Starting phenix.real_space_refine on Tue Sep 15 19:15:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7b0y_11972/09_2026/7b0y_11972.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b0y_11972/09_2026/7b0y_11972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7b0y_11972/09_2026/7b0y_11972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b0y_11972/09_2026/7b0y_11972.map" model { file = "/net/cci-nas-00/data/ceres_data/7b0y_11972/09_2026/7b0y_11972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b0y_11972/09_2026/7b0y_11972.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7b0y_11972/09_2026/7b0y_11972.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7b0y_11972/09_2026/7b0y_11972.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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 8 6.06 5 P 274 5.49 5 Mg 1 5.21 5 S 242 5.16 5 C 26605 2.51 5 N 7734 2.21 5 O 8928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 229 residue(s): 0.24s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43792 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 11263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1422, 11263 Classifications: {'peptide': 1422} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1352} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 9052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1131, 9052 Classifications: {'peptide': 1131} Link IDs: {'PTRANS': 53, 'TRANS': 1077} Chain breaks: 3 Chain: "C" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2089 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 15, 'TRANS': 244} Chain breaks: 1 Chain: "D" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1030 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 197} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} 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: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 949 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} 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: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "N" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 769 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "P" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 774 Classifications: {'RNAv2': 36} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 19, 'rna3p_pyr': 12} Link IDs: {'rna2p': 5, 'rna3p': 30} Chain: "T" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 749 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "a" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3485 Classifications: {'RNAv2': 164} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 15, 'rna3p_pur': 67, 'rna3p_pyr': 70} Link IDs: {'rna2p': 27, 'rna3p': 136} Chain: "b" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1543 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 12, 'TRANS': 173} Chain: "c" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 796 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "e" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 777 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Chain: "f" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "g" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 638 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "h" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 568 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "i" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 637 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "j" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 692 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "k" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 641 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 121.625 108.245 136.583 1.00 51.93 S ATOM 486 SG CYS A 74 121.156 112.528 136.060 1.00 48.48 S ATOM 533 SG CYS A 81 122.661 111.003 133.410 1.00 43.07 S ATOM 768 SG CYS A 111 165.708 103.396 153.093 1.00 61.14 S ATOM 796 SG CYS A 114 164.364 105.356 155.585 1.00 62.99 S ATOM 1109 SG CYS A 154 167.653 105.849 154.604 1.00 75.39 S ATOM 19885 SG CYS B1119 132.711 121.317 145.561 1.00 43.18 S ATOM 19907 SG CYS B1122 135.338 118.427 144.010 1.00 38.64 S ATOM 20022 SG CYS B1137 132.076 117.264 144.602 1.00 46.96 S ATOM 20043 SG CYS B1140 135.036 119.073 147.640 1.00 46.76 S ATOM 21009 SG CYS C 88 93.425 125.848 76.296 1.00 43.12 S ATOM 21022 SG CYS C 90 93.300 122.912 78.134 1.00 46.46 S ATOM 21057 SG CYS C 94 92.708 122.207 74.851 1.00 36.10 S ATOM 21079 SG CYS C 97 96.127 122.281 75.959 1.00 34.90 S ATOM 28417 SG CYS I 17 200.561 72.155 107.265 1.00 54.81 S ATOM 28441 SG CYS I 20 197.107 72.233 109.316 1.00 52.49 S ATOM 28602 SG CYS I 39 198.594 75.060 110.780 1.00 60.21 S ATOM 28627 SG CYS I 42 200.678 72.054 110.874 1.00 59.96 S ATOM 28979 SG CYS I 86 194.125 91.429 68.090 1.00 43.53 S ATOM 29003 SG CYS I 89 193.282 89.143 65.661 1.00 45.83 S ATOM 29207 SG CYS I 114 190.258 90.244 67.460 1.00 40.47 S ATOM 29242 SG CYS I 119 193.218 87.817 69.070 1.00 44.95 S ATOM 29352 SG CYS J 7 124.924 117.101 64.832 1.00 23.73 S ATOM 29376 SG CYS J 10 122.597 119.765 62.641 1.00 22.22 S ATOM 29640 SG CYS J 44 126.721 119.647 62.296 1.00 23.78 S ATOM 29646 SG CYS J 45 124.333 117.602 60.640 1.00 21.96 S ATOM 30808 SG CYS L 19 112.037 81.547 85.739 1.00 44.71 S ATOM 30827 SG CYS L 22 109.360 80.018 83.759 1.00 47.16 S ATOM 30944 SG CYS L 36 108.540 79.262 87.214 1.00 55.49 S ATOM 30970 SG CYS L 39 111.467 78.234 85.726 1.00 59.79 S Time building chain proxies: 8.86, per 1000 atoms: 0.20 Number of scatterers: 43792 At special positions: 0 Unit cell: (234.15, 197.4, 203.7, 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 8 29.99 S 242 16.00 P 274 15.00 Mg 1 11.99 O 8928 8.00 N 7734 7.00 C 26605 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 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 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " 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 94 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " 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 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb=" ZN J 101 " 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 ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " 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 