SER A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.890A pdb=" N CYS A 81 " --> pdb=" O MET A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 136 through 146 removed outlier: 4.060A pdb=" N LEU A 141 " --> pdb=" O PRO A 137 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.774A pdb=" N ILE A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 297 removed outlier: 4.421A pdb=" N GLN A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 398 through 409 removed outlier: 4.059A pdb=" N GLU A 404 " --> pdb=" O ASP A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.657A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 538 through 549 removed outlier: 3.750A pdb=" N LEU A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 564 Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 661 removed outlier: 3.566A pdb=" N GLY A 661 " --> pdb=" O TYR A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 684 removed outlier: 3.902A pdb=" N ASN A 677 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 695 through 722 removed outlier: 3.728A pdb=" N ASN A 722 " --> pdb=" O GLU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 759 removed outlier: 3.759A pdb=" N SER A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 771 Processing helix chain 'A' and resid 777 through 785 Processing helix chain 'A' and resid 832 through 868 removed outlier: 3.659A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 removed outlier: 3.678A pdb=" N ARG A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 934 removed outlier: 3.737A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG A 932 " --> pdb=" O ARG A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 removed outlier: 4.003A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.714A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 removed outlier: 3.720A pdb=" N GLN A1032 " --> pdb=" O PRO A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1079 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 4.044A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1192 through 1197 Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1227 through 1237 Processing helix chain 'A' and resid 1262 through 1266 Processing helix chain 'A' and resid 1283 through 1292 Processing helix chain 'A' and resid 1342 through 1348 Processing helix chain 'A' and resid 1361 through 1370 removed outlier: 3.560A pdb=" N GLY A1370 " --> pdb=" O PHE A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1386 removed outlier: 3.649A pdb=" N ILE A1386 " --> pdb=" O LEU A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1397 through 1406 Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1433 removed outlier: 4.018A pdb=" N GLU A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.952A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 4.365A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 54 through 62 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 295 through 307 Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'B' and resid 331 through 346 removed outlier: 3.991A pdb=" N LYS B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 378 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 422 Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.521A pdb=" N ALA B 434 " --> pdb=" O ASN B 430 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 430 through 435' Processing helix chain 'B' and resid 437 through 451 removed outlier: 3.763A pdb=" N SER B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 516 through 520 removed outlier: 4.419A pdb=" N ALA B 519 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.690A pdb=" N ALA B 560 " --> pdb=" O SER B 557 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 561 " --> pdb=" O PRO B 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 557 through 561' Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 636 through 644 removed outlier: 3.762A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 668 through 673 removed outlier: 3.917A pdb=" N VAL B 673 " --> pdb=" O GLU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.641A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 761 through 766 removed outlier: 3.565A pdb=" N GLU B 765 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 972 Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.046A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.633A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1058 Processing helix chain 'B' and resid 1077 through 1081 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1165 Processing helix chain 'C' and resid 27 through 40 removed outlier: 3.567A pdb=" N ALA C 31 " --> pdb=" O ASP C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 77 through 82 removed outlier: 3.875A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 98 removed outlier: 4.214A pdb=" N SER C 98 " --> pdb=" O PRO C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 removed outlier: 3.569A pdb=" N TRP C 176 " --> pdb=" O HIS C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.532A pdb=" N GLU C 202 " --> pdb=" O LYS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 269 removed outlier: 4.036A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.996A pdb=" N MET D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.733A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 removed outlier: 3.830A pdb=" N GLU D 119 " --> pdb=" O PRO D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 123 through 138 removed outlier: 3.532A pdb=" N ARG D 138 " --> pdb=" O ILE D 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.699A pdb=" N LEU E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 29 through 34' Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 54 through 58 Processing helix chain 'E' and resid 83 through 96 removed outlier: 3.876A pdb=" N GLU E 96 " --> pdb=" O GLN E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 122 Processing helix chain 'E' and resid 133 through 136 removed outlier: 3.933A pdb=" N LEU E 136 " --> pdb=" O GLN E 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 133 through 136' Processing helix chain 'E' and resid 138 through 142 removed outlier: 3.545A pdb=" N GLU E 141 " --> pdb=" O ASN E 138 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS E 142 " --> pdb=" O ILE E 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 142' Processing helix chain 'E' and resid 152 through 160 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 removed outlier: 3.659A pdb=" N ILE F 92 " --> pdb=" O ASP F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.620A pdb=" N GLU G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.534A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 removed outlier: 3.547A pdb=" N TYR J 21 " --> pdb=" O LYS J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 37 Processing helix chain 'J' and resid 42 through 51 Processing helix chain 'J' and resid 54 through 60 removed outlier: 3.801A pdb=" N LYS J 58 " --> pdb=" O ASP J 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 4.049A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.647A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 removed outlier: 3.710A pdb=" N GLY K 115 " --> pdb=" O ASP K 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 93 removed outlier: 3.999A pdb=" N SER M 92 " --> pdb=" O GLY M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 126 Processing helix chain 'M' and resid 131 through 149 removed outlier: 3.566A pdb=" N VAL M 135 " --> pdb=" O PRO M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 171 Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.666A pdb=" N VAL M 183 " --> pdb=" O GLU M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 203 removed outlier: 3.860A pdb=" N GLU M 203 " --> pdb=" O LEU M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 213 removed outlier: 3.643A pdb=" N ASP M 213 " --> pdb=" O THR M 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 210 through 213' Processing helix chain 'M' and resid 214 through 222 Processing helix chain 'M' and resid 225 through 243 removed outlier: 3.634A pdb=" N ASP M 243 " --> pdb=" O ALA M 239 " (cutoff:3.500A) Processing helix chain 'M' and resid 249 through 263 Processing helix chain 'M' and resid 270 through 279 Processing helix chain 'M' and resid 281 through 293 Processing helix chain 'O' and resid 179 through 187 Processing helix chain 'O' and resid 226 through 243 Processing helix chain 'O' and resid 269 through 277 Processing helix chain 'O' and resid 317 through 327 removed outlier: 3.594A pdb=" N ILE O 321 " --> pdb=" O VAL O 317 " (cutoff:3.500A) Processing helix chain 'O' and resid 328 through 334 removed outlier: 3.720A pdb=" N GLY O 334 " --> pdb=" O PRO O 330 " (cutoff:3.500A) Processing helix chain 'Q' and resid 156 through 164 removed outlier: 3.803A pdb=" N GLU Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 176 removed outlier: 3.504A pdb=" N