39 " Number of angles added : 39 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8916 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 58 sheets defined 35.2% alpha, 21.5% beta 77 base pairs and 159 stacking pairs defined. Time for finding SS restraints: 5.69 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.622A pdb=" N GLY A 63 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.853A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.606A pdb=" N ILE A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.519A pdb=" N PHE A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 274 through 296 removed outlier: 3.576A pdb=" N ASP A 282 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.526A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.984A pdb=" N ARG A 334 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.769A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 removed outlier: 3.643A pdb=" N GLY A 409 " --> pdb=" O LEU A 405 " (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 486 through 490 removed outlier: 3.648A pdb=" N THR A 489 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 486 through 490' Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 524 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 565 removed outlier: 3.560A pdb=" N MET A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 removed outlier: 4.172A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.623A pdb=" N THR A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 676 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.588A pdb=" N SER A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 773 removed outlier: 3.687A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 868 removed outlier: 3.729A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 removed outlier: 3.532A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.566A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 970 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 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1052 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1120 through 1129 removed outlier: 3.511A pdb=" N LEU A1127 " --> pdb=" O ARG A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 3.797A pdb=" N ARG A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.920A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1189 through 1198 removed outlier: 3.559A pdb=" N VAL A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1223 Processing helix chain 'A' and resid 1227 through 1239 Processing helix chain 'A' and resid 1280 through 1296 removed outlier: 4.296A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1347 Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.769A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1431 Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.707A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'B' and resid 18 through 37 removed outlier: 4.310A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 117 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 294 through 308 Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 325 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 357 through 377 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 424 removed outlier: 3.831A pdb=" N PHE B 402 " --> pdb=" O PRO B 398 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 495 through 500 removed outlier: 4.319A pdb=" N ARG B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.627A pdb=" N TRP B 506 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.741A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.595A pdb=" N LEU B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.866A 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 667 through 671 removed outlier: 3.849A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.575A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 763 through 768 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.328A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.891A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B 988 " --> pdb=" O CYS B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.671A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) 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 1164 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.803A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.816A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (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 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 268 removed outlier: 3.903A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 33 through 50 removed outlier: 3.522A pdb=" N SER D 50 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.614A pdb=" N MET D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 90 removed outlier: 4.124A pdb=" N ALA D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.561A pdb=" N LEU D 97 " --> pdb=" O HIS D 93 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N CYS D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 137 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.515A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 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 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 22 through 35 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 63 through 67 Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 26 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.582A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.577A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'b' and resid 64 through 89 removed outlier: 3.990A pdb=" N GLU b 68 " --> pdb=" O GLU b 64 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR b 84 " --> pdb=" O GLN b 80 " (cutoff:3.500A) Processing helix chain 'b' and resid 115 through 124 Processing helix chain 'b' and resid 153 through 165 removed outlier: 3.583A pdb=" N MET b 157 " --> pdb=" O HIS b 153 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS b 158 " --> pdb=" O GLU b 154 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA b 160 " --> pdb=" O ASP b 156 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS b 162 " --> pdb=" O HIS b 158 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS b 163 " --> pdb=" O