ILE Q 176 " --> pdb=" O HIS Q 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 14 Processing helix chain 'R' and resid 24 through 35 removed outlier: 3.512A pdb=" N SER R 28 " --> pdb=" O PRO R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 64 Processing helix chain 'R' and resid 123 through 136 removed outlier: 3.625A pdb=" N LEU R 127 " --> pdb=" O ASN R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 172 removed outlier: 3.822A pdb=" N LYS R 170 " --> pdb=" O GLU R 166 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU R 171 " --> pdb=" O ARG R 167 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP R 172 " --> pdb=" O LYS R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 194 removed outlier: 3.503A pdb=" N VAL R 183 " --> pdb=" O ASP R 179 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS R 193 " --> pdb=" O SER R 189 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS R 194 " --> pdb=" O ALA R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 207 Processing helix chain 'R' and resid 209 through 221 removed outlier: 4.077A pdb=" N GLU R 219 " --> pdb=" O GLU R 215 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE R 220 " --> pdb=" O ILE R 216 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 25 Processing helix chain 'U' and resid 25 through 33 Processing helix chain 'U' and resid 36 through 50 removed outlier: 3.764A pdb=" N MET U 40 " --> pdb=" O GLU U 36 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU U 50 " --> pdb=" O TRP U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 324 through 330 removed outlier: 4.137A pdb=" N LEU U 328 " --> pdb=" O GLU U 324 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP U 330 " --> pdb=" O GLN U 326 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 8 removed outlier: 3.830A pdb=" N ASN V 8 " --> pdb=" O LEU V 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 5 through 8' Processing helix chain 'V' and resid 9 through 25 Processing helix chain 'V' and resid 29 through 52 removed outlier: 4.087A pdb=" N VAL V 52 " --> pdb=" O LEU V 48 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 25 removed outlier: 3.699A pdb=" N LYS W 15 " --> pdb=" O PRO W 11 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 40 removed outlier: 3.768A pdb=" N ILE W 36 " --> pdb=" O LEU W 32 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU W 37 " --> pdb=" O ALA W 33 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 53 Processing helix chain 'W' and resid 55 through 69 removed outlier: 3.518A pdb=" N LEU W 59 " --> pdb=" O ASP W 55 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP W 69 " --> pdb=" O ASN W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 124 removed outlier: 3.640A pdb=" N ASN W 101 " --> pdb=" O ARG W 97 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU W 115 " --> pdb=" O ARG W 111 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR W 122 " --> pdb=" O GLU W 118 " (cutoff:3.500A) Processing helix chain 'W' and resid 137 through 145 Processing helix chain 'W' and resid 163 through 165 No H-bonds generated for 'chain 'W' and resid 163 through 165' Processing helix chain 'W' and resid 166 through 184 removed outlier: 4.511A pdb=" N LYS W 170 " --> pdb=" O SER W 166 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA W 178 " --> pdb=" O ARG W 174 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG W 179 " --> pdb=" O THR W 175 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE W 184 " --> pdb=" O PHE W 180 " (cutoff:3.500A) Processing helix chain 'W' and resid 184 through 194 removed outlier: 3.628A pdb=" N TYR W 188 " --> pdb=" O ILE W 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 91 removed outlier: 4.003A pdb=" N LYS X 80 " --> pdb=" O GLY X 76 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR X 84 " --> pdb=" O LYS X 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 98 through 106 removed outlier: 4.053A pdb=" N GLU X 105 " --> pdb=" O GLU X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 112 through 122 Processing helix chain 'X' and resid 147 through 162 Processing helix chain 'X' and resid 168 through 175 Processing helix chain 'X' and resid 177 through 186 removed outlier: 4.450A pdb=" N ALA X 181 " --> pdb=" O ASN X 177 " (cutoff:3.500A) Processing helix chain 'X' and resid 213 through 223 Processing helix chain 'X' and resid 229 through 241 removed outlier: 3.831A pdb=" N LEU X 237 " --> pdb=" O ILE X 233 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS X 238 " --> pdb=" O GLU X 234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 94 removed outlier: 3.578A pdb=" N LEU A 90 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 191 Processing sheet with id=AA5, first strand: chain 'A' and resid 328 through 329 Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA7, first strand: chain 'B' and resid 1060 through 1061 removed outlier: 3.605A pdb=" N MET A 470 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.111A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB1, first strand: chain 'A' and resid 604 through 605 Processing sheet with id=AB2, first strand: chain 'A' and resid 789 through 790 removed outlier: 3.725A pdb=" N GLY A 789 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.901A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 902 through 903 Processing sheet with id=AB5, first strand: chain 'A' and resid 1140 through 1142 Processing sheet with id=AB6, first strand: chain 'A' and resid 1170 through 1174 removed outlier: 3.709A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AB8, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.303A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.303A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 11.731A pdb=" N LEU G 67 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 10.582A pdb=" N ILE G 54 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N ASP G 52 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LYS G 71 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N THR G 50 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LYS G 73 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL G 48 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 65 through 66 removed outlier: 4.785A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.889A pdb=" N GLN R 143 " --> pdb=" O ILE B 91 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC4, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.423A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS B 524 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 208 through 209 removed outlier: 6.965A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC8, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC9, first strand: chain 'B' and resid 551 through 552 removed outlier: 3.519A pdb=" N GLU B 551 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 747 through 751 removed outlier: 3.524A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER B 925 " --> pdb=" O PHE B 810 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 747 through 751 removed outlier: 3.524A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER B 925 " --> pdb=" O PHE B 810 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD4, first strand: chain 'B' and resid 935 through 937 removed outlier: 4.392A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ILE B 965 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE B 779 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE B 967 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 781 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 935 through 937 Processing sheet with id=AD6, first strand: chain 'B' and resid 827 through 829 removed outlier: 3.648A pdb=" N VAL B 828 " --> pdb=" O THR B 870 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR B 870 " --> pdb=" O VAL B 828 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=AD8, first strand: chain 'C' and resid 8 through 11 removed outlier: 3.508A pdb=" N PHE C 21 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 121 through 122 removed outlier: 3.821A pdb=" N GLN C 157 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ARG C 162 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE C 52 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N TYR C 164 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N VAL C 50 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LYS C 166 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP C 48 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY C 168 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA C 46 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.480A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 26 through 27 removed outlier: 3.858A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL E 62 " --> pdb=" O MET E 72 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE4, first strand: chain 'E' and resid 103 through 106 Processing sheet with id=AE5, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AE6, first strand: chain 'G' and resid 142 through 146 removed outlier: 7.056A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU G 97 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 118 through 119 Processing sheet with id=AE8, first strand: chain 'H' and resid 90 through 91 removed outlier: 4.067A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 90 through 91 removed outlier: 6.844A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE H 99 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N SER H 113 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY H 101 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ARG H 111 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU H 121 " --> pdb=" O TYR H 118 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 25 through 28 Processing sheet with id=AF2, first strand: chain 'I' and resid 80 through 81 removed outlier: 3.729A pdb=" N PHE I 97 " --> pdb=" O TYR I 111 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU I 110 " --> pdb=" O GLU I 125 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU I 125 " --> pdb=" O LEU I 110 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 21 through 24 removed outlier: 4.552A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 24 through 26 Processing sheet with id=AF5, first strand: chain 'O' and resid 200 through 204 removed outlier: 5.306A pdb=" N LEU O 165 " --> pdb=" O SER O 261 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N SER O 261 " --> pdb=" O LEU O 165 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN O 167 " --> pdb=" O VAL O 259 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR O 171 " --> pdb=" O ILE O 255 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ILE O 255 " --> pdb=" O THR O 171 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ASN O 173 " --> pdb=" O PHE O 253 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE O 253 " --> pdb=" O ASN O 173 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 191 through 192 removed outlier: 3.699A pdb=" N TYR O 192 " --> pdb=" O PHE V 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'Q' and resid 45 through 49 removed outlier: 3.821A pdb=" N LYS Q 109 " --> pdb=" O LEU Q 149 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR Q 26 " --> pdb=" O ASN Q 142 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR Q 144 " --> pdb=" O TYR Q 26 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE Q 28 " --> pdb=" O TYR Q 144 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N PHE Q 146 " --> pdb=" O ILE Q 28 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA Q 30 " --> pdb=" O PHE Q 146 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE R 96 " --> pdb=" O ASN Q 27 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET Q 29 " --> pdb=" O THR R 94 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR R 94 " --> pdb=" O MET Q 29 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE Q 31 " --> pdb=" O THR R 92 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR R 92 " --> pdb=" O PHE Q 31 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU R 93 " --> pdb=" O VAL R 110 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY R 108 " --> pdb=" O VAL R 95 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR R 97 " --> pdb=" O LEU R 106 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU R 106 " --> pdb=" O THR R 97 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Q' and resid 135 through 136 removed outlier: 6.501A pdb=" N VAL Q 15 " --> pdb=" O PHE Q 135 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR Q 14 " --> pdb=" O LEU R 43 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU R 43 " --> pdb=" O TYR Q 14 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL Q 16 " --> pdb=" O GLY R 41 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLY R 41 " --> pdb=" O VAL Q 16 " (cutoff:3.500A) removed outlier: 10.781A pdb=" N THR R 52 " --> pdb=" O LEU R 85 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU R 85 " --> pdb=" O THR R 52 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL R 54 " --> pdb=" O PHE R 83 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ARG R 113 " --> pdb=" O GLN R 86 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL R 18 " --> pdb=" O GLN R 112 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ALA R 114 " --> pdb=" O VAL R 18 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU R 20 " --> pdb=" O ALA R 114 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N CYS R 116 " --> pdb=" O LEU R 20 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS R 22 " --> pdb=" O CYS R 116 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 125 through 126 Processing sheet with id=AG1, first strand: chain 'R' and resid 222 through 224 Processing sheet with id=AG2, first strand: chain 'U' and resid 333 through 344 removed outlier: 3.550A pdb=" N LYS U 341 " --> pdb=" O HIS U 352 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE U 351 " --> pdb=" O GLY U 372 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY U 372 " --> pdb=" O PHE U 351 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU U 353 " --> pdb=" O ALA U 370 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA U 370 " --> pdb=" O LEU U 353 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS U 369 " --> pdb=" O VAL V 56 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N PHE V 58 " --> pdb=" O LYS U 369 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE U 371 " --> pdb=" O PHE V 58 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N GLY V 60 " --> pdb=" O ILE U 371 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASP U 373 " --> pdb=" O GLY V 60 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU V 62 " --> pdb=" O ASP U 373 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER V 61 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ASP V 78 " --> pdb=" O SER V 61 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN V 63 " --> pdb=" O LEU V 76 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LEU V 76 " --> pdb=" O ASN V 63 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA V 97 " --> pdb=" O TRP V 72 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASP V 91 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLU V 80 " --> pdb=" O LYS V 89 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS V 89 " --> pdb=" O GLU V 80 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ARG V 82 " --> pdb=" O LEU V 87 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU V 87 " --> pdb=" O ARG V 82 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN U 333 " --> pdb=" O LYS V 94 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N VAL V 96 " --> pdb=" O ASN U 333 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL U 335 " --> pdb=" O VAL V 96 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N CYS V 98 " --> pdb=" O VAL U 335 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N CYS U 337 " --> pdb=" O CYS V 98 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'U' and resid 356 through 357 Processing sheet with id=AG4, first strand: chain 'W' and resid 42 through 44 Processing sheet with id=AG5, first strand: chain 'W' and resid 127 through 129 removed outlier: 3.697A pdb=" N PHE W 127 " --> pdb=" O PHE W 136 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS W 129 " --> pdb=" O SER W 134 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER W 134 " --> pdb=" O CYS W 129 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 130 through 133 Processing sheet with id=AG7, first strand: chain 'X' and resid 166 through 167 removed outlier: 3.615A pdb=" N ILE X 166 " --> pdb=" O LEU X 201 " (cutoff:3.500A) 1693 hydrogen bonds defined for protein. 4746 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 147 hydrogen bonds 294 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 108 stacking parallelities Total time for adding SS restraints: 28.92 Time building geometry restraints manager: 12.