SER b 159 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP b 165 " --> pdb=" O TYR b 161 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 193 Processing helix chain 'c' and resid 22 through 35 Processing helix chain 'c' and resid 36 through 38 No H-bonds generated for 'chain 'c' and resid 36 through 38' Processing helix chain 'c' and resid 61 through 73 Processing helix chain 'c' and resid 91 through 99 Processing helix chain 'e' and resid 18 through 27 Processing helix chain 'e' and resid 29 through 39 removed outlier: 3.870A pdb=" N THR e 33 " --> pdb=" O LEU e 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 6 through 14 Processing helix chain 'g' and resid 16 through 28 Processing helix chain 'i' and resid 4 through 13 Processing helix chain 'i' and resid 74 through 80 Processing helix chain 'j' and resid 7 through 11 Processing helix chain 'k' and resid 3 through 8 removed outlier: 3.698A pdb=" N LEU k 7 " --> pdb=" O LEU k 3 " (cutoff:3.500A) Processing helix chain 'k' and resid 75 through 80 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.669A pdb=" N ARG B1150 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 94 removed outlier: 11.210A pdb=" N LYS A 92 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL A 252 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.207A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.646A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 4.160A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 477 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.054A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.690A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB2, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.406A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.406A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 602 through 603 removed outlier: 6.800A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 872 through 873 removed outlier: 3.500A pdb=" N GLN A 888 " --> pdb=" O VAL A 879 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB8, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 3.728A pdb=" N THR A1338 " --> pdb=" O LEU A1139 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 3.532A pdb=" N GLN A1299 " --> pdb=" O THR A1164 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 4.785A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC3, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AC4, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AC5, first strand: chain 'B' and resid 87 through 93 removed outlier: 5.696A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC7, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC8, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AC9, first strand: chain 'B' and resid 206 through 208 removed outlier: 6.780A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N THR B 218 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL B 237 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU B 220 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE B 235 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ARG B 222 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N SER B 233 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 257 through 258 Processing sheet with id=AD2, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD3, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD4, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.309A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.571A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.571A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD8, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.351A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AE1, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.670A pdb=" N ILE B 867 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AE3, first strand: chain 'C' and resid 8 through 9 Processing sheet with id=AE4, first strand: chain 'C' and resid 8 through 9 removed outlier: 5.995A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 121 through 122 removed outlier: 3.560A pdb=" N LEU C 103 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.708A pdb=" N TYR C 164 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE8, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.546A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL G 76 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE G 11 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR G 68 " --> pdb=" O ILE G 11 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.546A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL G 76 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE G 11 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR G 68 " --> pdb=" O ILE G 11 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU G 67 " --> pdb=" O VAL G 58 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.459A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.772A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AF4, first strand: chain 'G' and resid 83 through 92 removed outlier: 6.895A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA G 159 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY G 161 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU G 145 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 127 through 129 Processing sheet with id=AF6, first strand: chain 'I' and resid 25 through 29 removed outlier: 3.512A pdb=" N ILE I 34 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF8, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF9, first strand: chain 'b' and resid 129 through 136 removed outlier: 5.348A pdb=" N TYR b 146 " --> pdb=" O VAL b 135 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA b 108 " --> pdb=" O LEU b 175 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU b 175 " --> pdb=" O ALA b 108 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'b' and resid 168 through 169 Processing sheet with id=AG2, first strand: chain 'c' and resid 40 through 46 removed outlier: 6.922A pdb=" N ILE c 58 " --> pdb=" O LEU c 41 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE c 43 " --> pdb=" O PHE c 56 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE c 56 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL c 45 " --> pdb=" O GLN c 54 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N GLN c 54 " --> pdb=" O VAL c 45 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'i' and resid 55 through 57 removed outlier: 3.753A pdb=" N ALA i 56 " --> pdb=" O VAL i 48 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL i 48 " --> pdb=" O ALA i 56 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN i 60 " --> pdb=" O ALA h 72 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET h 69 " --> pdb=" O LYS h 20 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLN h 28 " --> pdb=" O CYS h 45 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N CYS h 45 " --> pdb=" O GLN h 28 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL h 41 " --> pdb=" O ARG h 32 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU h 44 " --> pdb=" O GLY h 58 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N GLY h 58 " --> pdb=" O GLU h 44 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL h 46 " --> pdb=" O ASN h 56 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN h 56 " --> pdb=" O VAL h 46 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL h 61 " --> pdb=" O LEU g 87 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU g 86 " --> pdb=" O TRP g 34 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU g 35 " --> pdb=" O MET g 41 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N MET g 41 " --> pdb=" O LEU g 35 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ASN g 40 " --> pdb=" O HIS g 65 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N HIS g 65 " --> pdb=" O ASN g 40 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG g 42 " --> pdb=" O GLU g 63 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU g 63 " --> pdb=" O ARG g 42 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLU g 44 " --> pdb=" O ALA g 61 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA g 61 " --> pdb=" O GLU g 44 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N CYS g 46 " --> pdb=" O ASP g 59 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL g 57 " --> pdb=" O ILE g 48 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP g 60 " --> pdb=" O GLY g 75 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLY g 75 " --> pdb=" O ASP g 60 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU g 62 " --> pdb=" O GLN g 73 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLN g 73 " --> pdb=" O GLU g 62 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ARG g 76 " --> pdb=" O GLY f 74 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY f 74 " --> pdb=" O ARG g 76 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU f 28 " --> pdb=" O GLU f 49 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU f 49 " --> pdb=" O GLU f 28 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS f 30 " --> pdb=" O THR f 47 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR f 47 " --> pdb=" O LYS f 30 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLN f 43 " --> pdb=" O VAL f 34 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLN f 43 " --> pdb=" O VAL f 62 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL f 62 " --> pdb=" O GLN f 43 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA f 45 " --> pdb=" O GLY f 60 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY f 60 " --> pdb=" O ALA f 45 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR f 47 " --> pdb=" O HIS f 58 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N HIS f 58 " --> pdb=" O THR f 47 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU f 49 " --> pdb=" O SER f 56 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLU f 61 " --> pdb=" O ARG e 111 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG e 111 " --> pdb=" O GLU f 61 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASN e 45 " --> pdb=" O ILE e 107 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL e 109 " --> pdb=" O LEU e 43 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU e 43 " --> pdb=" O VAL e 109 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG e 55 " --> pdb=" O ASN e 69 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASN e 69 " --> pdb=" O ARG e 55 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL e 66 " --> pdb=" O PHE e 100 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N PHE e 100 " --> pdb=" O VAL e 66 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU e 68 " --> pdb=" O LYS e 98 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LYS e 98 " --> pdb=" O GLU e 68 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU k 18 " --> pdb=" O ARG k 66 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE k 68 " --> pdb=" O THR k 16 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR k 16 " --> pdb=" O PHE k 68 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL k 25 " --> pdb=" O MET k 45 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N MET k 45 " --> pdb=" O VAL k 25 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY k 27 " --> pdb=" O VAL k 43 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL k 43 " --> pdb=" O GLY k 27 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE k 29 " --> pdb=" O LYS k 41 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LYS k 41 " --> pdb=" O ILE k 29 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N HIS k 39 " --> pdb=" O SER k 59 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SER k 59 " --> pdb=" O HIS k 39 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS k 41 " --> pdb=" O THR k 57 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N THR k 57 " --> pdb=" O LYS k 41 " (cutoff:3.500A) removed outlier: 13.565A pdb=" N LEU k 55 " --> pdb=" O GLY j 84 " (cutoff:3.500A) removed outlier: 11.878A pdb=" N GLY j 84 " --> pdb=" O LEU k 55 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR k 57 " --> pdb=" O VAL j 82 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL j 82 " --> pdb=" O THR k 57 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER j 79 " --> pdb=" O ILE j 20 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ARG j 16 " --> pdb=" O GLU j 83 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE j 26 " --> pdb=" O GLU j 47 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU j 47 " --> pdb=" O ILE j 26 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE j 28 " --> pdb=" O CYS j 45 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N CYS j 45 " --> pdb=" O ILE j 28 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLY j 68 " --> pdb=" O ASP j 44 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP j 46 " --> pdb=" O VAL j 66 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL j 66 " --> pdb=" O ASP j 46 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU j 69 " --> pdb=" O LEU i 73 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU i 21 " --> pdb=" O ARG i 69 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU i 71 " --> pdb=" O THR i 19 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR i 19 " --> pdb=" O LEU i 71 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU i 73 " --> pdb=" O ILE i 17 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N ILE i 17 " --> pdb=" O LEU i 73 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL i 27 " --> pdb=" O VAL i 48 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL i 48 " --> pdb=" O VAL i 27 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ARG i 29 " --> pdb=" O ILE i 46 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE i 46 " --> pdb=" O ARG i 29 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN i 42 " --> pdb=" O ILE i 33 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'j' and resid 50 through 51 removed outlier: 3.686A pdb=" N ILE j 51 " --> pdb=" O ARG j 61 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG j 61 " --> pdb=" O ILE j 51 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 1534 hydrogen bonds defined for protein. 4212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 198 hydrogen bonds 376 hydrogen bond angles 0 basepair planarities 77 basepair parallelities 159 stacking parallelities Total time for adding SS restraints: 16.23 Time building geometry restraints manager: 4.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13396 1.34 - 1.45: 7591 1.45 - 1.57: 23246 1.57 - 1.69: 544 1.69 - 1.81: 391 Bond restraints: 45168 Sorted by residual: bond pdb=" C1' DT N 18 " pdb=" N1 DT N 18 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 1.00e+01 bond pdb=" C3' DC T 33 " pdb=" C2' DC T 33 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.10e+00 bond pdb=" C3' DT T 32 " pdb=" C2' DT T 32 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.54e+00 bond pdb=" C1' DC T 6 " pdb=" N1 DC T 6 " ideal model delta sigma weight residual 1.468 1.506 -0.038 1.40e-02 5.10e+03 7.46e+00 bond pdb=" C3' DG T 15 " pdb=" C2' DG T 15 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.99e+00 ... (remaining 45163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 60208 1.25 - 2.50: 1181 2.50 - 3.76: 769 3.76 - 5.01: 90 5.01 - 6.26: 8 Bond angle restraints: 62256 Sorted by residual: angle pdb=" C3' U a 90 " pdb=" O3' U a 90 " pdb=" P G a 91 " ideal model delta sigma weight residual 119.70 124.68 -4.98 1.20e+00 6.94e-01 1.72e+01 angle pdb=" N3 DT T 32 " pdb=" C4 DT T 32 " pdb=" O4 DT T 32 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT T 21 " pdb=" C4 DT T 21 " pdb=" O4 DT T 21 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 angle pdb=" N3 DT T 34 " pdb=" C4 DT T 34 " pdb=" O4 DT T 34 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 angle pdb=" N3 DT T 14 " pdb=" C4 DT T 14 " pdb=" O4 DT T 14 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.62e+01 ... (remaining 62251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 26042 35.96 - 71.92: 887 71.92 - 107.88: 46 107.88 - 143.84: 1 143.84 - 179.80: 9 Dihedral angle restraints: 26985 sinusoidal: 13200 harmonic: 13785 Sorted by residual: dihedral pdb=" C4' A a 29 " pdb=" C3' A a 29 " pdb=" C2' A a 29 " pdb=" C1' A a 29 " ideal model delta sinusoidal sigma weight residual 36.34 -36.71 73.06 1 3.10e+00 1.04e-01 7.08e+02 dihedral pdb=" C4' G a 11 " pdb=" C3' G a 11 " pdb=" C2' G a 11 " pdb=" C1' G a 11 " ideal model delta sinusoidal sigma weight residual 36.34 -36.68 73.02 1 3.10e+00 1.04e-01 7.07e+02 dihedral pdb=" C4' C a 31 " pdb=" C3' C a 31 " pdb=" C2' C a 31 " pdb=" C1' C a 31 " ideal model delta sinusoidal sigma weight residual 36.34 -35.76 72.10 1 3.10e+00 1.04e-01 6.92e+02 ... (remaining 26982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 5888 0.062 - 0.125: 862 0.125 - 0.187: 91 0.187 - 0.249: 208 0.249 - 0.312: 54 Chirality restraints: 7103 Sorted by residual: chirality pdb=" C2' U a 90 " pdb=" C3' U a 90 " pdb=" O2' U a 90 " pdb=" C1' U a 90 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" P G a 91 " pdb=" OP1 G a 91 " pdb=" OP2 G a 91 " pdb=" O5' G a 91 " both_signs ideal model delta sigma weight residual True 2.17 -2.46 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C2' C a 92 " pdb=" C3' C a 92 " pdb=" O2' C a 92 " pdb=" C1' C a 92 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 7100 not shown) Planarity restraints: 7060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE c 75 " 0.038 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO c 76 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO c 76 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO c 76 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR c 78 " -0.004 2.00e-02 2.50e+03 8.45e-03 1.43e+00 pdb=" CG TYR c 78 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR c 78 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR c 78 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR c 78 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR c 78 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR c 78 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR c 78 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO b 55 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO b 56 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO b 56 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO b 56 " 0.016 5.00e-02 4.00e+02 ... (remaining 7057 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 356 2.54 - 3.13: 34656 3.13 - 3.72: 68992 3.72 - 4.31: 100552 4.31 - 4.90: 162621 Nonbonded interactions: 367177 Sorted by model distance: nonbonded pdb=" O2' U a 90 " pdb=" OP2 G a 91 " model vdw 1.954 3.040 nonbonded pdb=" O MET A 535 " pdb=" OH TYR A 669 " model vdw 1.976 3.040 nonbonded pdb=" O2' G a 