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11403 1.33 - 1.45: 9087 1.45 - 1.58: 24659 1.58 - 1.70: 253 1.70 - 1.82: 394 Bond restraints: 45796 Sorted by residual: bond pdb=" N MET B1165 " pdb=" CA MET B1165 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.26e-02 6.30e+03 9.55e+00 bond pdb=" N ILE B 612 " pdb=" CA ILE B 612 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.83e+00 bond pdb=" N ASP G 165 " pdb=" CA ASP G 165 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.32e+00 bond pdb=" N LEU M 242 " pdb=" CA LEU M 242 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.33e-02 5.65e+03 6.90e+00 bond pdb=" N ASP G 156 " pdb=" CA ASP G 156 " ideal model delta sigma weight residual 1.457 1.488 -0.032 1.26e-02 6.30e+03 6.33e+00 ... (remaining 45791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 60783 2.81 - 5.63: 1361 5.63 - 8.44: 199 8.44 - 11.25: 26 11.25 - 14.07: 3 Bond angle restraints: 62372 Sorted by residual: angle pdb=" CA PRO A 60 " pdb=" N PRO A 60 " pdb=" CD PRO A 60 " ideal model delta sigma weight residual 112.00 104.79 7.21 1.40e+00 5.10e-01 2.65e+01 angle pdb=" C5' DG T 49 " pdb=" C4' DG T 49 " pdb=" C3' DG T 49 " ideal model delta sigma weight residual 114.90 107.33 7.57 1.50e+00 4.44e-01 2.54e+01 angle pdb=" N ILE B 972 " pdb=" CA ILE B 972 " pdb=" C ILE B 972 " ideal model delta sigma weight residual 108.88 119.77 -10.89 2.16e+00 2.14e-01 2.54e+01 angle pdb=" C GLY B1077 " pdb=" N ARG B1078 " pdb=" CA ARG B1078 " ideal model delta sigma weight residual 120.38 127.03 -6.65 1.37e+00 5.33e-01 2.36e+01 angle pdb=" O2' C P 2 " pdb=" C2' C P 2 " pdb=" C1' C P 2 " ideal model delta sigma weight residual 111.80 104.68 7.12 1.50e+00 4.44e-01 2.25e+01 ... (remaining 62367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 26807 35.33 - 70.66: 865 70.66 - 105.99: 66 105.99 - 141.33: 0 141.33 - 176.66: 1 Dihedral angle restraints: 27739 sinusoidal: 12448 harmonic: 15291 Sorted by residual: dihedral pdb=" CA LYS O 297 " pdb=" C LYS O 297 " pdb=" N PRO O 298 " pdb=" CA PRO O 298 " ideal model delta harmonic sigma weight residual 180.00 152.50 27.50 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ARG B1085 " pdb=" C ARG B1085 " pdb=" N PHE B1086 " pdb=" CA PHE B1086 " ideal model delta harmonic sigma weight residual 180.00 154.08 25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" O4' A P 3 " pdb=" C2' A P 3 " pdb=" C1' A P 3 " pdb=" C3' A P 3 " ideal model delta sinusoidal sigma weight residual 25.00 -9.76 34.76 1 8.00e+00 1.56e-02 2.68e+01 ... (remaining 27736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 6583 0.127 - 0.253: 342 0.253 - 0.380: 13 0.380 - 0.507: 11 0.507 - 0.634: 19 Chirality restraints: 6968 Sorted by residual: chirality pdb=" P DC T 69 " pdb=" OP1 DC T 69 " pdb=" OP2 DC T 69 " pdb=" O5' DC T 69 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" P DG N 25 " pdb=" OP1 DG N 25 " pdb=" OP2 DG N 25 " pdb=" O5' DG N 25 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" P DG T 70 " pdb=" OP1 DG T 70 " pdb=" OP2 DG T 70 " pdb=" O5' DG T 70 " both_signs ideal model delta sigma weight residual True 2.35 -2.97 -0.63 2.00e-01 2.50e+01 9.86e+00 ... (remaining 6965 not shown) Planarity restraints: 7631 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC T 30 " -0.109 2.00e-02 2.50e+03 5.12e-02 5.90e+01 pdb=" N1 DC T 30 " 0.042 2.00e-02 2.50e+03 pdb=" C2 DC T 30 " 0.015 2.00e-02 2.50e+03 pdb=" O2 DC T 30 " 0.045 2.00e-02 2.50e+03 pdb=" N3 DC T 30 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DC T 30 " -0.008 2.00e-02 2.50e+03 pdb=" N4 DC T 30 " -0.061 2.00e-02 2.50e+03 pdb=" C5 DC T 30 " 0.036 2.00e-02 2.50e+03 pdb=" C6 DC T 30 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG T 28 " -0.101 2.00e-02 2.50e+03 4.23e-02 5.37e+01 pdb=" N9 DG T 28 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG T 28 " 0.046 2.00e-02 2.50e+03 pdb=" N7 DG T 28 " 0.043 2.00e-02 2.50e+03 pdb=" C5 DG T 28 " 0.014 2.00e-02 2.50e+03 pdb=" C6 DG T 28 " -0.015 2.00e-02 2.50e+03 pdb=" O6 DG T 28 " -0.069 2.00e-02 2.50e+03 pdb=" N1 DG T 28 " -0.009 2.00e-02 2.50e+03 pdb=" C2 DG T 28 " 0.008 2.00e-02 2.50e+03 pdb=" N2 DG T 28 " 0.032 2.00e-02 2.50e+03 pdb=" N3 DG T 28 " 0.011 2.00e-02 2.50e+03 pdb=" C4 DG T 28 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG T 37 " -0.093 2.00e-02 2.50e+03 4.09e-02 5.02e+01 pdb=" N9 DG T 37 " 0.015 2.00e-02 2.50e+03 pdb=" C8 DG T 37 " 0.070 2.00e-02 2.50e+03 pdb=" N7 DG T 37 " 0.032 2.00e-02 2.50e+03 pdb=" C5 DG T 37 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DG T 37 " -0.022 2.00e-02 2.50e+03 pdb=" O6 DG T 37 " -0.055 2.00e-02 2.50e+03 pdb=" N1 DG T 37 " -0.009 2.00e-02 2.50e+03 pdb=" C2 DG T 37 " 0.007 2.00e-02 2.50e+03 pdb=" N2 DG T 37 " 0.040 2.00e-02 2.50e+03 pdb=" N3 DG T 37 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DG T 37 " 0.006 2.00e-02 2.50e+03 ... (remaining 7628 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.95: 4 1.95 - 2.69: 932 2.69 - 3.42: 61284 3.42 - 4.16: 106992 4.16 - 4.90: 188181 Nonbonded interactions: 357393 Sorted by model distance: nonbonded pdb=" NH1 ARG C 193 " pdb=" OE1 GLN C 217 " model vdw 1.208 3.120 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2003 " model vdw 1.905 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2003 " model vdw 1.907 2.170 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG A2003 " model vdw 1.930 2.170 nonbonded pdb=" CZ ARG C 193 " pdb=" OE1 GLN C 217 " model vdw 2.062 3.270 ... (remaining 357388 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=1.00 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: 4.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 1.480 Check model and map are aligned: 0.290 Set scattering table: 0.360 Process input model: 118.380 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 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 : 0.008 0.081 45796 Z= 0.531 Angle : 0.993 14.065 62372 Z= 0.533 Chirality : 0.072 0.634 6968 Planarity : 0.008 0.195 7631 Dihedral : 16.298 176.658 17835 Min Nonbonded Distance : 1.208 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.63 % Favored : 94.35 % Rotamer: Outliers : 0.06 % Allowed : 0.67 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.11), residues: 5183 helix: -0.71 (0.11), residues: 1836 sheet: -0.65 (0.19), residues: 706 loop : -1.53 (0.11), residues: 2641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP B 548 HIS 0.013 0.002 HIS E 142 PHE 0.047 0.003 PHE A 458 TYR 0.057 0.003 TYR M 27 ARG 0.016 0.001 ARG B 438 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10366 Ramachandran restraints generated. 5183 Oldfield, 0 Emsley, 5183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10366 Ramachandran restraints generated. 5183 Oldfield, 0 Emsley, 5183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 4642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 779 time to evaluate : 4.752 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: B 222 ARG cc_start: 0.8515 (ttm110) cc_final: 0.7911 (mtp85) REVERT: B 266 GLU cc_start: 0.7961 (mp0) cc_final: 0.7755 (pm20) REVERT: B 577 HIS cc_start: 0.7827 (t-170) cc_final: 0.7239 (t-170) REVERT: B 650 ASN cc_start: 0.7376 (t0) cc_final: 0.7125 (t0) REVERT: F 66 LEU cc_start: 0.8442 (mp) cc_final: 0.8198 (mp) REVERT: G 33 GLU cc_start: 0.7543 (tt0) cc_final: 0.7224 (tt0) REVERT: H 13 LYS cc_start: 0.8772 (mmmt) cc_final: 0.8461 (mmtt) REVERT: H 37 MET cc_start: 0.8144 (mmm) cc_final: 0.7689 (mmt) REVERT: J 54 ASP cc_start: 0.7347 (p0) cc_final: 0.7064 (p0) REVERT: M 230 MET cc_start: 0.7018 (tpt) cc_final: 0.6809 (tpp) REVERT: U 51 MET cc_start: 0.3905 (mpp) cc_final: 0.3629 (mpp) outliers start: 3 outliers final: 2 residues processed: 780 average time/residue: 0.5716 time to fit residues: 744.6575 Evaluate side-chains 644 residues out of total 4642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 642 time to evaluate : 5.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain B residue 1069 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 444 optimal weight: 50.0000 chunk 398 optimal weight: 5.9990 chunk 221 optimal weight: 0.0980 chunk 136 optimal weight: 0.7980 chunk 268 optimal weight: 0.8980 chunk 212 optimal weight: 0.6980 chunk 412 optimal weight: 9.9990 chunk 159 optimal weight: 0.8980 chunk 250 optimal weight: 3.9990 chunk 306 optimal weight: 0.7980 chunk 477 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS A 353 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 GLN A 711 GLN A 735 GLN ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN A 904 GLN A1005 HIS A1078 GLN A1093 GLN A1248 ASN A1420 ASN B 23 GLN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 631 GLN B 642 GLN B 777 ASN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1007 ASN B1073 GLN B1101 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN E 138 ASN E 210 GLN H 130 ASN I 100 HIS J 61 ASN K 2 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 ASN ** Q 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 162 ASN W 109 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 45796 Z= 0.193 Angle : 0.607 10.022 62372 Z= 0.319 Chirality : 0.044 0.217 6968 Planarity : 0.004 0.081 7631 Dihedral : 13.873 163.955 7169 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.06 % Allowed : 7.43 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.11), residues: 5183 helix: 0.37 (0.12), residues: 1876 sheet: -0.58 (0.20), residues: 698 loop : -1.27 (0.12), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 349 HIS 0.006 0.001 HIS A 465 PHE 0.020 0.001 PHE A 458 TYR 0.020 0.001 TYR H 118 ARG 0.007 0.000 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10366 Ramachandran restraints generated. 5183 Oldfield, 0 Emsley, 5183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10366 Ramachandran restraints generated. 