15 " pdb=" OP1 G a 16 " model vdw 2.001 3.040 nonbonded pdb=" OG1 THR B 565 " pdb=" O ARG B 610 " model vdw 2.003 3.040 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2003 " model vdw 2.020 2.170 ... (remaining 367172 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.900 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 54.800 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.080 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 : 0.004 0.215 45199 Z= 0.190 Angle : 0.688 48.545 62295 Z= 0.316 Chirality : 0.062 0.312 7103 Planarity : 0.002 0.058 7060 Dihedral : 16.368 179.804 18069 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.02 % Allowed : 0.95 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.11), residues: 4687 helix: -2.05 (0.11), residues: 1409 sheet: -2.09 (0.16), residues: 781 loop : -1.81 (0.12), residues: 2497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG c 83 TYR 0.011 0.001 TYR c 78 PHE 0.007 0.001 PHE j 48 TRP 0.004 0.000 TRP C 49 HIS 0.006 0.000 HIS k 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.16 (45168) covalent geometry : angle 0.53970 / 0.31 (62256) hydrogen bonds : bond 0.23159 / 15.26 ( 1696) hydrogen bonds : angle 8.33087 / 5.84 ( 4588) metal coordination : bond 0.11306 / 7.55 ( 31) metal coordination : angle 17.07232 / 10.68 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 771 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 941 ASP cc_start: 0.7104 (t0) cc_final: 0.6795 (t0) REVERT: A 1130 ILE cc_start: 0.8282 (mp) cc_final: 0.7974 (mm) REVERT: A 1289 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7791 (tm-30) REVERT: A 1351 ASP cc_start: 0.6911 (m-30) cc_final: 0.6674 (m-30) REVERT: A 1412 MET cc_start: 0.8090 (tmm) cc_final: 0.7845 (tmm) REVERT: A 1414 ILE cc_start: 0.8748 (mm) cc_final: 0.8390 (mm) REVERT: B 146 LYS cc_start: 0.8257 (mttm) cc_final: 0.8012 (mttp) REVERT: B 262 TYR cc_start: 0.8445 (m-10) cc_final: 0.8106 (m-80) REVERT: B 677 MET cc_start: 0.9005 (tpp) cc_final: 0.8181 (tpp) REVERT: B 934 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8572 (mtpt) REVERT: B 1039 SER cc_start: 0.8645 (t) cc_final: 0.8405 (p) REVERT: C 48 ASP cc_start: 0.7394 (t70) cc_final: 0.7106 (t0) REVERT: C 186 TYR cc_start: 0.8553 (p90) cc_final: 0.8038 (p90) REVERT: E 61 LEU cc_start: 0.8468 (tp) cc_final: 0.8155 (tp) REVERT: F 115 TYR cc_start: 0.8096 (p90) cc_final: 0.7721 (p90) REVERT: G 104 MET cc_start: 0.0040 (mmp) cc_final: -0.0181 (mmp) REVERT: I 25 TYR cc_start: 0.8159 (m-80) cc_final: 0.7483 (m-80) REVERT: I 51 SER cc_start: 0.7967 (t) cc_final: 0.7294 (p) REVERT: I 54 TYR cc_start: 0.8208 (t80) cc_final: 0.8003 (t80) REVERT: J 50 LEU cc_start: 0.8532 (tp) cc_final: 0.8282 (tt) REVERT: J 58 LYS cc_start: 0.8560 (mttt) cc_final: 0.8270 (mtpp) REVERT: K 17 LYS cc_start: 0.8272 (mtmm) cc_final: 0.8009 (mtmm) REVERT: b 158 HIS cc_start: 0.7844 (m90) cc_final: 0.7577 (m90) REVERT: g 41 MET cc_start: 0.3200 (mtt) cc_final: 0.2934 (ptp) REVERT: k 8 MET cc_start: 0.4463 (mpp) cc_final: 0.4194 (mmt) REVERT: k 36 MET cc_start: 0.0674 (ttm) cc_final: -0.0179 (mpp) REVERT: k 45 MET cc_start: -0.0369 (ttp) cc_final: -0.0798 (tpt) outliers start: 1 outliers final: 1 residues processed: 772 average time/residue: 0.3008 time to fit residues: 371.1829 Evaluate side-chains 450 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 449 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 8 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 40.0000 chunk 455 optimal weight: 0.1980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 470 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 HIS B 430 ASN B1030 ASN H 131 ASN b 153 HIS b 210 HIS c 10 HIS c 39 GLN g 19 ASN h 26 HIS h 39 ASN j 55 ASN j 76 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.204409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.155465 restraints weight = 67521.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.149218 restraints weight = 50478.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.149598 restraints weight = 45365.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.149994 restraints weight = 37489.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.150251 restraints weight = 34055.724| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 45199 Z= 0.205 Angle : 0.926 23.903 62295 Z= 0.406 Chirality : 0.082 1.696 7103 Planarity : 0.005 0.058 7060 Dihedral : 15.520 178.419 8358 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.54 % Allowed : 8.70 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.12), residues: 4687 helix: -0.14 (0.13), residues: 1468 sheet: -1.70 (0.16), residues: 807 loop : -1.11 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG b 69 TYR 0.018 0.002 TYR b 161 PHE 0.034 0.002 PHE c 77 TRP 0.024 0.001 TRP C 203 HIS 0.005 0.001 HIS b 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (45168) covalent geometry : angle 0.91406 / 0.40 (62256) hydrogen bonds : bond 0.05287 / 3.56 ( 1696) hydrogen bonds : angle 5.49658 / 3.87 ( 4588) metal coordination : bond 0.01282 / 0.84 ( 31) metal coordination : angle 6.01175 / 3.97 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 471 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 SER cc_start: 0.8646 (m) cc_final: 0.8333 (p) REVERT: A 711 GLN cc_start: 0.7237 (tm-30) cc_final: 0.7007 (tm-30) REVERT: A 1344 MET cc_start: 0.7780 (mmm) cc_final: 0.7176 (mtt) REVERT: A 1351 ASP cc_start: 0.6898 (m-30) cc_final: 0.6362 (m-30) REVERT: A 1412 MET cc_start: 0.8339 (tmm) cc_final: 0.8022 (tmm) REVERT: B 262 TYR cc_start: 0.8356 (m-10) cc_final: 0.8142 (m-80) REVERT: B 438 ARG cc_start: 0.7270 (ttp-110) cc_final: 0.7061 (ptm-80) REVERT: B 726 SER cc_start: 0.9006 (m) cc_final: 0.8752 (t) REVERT: B 934 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8578 (mtpt) REVERT: C 48 ASP cc_start: 0.7814 (t70) cc_final: 0.7474 (t0) REVERT: C 186 TYR cc_start: 0.8761 (p90) cc_final: 0.8443 (p90) REVERT: E 61 LEU cc_start: 0.8424 (tp) cc_final: 0.8176 (tp) REVERT: E 193 ILE cc_start: 0.8354 (mt) cc_final: 0.8126 (mt) REVERT: F 107 ARG cc_start: 0.8915 (ttm-80) cc_final: 0.8602 (tpp80) REVERT: F 115 TYR cc_start: 0.8166 (p90) cc_final: 0.7819 (p90) REVERT: G 104 MET cc_start: 0.1220 (mmp) cc_final: 0.0968 (mmp) REVERT: I 25 TYR cc_start: 0.8170 (m-80) cc_final: 