5183 Oldfield, 0 Emsley, 5183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 4642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 744 time to evaluate : 5.107 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 1011 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6935 (tp30) REVERT: B 312 GLN cc_start: 0.8162 (mm110) cc_final: 0.7893 (mm110) REVERT: B 577 HIS cc_start: 0.7847 (t-170) cc_final: 0.7088 (t-170) REVERT: B 650 ASN cc_start: 0.7439 (t0) cc_final: 0.7118 (t0) REVERT: B 674 MET cc_start: 0.7655 (mmm) cc_final: 0.7046 (tpt) REVERT: B 930 GLN cc_start: 0.8219 (mt0) cc_final: 0.8002 (mt0) REVERT: B 1136 GLU cc_start: 0.6939 (tt0) cc_final: 0.6570 (tm-30) REVERT: F 86 GLU cc_start: 0.6735 (mp0) cc_final: 0.6374 (mp0) REVERT: G 33 GLU cc_start: 0.7626 (tt0) cc_final: 0.7298 (tt0) REVERT: G 117 MET cc_start: -0.1870 (ptm) cc_final: -0.2885 (tpp) REVERT: H 37 MET cc_start: 0.8148 (mmm) cc_final: 0.7691 (mmt) REVERT: I 18 GLN cc_start: 0.7856 (mp10) cc_final: 0.7613 (mp10) REVERT: I 41 ASN cc_start: 0.5983 (p0) cc_final: 0.5565 (p0) REVERT: I 44 TYR cc_start: 0.6233 (t80) cc_final: 0.5897 (t80) REVERT: I 67 GLN cc_start: 0.6820 (pm20) cc_final: 0.6063 (mm-40) REVERT: J 54 ASP cc_start: 0.7374 (p0) cc_final: 0.7115 (p0) REVERT: O 295 MET cc_start: 0.5968 (pmm) cc_final: 0.5381 (pmm) REVERT: O 329 TYR cc_start: 0.7884 (t80) cc_final: 0.7680 (t80) REVERT: R 125 MET cc_start: 0.0425 (mtt) cc_final: 0.0146 (mtt) outliers start: 49 outliers final: 28 residues processed: 766 average time/residue: 0.5541 time to fit residues: 718.2399 Evaluate side-chains 700 residues out of total 4642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 671 time to evaluate : 5.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 111 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 265 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 397 optimal weight: 4.9990 chunk 325 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 478 optimal weight: 50.0000 chunk 516 optimal weight: 0.0770 chunk 426 optimal weight: 7.9990 chunk 474 optimal weight: 50.0000 chunk 163 optimal weight: 10.0000 chunk 383 optimal weight: 2.9990 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 HIS ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1360 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 GLN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 168 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 45796 Z= 0.339 Angle : 0.623 12.640 62372 Z= 0.325 Chirality : 0.045 0.265 6968 Planarity : 0.004 0.074 7631 Dihedral : 14.074 161.374 7164 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.74 % Allowed : 9.46 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.12), residues: 5183 helix: 0.68 (0.12), residues: 1886 sheet: -0.56 (0.20), residues: 711 loop : -1.21 (0.12), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A1210 HIS 0.006 0.001 HIS A 465 PHE 0.025 0.001 PHE A1471 TYR 0.022 0.002 TYR E 26 ARG 0.008 0.000 ARG O 318 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10366 Ramachandran restraints generated. 5183 Oldfield, 0 Emsley, 5183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10366 Ramachandran restraints generated. 5183 Oldfield, 0 Emsley, 5183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 4642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 688 time to evaluate : 5.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7913 (tm-30) REVERT: A 85 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.5788 (m-80) REVERT: A 305 GLU cc_start: 0.8317 (pp20) cc_final: 0.7877 (pp20) REVERT: A 322 LEU cc_start: 0.8065 (pt) cc_final: 0.7469 (pp) REVERT: A 1011 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6868 (tp30) REVERT: A 1303 GLN cc_start: 0.8519 (mp10) cc_final: 0.8249 (mp10) REVERT: B 577 HIS cc_start: 0.7947 (t-170) cc_final: 0.7261 (t-170) REVERT: B 671 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7948 (mm-30) REVERT: B 744 MET cc_start: 0.8039 (ptp) cc_final: 0.7785 (mtm) REVERT: B 818 GLU cc_start: 0.7373 (tt0) cc_final: 0.7055 (tt0) REVERT: B 1136 GLU cc_start: 0.7108 (tt0) cc_final: 0.6755 (tm-30) REVERT: G 33 GLU cc_start: 0.7682 (tt0) cc_final: 0.7310 (tt0) REVERT: G 117 MET cc_start: -0.2151 (ptm) cc_final: -0.3106 (tpp) REVERT: H 37 MET cc_start: 0.8286 (mmm) cc_final: 0.7844 (mmt) REVERT: I 41 ASN cc_start: 0.6242 (p0) cc_final: 0.5864 (p0) REVERT: I 46 GLN cc_start: 0.8615 (tp40) cc_final: 0.8179 (tp40) REVERT: J 54 ASP cc_start: 0.7430 (p0) cc_final: 0.7186 (p0) REVERT: M 230 MET cc_start: 0.7094 (tpp) cc_final: 0.6855 (tpp) REVERT: O 257 ASN cc_start: 0.7253 (t0) cc_final: 0.7030 (t0) REVERT: O 258 MET cc_start: 0.8563 (ptp) cc_final: 0.7907 (ptp) REVERT: O 329 TYR cc_start: 0.7938 (t80) cc_final: 0.7631 (t80) REVERT: R 125 MET cc_start: 0.0455 (mtt) cc_final: -0.0011 (mtt) outliers start: 81 outliers final: 53 residues processed: 728 average time/residue: 0.5486 time to fit residues: 679.9049 Evaluate side-chains 692 residues out of total 4642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 637 time to evaluate : 4.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1459 MET Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain O residue 303 LEU Chi-restraints excluded: chain O residue 307 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 472 optimal weight: 10.0000 chunk 359 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 228 optimal weight: 2.9990 chunk 321 optimal weight: 9.9990 chunk 480 optimal weight: 40.0000 chunk 508 optimal weight: 40.0000 chunk 250 optimal weight: 6.9990 chunk 455 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 HIS ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN A 671 ASN ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B1097 HIS C 190 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 145 ASN W 109 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 45796 Z= 0.324 Angle : 0.606 10.195 62372 Z= 0.317 Chirality : 0.044 0.242 6968 Planarity : 0.004 0.068 7631 Dihedral : 14.204 160.319 7164 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.98 % Allowed : 11.57 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.12), residues: 5183 helix: 0.79 (0.12), residues: 1889 sheet: -0.45 (0.20), residues: 710 loop : -1.16 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A1210 HIS 0.008 0.001 HIS A1005 PHE 0.022 0.001 PHE A1471 TYR 0.022 0.001 TYR K 81 ARG 0.007 0.000 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10366 Ramachandran restraints generated. 5183 Oldfield, 0 Emsley, 5183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10366 Ramachandran restraints generated. 5183 Oldfield, 0 Emsley, 5183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 4642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 684 time to evaluate : 5.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.6323 (m-80) REVERT: A 305 GLU cc_start: 0.8273 (pp20) cc_final: 0.7829 (pp20) REVERT: A 306 ASP cc_start: 0.7834 (t70) cc_final: 0.7349 (t70) REVERT: A 486 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8522 (mm) REVERT: A 1011 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6862 (tp30) REVERT: A 1210 TRP cc_start: 0.7664 (m100) cc_final: 0.7295 (m-10) REVERT: A 1282 ASP cc_start: 0.5952 (OUTLIER) cc_final: 0.5702 (t70) REVERT: B 89 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6781 (mm-30) REVERT: B 312 GLN cc_start: 0.8179 (mm110) cc_final: 0.7959 (mm110) REVERT: B 344 GLN cc_start: 0.8761 (tp40) cc_final: 0.8200 (tm-30) REVERT: B 596 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7638 (mp) REVERT: B 671 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7938 (mm-30) REVERT: B 744 MET cc_start: 0.7970 (ptp) cc_final: 0.7765 (mtm) REVERT: B 818 GLU cc_start: 0.7326 (tt0) cc_final: 0.7024 (tt0) REVERT: B 1136 GLU cc_start: 0.7102 (tt0) cc_final: 0.6803 (tm-30) REVERT: E 133 GLN cc_start: 0.7739 (tp40) cc_final: 0.7505 (tp40) REVERT: G 33 GLU cc_start: 0.7607 (tt0) cc_final: 0.7239 (tt0) REVERT: G 117 MET cc_start: -0.2171 (ptm) cc_final: -0.3067 (tpp) REVERT: H 37 MET cc_start: 0.8376 (mmm) cc_final: 0.7967 (mmt) REVERT: H 42 ASP cc_start: 0.7510 (m-30) cc_final: 0.7132 (m-30) REVERT: I 41 ASN cc_start: 0.6177 (p0) cc_final: 0.5758 (p0) REVERT: I 67 GLN cc_start: 0.6932 (pm20) cc_final: 0.6324 (mm-40) REVERT: J 54 ASP cc_start: 0.7431 (p0) cc_final: 0.7209 (p0) REVERT: O 329 TYR cc_start: 0.7935 (t80) cc_final: 0.7632 (t80) REVERT: R 125 MET cc_start: 0.0262 (mtt) cc_final: -0.0354 (mtt) outliers start: 92 outliers final: 65 residues processed: 731 average time/residue: 0.5769 time to fit residues: 715.1440 Evaluate side-chains 707 residues out of total 4642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 637 time to evaluate : 5.