0.7794 (m-80) REVERT: I 51 SER cc_start: 0.7989 (t) cc_final: 0.7774 (p) REVERT: I 54 TYR cc_start: 0.8167 (t80) cc_final: 0.7888 (t80) REVERT: K 110 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7881 (mtmt) REVERT: g 41 MET cc_start: 0.3581 (mtt) cc_final: 0.3247 (ptp) REVERT: k 45 MET cc_start: 0.0118 (ttp) cc_final: -0.0438 (tpt) outliers start: 65 outliers final: 34 residues processed: 509 average time/residue: 0.2722 time to fit residues: 230.5765 Evaluate side-chains 428 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 394 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 758 LYS Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain f residue 20 MET Chi-restraints excluded: chain f residue 63 LEU Chi-restraints excluded: chain k residue 76 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 362 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 397 optimal weight: 20.0000 chunk 465 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 365 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 469 optimal weight: 30.0000 chunk 82 optimal weight: 0.6980 chunk 414 optimal weight: 7.9990 chunk 325 optimal weight: 40.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1145 GLN E 35 GLN K 89 ASN ** b 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 62 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.202989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.151443 restraints weight = 66428.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.147415 restraints weight = 58274.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.148878 restraints weight = 50320.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.149609 restraints weight = 37072.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.149709 restraints weight = 32443.055| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 45199 Z= 0.183 Angle : 0.746 18.347 62295 Z= 0.340 Chirality : 0.061 1.010 7103 Planarity : 0.004 0.047 7060 Dihedral : 16.032 179.622 8355 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.92 % Allowed : 10.53 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.12), residues: 4687 helix: 0.41 (0.14), residues: 1463 sheet: -1.54 (0.16), residues: 820 loop : -0.89 (0.13), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 416 TYR 0.019 0.001 TYR b 161 PHE 0.022 0.002 PHE b 106 TRP 0.024 0.001 TRP A1192 HIS 0.005 0.001 HIS B 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (45168) covalent geometry : angle 0.73450 / 0.34 (62256) hydrogen bonds : bond 0.04615 / 3.07 ( 1696) hydrogen bonds : angle 5.12476 / 3.60 ( 4588) metal coordination : bond 0.00947 / 0.61 ( 31) metal coordination : angle 5.16238 / 3.34 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 433 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.6989 (mtp) REVERT: A 556 GLU cc_start: 0.7329 (mp0) cc_final: 0.6244 (mp0) REVERT: A 559 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6597 (mt-10) REVERT: A 593 SER cc_start: 0.8683 (m) cc_final: 0.8358 (p) REVERT: A 1086 MET cc_start: 0.8456 (mmm) cc_final: 0.8162 (mmm) REVERT: A 1344 MET cc_start: 0.7615 (mmm) cc_final: 0.7183 (mtt) REVERT: A 1351 ASP cc_start: 0.7020 (m-30) cc_final: 0.6442 (m-30) REVERT: A 1412 MET cc_start: 0.8414 (tmm) cc_final: 0.8082 (tmm) REVERT: A 1423 ASP cc_start: 0.6566 (t0) cc_final: 0.6023 (t0) REVERT: A 1428 MET cc_start: 0.7552 (mtp) cc_final: 0.7329 (mtp) REVERT: A 1451 MET cc_start: 0.7615 (mmp) cc_final: 0.7388 (mmp) REVERT: B 93 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7820 (tp) REVERT: B 262 TYR cc_start: 0.8365 (m-10) cc_final: 0.8082 (m-80) REVERT: B 456 GLN cc_start: 0.7720 (tt0) cc_final: 0.7200 (tt0) REVERT: C 48 ASP cc_start: 0.8024 (t70) cc_final: 0.7739 (t0) REVERT: C 186 TYR cc_start: 0.8778 (p90) cc_final: 0.8404 (p90) REVERT: E 61 LEU cc_start: 0.8420 (tp) cc_final: 0.8173 (tp) REVERT: F 107 ARG cc_start: 0.8882 (ttm-80) cc_final: 0.7846 (tpp80) REVERT: G 104 MET cc_start: 0.1744 (mmp) cc_final: 0.1488 (mmp) REVERT: I 25 TYR cc_start: 0.8188 (m-80) cc_final: 0.7755 (m-80) REVERT: I 51 SER cc_start: 0.8130 (t) cc_final: 0.7847 (p) REVERT: K 110 LYS cc_start: 0.8206 (mtpt) cc_final: 0.6586 (mtmt) REVERT: b 77 ARG cc_start: 0.7615 (tpp-160) cc_final: 0.7314 (tpp-160) REVERT: b 155 ARG cc_start: 0.8205 (tmt-80) cc_final: 0.7914 (tpt-90) REVERT: e 65 MET cc_start: -0.3275 (mmt) cc_final: -0.3601 (mmt) REVERT: g 41 MET cc_start: 0.3678 (mtt) cc_final: 0.3283 (ptp) REVERT: i 43 MET cc_start: 0.5629 (mmm) cc_final: 0.5216 (tpp) outliers start: 81 outliers final: 46 residues processed: 489 average time/residue: 0.2658 time to fit residues: 218.4686 Evaluate side-chains 429 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 381 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 758 LYS Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain b residue 83 GLU Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain f residue 20 MET Chi-restraints excluded: chain f residue 63 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 354 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 378 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 184 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 262 optimal weight: 0.9980 chunk 368 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 825 GLN C 66 HIS H 131 ASN ** b 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.202040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.150927 restraints weight = 66365.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.148527 restraints weight = 85897.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.151004 restraints weight = 59940.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.150773 restraints weight = 44827.