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 651 SER Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1459 MET Chi-restraints excluded: chain A residue 1462 GLN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain M residue 216 SER Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 303 LEU Chi-restraints excluded: chain Q residue 18 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 423 optimal weight: 9.9990 chunk 288 optimal weight: 30.0000 chunk 7 optimal weight: 0.9990 chunk 378 optimal weight: 6.9990 chunk 209 optimal weight: 0.8980 chunk 433 optimal weight: 0.0770 chunk 351 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 chunk 456 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 45796 Z= 0.267 Angle : 0.588 12.167 62372 Z= 0.305 Chirality : 0.043 0.250 6968 Planarity : 0.004 0.068 7631 Dihedral : 14.265 160.747 7164 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.00 % Allowed : 12.69 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.12), residues: 5183 helix: 0.92 (0.12), residues: 1892 sheet: -0.43 (0.20), residues: 718 loop : -1.12 (0.12), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1210 HIS 0.008 0.001 HIS A1005 PHE 0.017 0.001 PHE A1471 TYR 0.024 0.001 TYR K 81 ARG 0.007 0.000 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10366 Ramachandran restraints generated. 5183 Oldfield, 0 Emsley, 5183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10366 Ramachandran restraints generated. 5183 Oldfield, 0 Emsley, 5183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 4642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 681 time to evaluate : 4.858 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 85 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.6254 (m-80) REVERT: A 305 GLU cc_start: 0.8324 (pp20) cc_final: 0.7853 (pp20) REVERT: A 306 ASP cc_start: 0.7861 (t70) cc_final: 0.7341 (t70) REVERT: A 486 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8470 (mm) REVERT: A 924 TYR cc_start: 0.7669 (p90) cc_final: 0.7252 (p90) REVERT: A 1011 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6893 (tp30) REVERT: A 1144 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7509 (tt) REVERT: A 1210 TRP cc_start: 0.7505 (m100) cc_final: 0.7293 (m-10) REVERT: A 1282 ASP cc_start: 0.6030 (t70) cc_final: 0.5655 (t70) REVERT: A 1292 MET cc_start: 0.7295 (tmm) cc_final: 0.6374 (tmm) REVERT: B 89 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6772 (mm-30) REVERT: B 312 GLN cc_start: 0.8176 (mm110) cc_final: 0.7938 (mm110) REVERT: B 358 GLU cc_start: 0.8008 (tp30) cc_final: 0.7672 (tp30) REVERT: B 577 HIS cc_start: 0.8148 (t-170) cc_final: 0.7613 (t-170) REVERT: B 671 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7942 (mm-30) REVERT: B 744 MET cc_start: 0.7956 (ptp) cc_final: 0.7751 (mtm) REVERT: B 1136 GLU cc_start: 0.7053 (tt0) cc_final: 0.6782 (tm-30) REVERT: E 133 GLN cc_start: 0.7724 (tp40) cc_final: 0.7461 (tp40) REVERT: G 117 MET cc_start: -0.2147 (ptm) cc_final: -0.2751 (tpt) REVERT: H 37 MET cc_start: 0.8400 (mmm) cc_final: 0.8015 (mmt) REVERT: H 42 ASP cc_start: 0.7528 (m-30) cc_final: 0.7174 (m-30) REVERT: H 48 TYR cc_start: 0.8084 (t80) cc_final: 0.7034 (t80) REVERT: I 41 ASN cc_start: 0.6124 (p0) cc_final: 0.5723 (p0) REVERT: I 67 GLN cc_start: 0.7084 (pm20) cc_final: 0.6407 (mm-40) REVERT: J 54 ASP cc_start: 0.7416 (p0) cc_final: 0.7193 (p0) REVERT: O 322 TYR cc_start: 0.7819 (m-80) cc_final: 0.7550 (m-80) REVERT: O 329 TYR cc_start: 0.7932 (t80) cc_final: 0.7646 (t80) REVERT: R 125 MET cc_start: 0.0118 (mtt) cc_final: -0.0337 (mtt) outliers start: 93 outliers final: 71 residues processed: 733 average time/residue: 0.5713 time to fit residues: 709.0402 Evaluate side-chains 715 residues out of total 4642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 640 time to evaluate : 5.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1459 MET Chi-restraints excluded: chain A residue 1462 GLN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain M residue 202 LEU Chi-restraints excluded: chain M residue 216 SER Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain O residue 303 LEU Chi-restraints excluded: chain O residue 307 SER Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain V residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 171 optimal weight: 0.9980 chunk 457 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 298 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 508 optimal weight: 40.0000 chunk 422 optimal weight: 1.9990 chunk 235 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 chunk 267 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 45796 Z= 0.225 Angle : 0.579 12.595 62372 Z= 0.299 Chirality : 0.042 0.265 6968 Planarity : 0.004 0.069 7631 Dihedral : 14.336 160.973 7164 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.09 % Allowed : 13.64 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.12), residues: 5183 helix: 1.04 (0.12), residues: 1884 sheet: -0.41 (0.20), residues: 722 loop : -1.08 (0.12), residues: 2577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1210 HIS 0.007 0.001 HIS A1005 PHE 0.016 0.001 PHE A 592 TYR 0.031 0.001 TYR K 81 ARG 0.007 0.000 ARG L 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10366 Ramachandran restraints generated. 5183 Oldfield, 0 Emsley, 5183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10366 Ramachandran restraints generated. 5183 Oldfield, 0 Emsley, 5183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 4642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 676 time to evaluate : 5.555 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 85 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.6224 (m-80) REVERT: A 305 GLU cc_start: 0.8262 (pp20) cc_final: 0.7811 (pp20) REVERT: A 486 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8419 (mm) REVERT: A 924 TYR cc_start: 0.7691 (p90) cc_final: 0.7280 (p90) REVERT: A 1011 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6878 (tp30) REVERT: A 1144 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7385 (tt) REVERT: A 1158 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8308 (tp) REVERT: A 1282 ASP cc_start: 0.5905 (t70) cc_final: 0.5561 (t70) REVERT: A 1292 MET cc_start: 0.7179 (tmm) cc_final: 0.6450 (tmm) REVERT: B 312 GLN cc_start: 0.8189 (mm110) cc_final: 0.7913 (mm110) REVERT: B 358 GLU cc_start: 0.7971 (tp30) cc_final: 0.7661 (tp30) REVERT: B 577 HIS cc_start: 0.8034 (t-170) cc_final: 0.7680 (t-170) REVERT: B 596 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7548 (mp) REVERT: B 744 MET cc_start: 0.7951 (ptp) cc_final: 0.7698 (mtm) REVERT: B 1125 MET cc_start: 0.8839 (mtp) cc_final: 0.8588 (mtt) REVERT: B 1136 GLU cc_start: 0.7049 (tt0) cc_final: 0.6797 (tm-30) REVERT: E 133 GLN cc_start: 0.7704 (tp40) cc_final: 0.7468 (tp40) REVERT: G 117 MET cc_start: -0.2358 (ptm) cc_final: -0.2864 (tpt) REVERT: H 37 MET cc_start: 0.8373 (mmm) cc_final: 0.7998 (mmt) REVERT: H 42 ASP cc_start: 0.7476 (m-30) cc_final: 0.7200 (m-30) REVERT: H 48 TYR cc_start: 0.8079 (t80) cc_final: 0.7093 (t80) REVERT: I 41 ASN cc_start: 0.6054 (p0) cc_final: 0.5752 (p0) REVERT: J 54 ASP cc_start: 0.7380 (p0) cc_final: 0.7169 (p0) REVERT: K 81 TYR cc_start: 0.8236 (t80) cc_final: 0.7887 (t80) REVERT: O 258 MET cc_start: 0.7999 (ptp) cc_final: 0.7760 (pmm) REVERT: O 322 TYR cc_start: 0.7768 (m-80) cc_final: 0.7284 (m-80) REVERT: O 329 TYR cc_start: 0.7924 (t80) cc_final: 0.7656 (t80) REVERT: Q 177 MET cc_start: 0.6655 (mmm) cc_final: 0.6452 (mmp) REVERT: R 125 MET cc_start: 0.0181 (mtt) cc_final: -0.0344 (mtt) outliers start: 97 outliers final: 68 residues processed: 730 average time/residue: 0.5614 time to fit residues: 692.6863 Evaluate side-chains 713 residues out of total 4642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 639 time to evaluate : 4.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1459 MET Chi-restraints excluded: chain A residue 1462 GLN Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain B residue 1167 ILE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain M residue 202 LEU Chi-restraints excluded: chain M residue 216 SER Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain O residue 302 LEU Chi-restraints excluded: chain O residue 303 LEU Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain V residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 490 optimal weight: 0.4980 chunk 57 optimal weight: 0.0370 chunk 289 optimal weight: 7.9990 chunk 371 optimal weight: 0.9990 chunk 287 optimal weight: 40.0000 chunk 428 optimal weight: 0.1980 chunk 284 optimal weight: 9.9990 chunk 506 optimal weight: 8.9990 chunk 317 optimal weight: 0.2980 chunk 309 optimal weight: 3.9990 chunk 234 optimal weight: 0.2980 overall best weight: 0.2658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS A 372 ASN ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 HIS A1005 HIS ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 HIS B 725 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN K 2 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 45796 Z= 0.162 Angle : 0.570 9.896 62372 Z= 0.293 Chirality : 0.042 0.263 6968 Planarity : 0.004 0.065 7631 Dihedral : 14.305 161.380 7164 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.79 % Allowed : 14.52 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.12), residues: 5183 helix: 1.11 (0.12), residues: 1889 sheet: -0.31 (0.20), residues: 726 loop : -1.03 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP A1210 HIS 0.006 0.001 HIS A1005 PHE 0.014 0.001 PHE A 458 TYR 0.023 0.001 TYR K 81 ARG 0.012 0.000 ARG R 113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10366 Ramachandran restraints generated. 5183 Oldfield, 0 Emsley, 5183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10366 Ramachandran restraints generated. 5183 Oldfield, 0 Emsley, 5183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 4642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 710 time to evaluate : 5.125 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 22 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7727 (tm-30) REVERT: A 85 PHE cc_start: 0.7521 (OUTLIER) cc_final: 0.6091 (m-80) REVERT: A 305 GLU cc_start: 0.8227 (pp20) cc_final: 0.7752 (pp20) REVERT: A 486 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8302 (mm) REVERT: A 520 MET cc_start: 0.7123 (mmm) cc_final: 0.6769 (mmm) REVERT: A 1011 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6715 (tp30) REVERT: A 1158 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8372 (tp) REVERT: A 1292 MET cc_start: 0.7054 (tmm) cc_final: 0.6624 (tmm) REVERT: A 1414 ILE cc_start: 0.8780 (mm) cc_final: 0.8007 (mm) REVERT: B 358 GLU cc_start: 0.7966 (tp30) cc_final: 0.7608 (tp30) REVERT: B 577 HIS cc_start: 0.7903 (t-170) cc_final: 0.7644 (t-170) REVERT: B 596 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7371 (mp) REVERT: B 671 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7887 (mm-30) REVERT: B 674 MET cc_start: 0.7709 (mmm) cc_final: 0.7227 (tpt) REVERT: B 744 MET cc_start: 0.7815 (ptp) cc_final: 0.7589 (mtm) REVERT: B 930 GLN cc_start: 0.8182 (mt0) cc_final: 0.7912 (mt0) REVERT: B 1060 HIS cc_start: 0.8192 (t70) cc_final: 0.7914 (t70) REVERT: B 1125 MET cc_start: 0.8707 (mtp) cc_final: 0.8453 (mtt) REVERT: B 1136 GLU cc_start: 0.6967 (tt0) cc_final: 0.6753 (tm-30) REVERT: B 1163 MET cc_start: 0.8036 (mtm) cc_final: 0.7660 (mtm) REVERT: D 44 ARG cc_start: 0.8445 (tpt90) cc_final: 0.8171 (tpm170) REVERT: F 60 TYR cc_start: 0.8648 (m-80) cc_final: 0.8443 (m-80) REVERT: G 117 MET cc_start: -0.2567 (ptm) cc_final: -0.3081 (tpp) REVERT: H 37 MET cc_start: 0.8290 (mmm) cc_final: 0.7759 (mmt) REVERT: H 42 ASP cc_start: 0.7417 (m-30) cc_final: 0.7167 (m-30) REVERT: H 48 TYR cc_start: 0.8017 (t80) cc_final: 0.7086 (t80) REVERT: I 41 ASN cc_start: 0.5882 (p0) cc_final: 0.5574 (p0) REVERT: I 67 GLN cc_start: 0.6777 (pm20) cc_final: 0.6004 (mm-40) REVERT: M 83 MET cc_start: 0.6844 (ttm) cc_final: 0.6411 (ttt) REVERT: O 219 MET cc_start: 0.8887 (tpp) cc_final: 0.8529 (tpp) REVERT: O 292 ILE cc_start: 0.8726 (mm) cc_final: 0.8519 (mm) REVERT: O 322 TYR cc_start: 0.7781 (m-80) cc_final: 0.7311 (m-80) REVERT: O 329 TYR cc_start: 0.7923 (t80) cc_final: 0.7660 (t80) REVERT: R 125 MET cc_start: 0.0257 (OUTLIER) cc_final: -0.0138 (mtt) outliers start: 83 outliers final: 52 residues processed: 758 average time/residue: 0.5615 time to fit residues: 724.5178 Evaluate side-chains 715 residues out of total 4642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 657 time to evaluate : 5.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1459 MET Chi-restraints excluded: chain A residue 1462 GLN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 817 GLN Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 1093 CYS Chi-restraints excluded: chain B residue 1167 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain M residue 216 SER Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain O residue 302 LEU Chi-restraints excluded: chain O residue 303 LEU Chi-restraints excluded: chain O residue 307 SER Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain R residue 125 MET Chi-restraints excluded: chain V residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 313 optimal weight: 2.9990 chunk 202 optimal weight: 0.4980 chunk 302 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 322 optimal weight: 9.9990 chunk 345 optimal weight: 9.9990 chunk 250 optimal weight: 6.9990 chunk 47 optimal weight: 0.0070 chunk 398 optimal weight: 6.9990 overall best weight: 1.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN B1094 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 45796 Z= 0.315 Angle : 0.618 11.474 62372 Z= 0.317 Chirality : 0.044 0.305 6968 Planarity : 0.004 0.070 7631 Dihedral : 14.354 160.472 7164 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.87 % Allowed : 15.08 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.12), residues: 5183 helix: 1.09 (0.12), residues: 1883 sheet: -0.41 (0.20), residues: 751 loop : -1.00 (0.12), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP Q 98 HIS 0.005 0.001 HIS A 87 PHE 0.022 0.001 PHE A1471 TYR 0.034 0.001 TYR B 217 ARG 0.008 0.000 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10366 Ramachandran restraints generated. 5183 Oldfield, 0 Emsley, 5183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10366 Ramachandran restraints generated. 5183 Oldfield, 0 Emsley, 5183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 4642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 650 time to evaluate : 4.823 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 85 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.6229 (m-80) REVERT: A 305 GLU cc_start: 0.8337 (pp20) cc_final: 0.7832 (pp20) REVERT: A 486 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8460 (mm) REVERT: A 520 MET cc_start: 0.7510 (mmm) cc_final: 0.7210 (mmm) REVERT: A 561 MET cc_start: 0.8248 (mtt) cc_final: 0.7995 (mtt) REVERT: A 1011 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6938 (tp30) REVERT: A 1292 MET cc_start: 0.7227 (tmm) cc_final: 0.6884 (tmm) REVERT: A 1414 ILE cc_start: 0.8866 (mm) cc_final: 0.8349 (mm) REVERT: B 358 GLU cc_start: 0.7973 (tp30) cc_final: 0.7756 (tp30) REVERT: B 577 HIS cc_start: 0.8015 (t-170) cc_final: 0.7655 (t-170) REVERT: B 596 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7417 (mp) REVERT: B 677 MET cc_start: 0.8482 (mmm) cc_final: 0.8135 (tpp) REVERT: B 744 MET cc_start: 0.7983 (ptp) cc_final: 0.7719 (mtm) REVERT: E 94 MET cc_start: 0.6651 (tpt) cc_final: 0.6335 (tpt) REVERT: E 133 GLN cc_start: 0.7647 (tp40) cc_final: 0.7425 (tp40) REVERT: G 117 MET cc_start: -0.2534 (ptm) cc_final: -0.3018 (tpp) REVERT: H 42 ASP cc_start: 0.7497 (m-30) cc_final: 0.7211 (m-30) REVERT: H 48 TYR cc_start: 0.8092 (t80) cc_final: 0.7185 (t80) REVERT: I 41 ASN cc_start: 0.6165 (p0) cc_final: 0.5854 (p0) REVERT: M 83 MET cc_start: 0.6905 (ttm) cc_final: 0.6470 (ttt) REVERT: O 219 MET cc_start: 0.8918 (tpp) cc_final: 0.8656 (tpp) REVERT: O 322 TYR cc_start: 0.7801 (m-80) cc_final: 0.7274 (m-80) REVERT: O 329 TYR cc_start: 0.7907 (t80) cc_final: 0.7671 (t80) REVERT: R 125 MET cc_start: 0.0280 (OUTLIER) cc_final: -0.0290 (mtt) outliers start: 87 outliers final: 64 residues processed: 703 average time/residue: 0.6070 time to fit residues: 731.5223 Evaluate side-chains 698 residues out of total 4642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 629 time to evaluate : 4.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1459 MET Chi-restraints excluded: chain A residue 1462 GLN Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain M residue 216 SER Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain O residue 302 LEU Chi-restraints excluded: chain O residue 303 LEU Chi-restraints excluded: chain O residue 307 SER Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain R residue 125 MET Chi-restraints excluded: chain V residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 461 optimal weight: 9.9990 chunk 485 optimal weight: 40.0000 chunk 443 optimal weight: 3.9990 chunk 472 optimal weight: 10.0000 chunk 284 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 chunk 370 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 426 optimal weight: 10.0000 chunk 446 optimal weight: 0.9990 chunk 470 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 ASN B 312 GLN ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 GLN C 114 HIS ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 167 ASN ** O 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 45796 Z= 0.326 Angle : 0.632 12.313 62372 Z= 0.324 Chirality : 0.044 0.326 6968 Planarity : 0.004 0.071 7631 Dihedral : 14.411 159.975 7164 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.87 % Allowed : 15.60 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.12), residues: 5183 helix: 1.00 (0.12), residues: 1891 sheet: -0.36 (0.20), residues: 754 loop : -1.04 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP Q 98 HIS 0.005 0.001 HIS B 387 PHE 0.029 0.001 PHE A1471 TYR 0.030 0.001 TYR K 81 ARG 0.010 0.000 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10366 Ramachandran restraints generated. 5183 Oldfield, 0 Emsley, 5183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10366 Ramachandran restraints generated. 5183 Oldfield, 0 Emsley, 5183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 4642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 651 time to evaluate : 5.037 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 22 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7784 (tm-30) REVERT: A 85 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.6238 (m-80) REVERT: A 305 GLU cc_start: 0.8332 (pp20) cc_final: 0.7837 (pp20) REVERT: A 486 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8478 (mm) REVERT: A 524 MET cc_start: 0.7161 (tpp) cc_final: 0.6617 (ttp) REVERT: A 1292 MET cc_start: 0.7338 (tmm) cc_final: 0.7137 (tmm) REVERT: B 312 GLN cc_start: 0.8066 (mm110) cc_final: 0.7835 (mm-40) REVERT: B 358 GLU cc_start: 0.7996 (tp30) cc_final: 0.7654 (tp30) REVERT: B 577 HIS cc_start: 0.8097 (t-170) cc_final: 0.7666 (t-170) REVERT: B 596 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7431 (mp) REVERT: B 603 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7355 (mtp) REVERT: B 677 MET cc_start: 0.8536 (mmm) cc_final: 0.8262 (tpp) REVERT: B 744 MET cc_start: 0.7966 (ptp) cc_final: 0.7712 (mtm) REVERT: B 849 ASP cc_start: 0.6949 (m-30) cc_final: 0.6675 (t70) REVERT: D 44 ARG cc_start: 0.8368 (tpt90) cc_final: 0.8066 (tpm170) REVERT: E 133 GLN cc_start: 0.7644 (tp40) cc_final: 0.7369 (tp40) REVERT: G 117 MET cc_start: -0.2322 (ptm) cc_final: -0.2873 (tpt) REVERT: G 164 MET cc_start: 0.6552 (mmp) cc_final: 0.6210 (mmp) REVERT: H 42 ASP cc_start: 0.7651 (m-30) cc_final: 0.7379 (m-30) REVERT: H 48 TYR cc_start: 0.8109 (t80) cc_final: 0.7184 (t80) REVERT: I 41 ASN cc_start: 0.6340 (p0) cc_final: 0.5990 (p0) REVERT: I 67 GLN cc_start: 0.6993 (pm20) cc_final: 0.6370 (mm-40) REVERT: M 20 ASP cc_start: 0.6645 (t70) cc_final: 0.6390 (t0) REVERT: M 83 MET cc_start: 0.6954 (ttm) cc_final: 0.6517 (ttt) REVERT: O 219 MET cc_start: 0.8899 (tpp) cc_final: 0.8657 (tpp) REVERT: O 322 TYR cc_start: 0.7826 (m-80) cc_final: 0.7470 (m-80) REVERT: O 329 TYR cc_start: 0.7974 (t80) cc_final: 0.7701 (t80) REVERT: R 125 MET cc_start: 0.0068 (OUTLIER) cc_final: -0.0516 (mtt) outliers start: 87 outliers final: 67 residues processed: 701 average time/residue: 0.5800 time to fit residues: 686.5753 Evaluate side-chains 707 residues out of total 4642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 635 time to evaluate : 4.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1459 MET Chi-restraints excluded: chain A residue 1462 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 570 ASN Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 622 CYS Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain M residue 216 SER Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain O residue 302 LEU Chi-restraints excluded: chain O residue 303 LEU Chi-restraints excluded: chain O residue 307 SER Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain R residue 125 MET Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 90 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 310 optimal weight: 0.6980 chunk 499 optimal weight: 50.0000 chunk 304 optimal weight: 0.7980 chunk 236 optimal weight: 0.9980 chunk 347 optimal weight: 0.9980 chunk 524 optimal weight: 4.9990 chunk 482 optimal weight: 20.0000 chunk 417 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 322 optimal weight: 5.9990 chunk 255 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 45796 Z= 0.234 Angle : 0.618 10.603 62372 Z= 0.317 Chirality : 0.043 0.325 6968 Planarity : 0.004 0.073 7631 Dihedral : 14.387 160.587 7164 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.66 % Allowed : 15.70 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.12), residues: 5183 helix: 1.05 (0.12), residues: 1891 sheet: -0.35 (0.20), residues: 744 loop : -1.03 (0.12), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP Q 98 HIS 0.015 0.001 HIS A1005 PHE 0.022 0.001 PHE A1388 TYR 0.028 0.001 TYR K 81 ARG 0.008 0.000 ARG J 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10366 Ramachandran restraints generated. 5183 Oldfield, 0 Emsley, 5183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10366 Ramachandran restraints generated. 5183 Oldfield, 0 Emsley, 5183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 4642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 657 time to evaluate : 5.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7653 (tm-30) REVERT: A 85 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.5858 (m-80) REVERT: A 305 GLU cc_start: 0.8299 (pp20) cc_final: 0.7800 (pp20) REVERT: A 486 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8415 (mm) REVERT: A 524 MET cc_start: 0.6975 (tpp) cc_final: 0.6472 (ttp) REVERT: A 1292 MET cc_start: 0.7273 (tmm) cc_final: 0.6885 (tmm) REVERT: B 312 GLN cc_start: 0.8072 (mm110) cc_final: 0.7816 (mm-40) REVERT: B 358 GLU cc_start: 0.7978 (tp30) cc_final: 0.7641 (tp30) REVERT: B 577 HIS cc_start: 0.7974 (t-170) cc_final: 0.7585 (t-170) REVERT: B 596 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7383 (mp) REVERT: B 603 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.7165 (mtp) REVERT: B 677 MET cc_start: 0.8486 (mmm) cc_final: 0.8235 (tpp) REVERT: B 744 MET cc_start: 0.7933 (ptp) cc_final: 0.7685 (mtm) REVERT: B 849 ASP cc_start: 0.6890 (m-30) cc_final: 0.6465 (t0) REVERT: B 1125 MET cc_start: 0.8762 (mtp) cc_final: 0.8494 (mtt) REVERT: D 44 ARG cc_start: 0.8392 (tpt90) cc_final: 0.8086 (tpm170) REVERT: E 94 MET cc_start: 0.6618 (tpt) cc_final: 0.6260 (tpt) REVERT: E 133 GLN cc_start: 0.7546 (tp40) cc_final: 0.7277 (tp40) REVERT: G 117 MET cc_start: -0.2422 (ptm) cc_final: -0.2902 (tpt) REVERT: G 164 MET cc_start: 0.6549 (mmp) cc_final: 0.6227 (mmp) REVERT: H 42 ASP cc_start: 0.7611 (m-30) cc_final: 0.7343 (m-30) REVERT: H 48 TYR cc_start: 0.8036 (t80) cc_final: 0.7200 (t80) REVERT: I 41 ASN cc_start: 0.6255 (p0) cc_final: 0.5920 (p0) REVERT: I 67 GLN cc_start: 0.6951 (pm20) cc_final: 0.6426 (mm-40) REVERT: I 122 ARG cc_start: 0.8413 (ptp90) cc_final: 0.7992 (ptp90) REVERT: J 19 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7446 (mm-30) REVERT: M 20 ASP cc_start: 0.6631 (t70) cc_final: 0.6372 (t0) REVERT: M 83 MET cc_start: 0.6895 (ttm) cc_final: 0.6488 (ttt) REVERT: O 219 MET cc_start: 0.8899 (tpp) cc_final: 0.8677 (tpp) REVERT: O 322 TYR cc_start: 0.7857 (m-80) cc_final: 0.7462 (m-80) REVERT: O 329 TYR cc_start: 0.7965 (t80) cc_final: 0.7701 (t80) REVERT: Q 98 TRP cc_start: 0.4106 (m100) cc_final: 0.3814 (m100) REVERT: Q 177 MET cc_start: 0.6479 (mmp) cc_final: 0.6252 (mmp) REVERT: R 125 MET cc_start: 0.0167 (OUTLIER) cc_final: -0.0320 (mtt) outliers start: 77 outliers final: 62 residues processed: 699 average time/residue: 0.5744 time to fit residues: 676.7823 Evaluate side-chains 701 residues out of total 4642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 634 time to evaluate : 5.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1459 MET Chi-restraints excluded: chain A residue 1462 GLN Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain M residue 216 SER Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 273 LEU Chi-restraints excluded: chain O residue 302 LEU Chi-restraints excluded: chain O residue 303 LEU Chi-restraints excluded: chain O residue 307 SER Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain R residue 125 MET Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 90 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 331 optimal weight: 4.9990 chunk 444 optimal weight: 40.0000 chunk 127 optimal weight: 2.9990 chunk 384 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 417 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 429 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B1101 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.181559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.105891 restraints weight = 68038.399| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.68 r_work: 0.3022 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 45796 Z= 0.461 Angle : 0.710 12.993 62372 Z= 0.365 Chirality : 0.046 0.337 6968 Planarity : 0.005 0.075 7631 Dihedral : 14.500 159.413 7164 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.90 % Allowed : 15.64 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.12), residues: 5183 helix: 0.86 (0.12), residues: 1901 sheet: -0.44 (0.20), residues: 720 loop : -1.11 (0.12), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP Q 98 HIS 0.012 0.001 HIS A1005 PHE 0.036 0.002 PHE A1388 TYR 0.033 0.002 TYR B 217 ARG 0.008 0.001 ARG J 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11947.79 seconds wall clock time: 219 minutes 30.12 seconds (13170.12 seconds total)