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.151391 restraints weight = 39220.484| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 45199 Z= 0.158 Angle : 0.695 15.652 62295 Z= 0.319 Chirality : 0.055 0.812 7103 Planarity : 0.004 0.047 7060 Dihedral : 16.199 179.684 8355 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.81 % Allowed : 12.24 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.12), residues: 4687 helix: 0.70 (0.14), residues: 1457 sheet: -1.38 (0.17), residues: 823 loop : -0.78 (0.13), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 51 TYR 0.019 0.001 TYR A 669 PHE 0.026 0.001 PHE b 106 TRP 0.013 0.001 TRP C 49 HIS 0.006 0.001 HIS b 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (45168) covalent geometry : angle 0.68657 / 0.32 (62256) hydrogen bonds : bond 0.03981 / 2.66 ( 1696) hydrogen bonds : angle 4.90253 / 3.44 ( 4588) metal coordination : bond 0.00841 / 0.55 ( 31) metal coordination : angle 4.45808 / 2.93 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 413 time to evaluate : 1.551 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 556 GLU cc_start: 0.7440 (mp0) cc_final: 0.6458 (mp0) REVERT: A 559 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6691 (mt-10) REVERT: A 593 SER cc_start: 0.8655 (m) cc_final: 0.8292 (p) REVERT: A 711 GLN cc_start: 0.7335 (tm-30) cc_final: 0.7127 (tm-30) REVERT: A 828 LEU cc_start: 0.8111 (tp) cc_final: 0.7611 (mp) REVERT: A 1351 ASP cc_start: 0.7013 (m-30) cc_final: 0.6451 (m-30) REVERT: A 1412 MET cc_start: 0.8426 (tmm) cc_final: 0.7957 (tmm) REVERT: A 1423 ASP cc_start: 0.6583 (t0) cc_final: 0.6368 (t0) REVERT: A 1428 MET cc_start: 0.7522 (mtp) cc_final: 0.7315 (mtp) REVERT: B 93 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7714 (tp) REVERT: B 262 TYR cc_start: 0.8329 (m-10) cc_final: 0.8035 (m-80) REVERT: B 456 GLN cc_start: 0.7666 (tt0) cc_final: 0.7229 (tt0) REVERT: B 733 MET cc_start: 0.7139 (mtt) cc_final: 0.6905 (mtt) REVERT: C 48 ASP cc_start: 0.7984 (t70) cc_final: 0.7677 (t0) REVERT: C 186 TYR cc_start: 0.8743 (p90) cc_final: 0.8430 (p90) REVERT: E 61 LEU cc_start: 0.8424 (tp) cc_final: 0.8198 (tp) REVERT: F 115 TYR cc_start: 0.7760 (p90) cc_final: 0.7423 (p90) REVERT: G 104 MET cc_start: 0.2704 (mmp) cc_final: 0.2327 (mmp) REVERT: I 25 TYR cc_start: 0.8134 (m-80) cc_final: 0.7783 (m-80) REVERT: I 51 SER cc_start: 0.7927 (t) cc_final: 0.7686 (p) REVERT: I 54 TYR cc_start: 0.7961 (t80) cc_final: 0.7661 (t80) REVERT: b 155 ARG cc_start: 0.7927 (tmt-80) cc_final: 0.7699 (tpt-90) REVERT: e 99 MET cc_start: 0.3734 (tmm) cc_final: 0.3369 (tpp) REVERT: g 41 MET cc_start: 0.3862 (mtt) cc_final: 0.3369 (ptp) outliers start: 76 outliers final: 48 residues processed: 469 average time/residue: 0.2607 time to fit residues: 206.7737 Evaluate side-chains 434 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 385 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 942 LYS Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain f residue 20 MET Chi-restraints excluded: chain f residue 63 LEU Chi-restraints excluded: chain g residue 77 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 484 optimal weight: 50.0000 chunk 244 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 211 optimal weight: 0.6980 chunk 311 optimal weight: 2.9990 chunk 335 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 462 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN A 387 ASN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 GLN A1042 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN K 29 ASN b 158 HIS b 207 ASN b 210 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.198777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.147208 restraints weight = 66543.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.144248 restraints weight = 84707.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.145213 restraints weight = 77785.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.145989 restraints weight = 49688.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.148592 restraints weight = 39668.001| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 45199 Z= 0.222 Angle : 0.721 15.961 62295 Z= 0.335 Chirality : 0.054 0.637 7103 Planarity : 0.004 0.046 7060 Dihedral : 16.327 177.866 8355 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.42 % Allowed : 13.21 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.12), residues: 4687 helix: 0.77 (0.14), residues: 1453 sheet: -1.36 (0.17), residues: 799 loop : -0.77 (0.12), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 71 TYR 0.025 0.002 TYR B 92 PHE 0.025 0.002 PHE b 106 TRP 0.011 0.001 TRP C 49 HIS 0.012 0.001 HIS B1097 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (45168) covalent geometry : angle 0.70986 / 0.33 (62256) hydrogen bonds : bond 0.04072 / 2.73 ( 1696) hydrogen bonds : angle 4.90860 / 3.46 ( 4588) metal coordination : bond 0.01166 / 0.74 ( 31) metal coordination : angle 5.00526 / 3.33 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 417 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 GLU cc_start: 0.7525 (mp0) cc_final: 0.6580 (mp0) REVERT: A 559 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7000 (mt-10) REVERT: A 593 SER cc_start: 0.8828 (m) cc_final: 0.8506 (p) REVERT: A 1351 ASP cc_start: 0.7094 (m-30) cc_final: 0.6540 (m-30) REVERT: A 1412 MET cc_start: 0.8420 (tmm) cc_final: 0.7930 (tmm) REVERT: A 1423 ASP cc_start: 0.6687 (t0) cc_final: 0.6438 (t0) REVERT: A 1428 MET cc_start: 0.7586 (mtp) cc_final: 0.7357 (mtp) REVERT: B 93 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7816 (tp) REVERT: B 108 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7724 (ttm) REVERT: B 187 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8851 (mm) REVERT: B 456 GLN cc_start: 0.7776 (tt0) cc_final: 0.7358 (tt0) REVERT: B 494 LYS cc_start: 0.8424 (mmtt) cc_final: 0.7980 (tmtt) REVERT: B 554 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: B 864 ASP cc_start: 0.7066 (t0) cc_final: 0.6806 (m-30) REVERT: B 1070 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8295 (tp) REVERT: C 48 ASP cc_start: 0.8097 (t70) cc_final: 0.7690 (t0) REVERT: C 94 CYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7085 (p) REVERT: C 103 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8957 (tt) REVERT: C 186 TYR cc_start: 0.8799 (p90) cc_final: 0.8409 (p90) REVERT: C 246 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8854 (mm) REVERT: E 182 TYR cc_start: 0.8632 (t80) cc_final: 0.8341 (t80) REVERT: F 115 TYR cc_start: 0.7723 (p90) cc_final: 0.7314 (p90) REVERT: G 104 MET cc_start: 0.2406 (mmp) cc_final: 0.1978 (mmp) REVERT: I 23 MET cc_start: 0.7664 (ptm) cc_final: 0.7424 (ttp) REVERT: I 51 SER cc_start: 0.8034 (t) cc_final: 0.7789 (p) REVERT: b 155 ARG cc_start: 0.7959 (tmt-80) cc_final: 0.7690 (tpt-90) REVERT: c 82 MET cc_start: 0.0117 (mmt) cc_final: -0.0158 (mmt) REVERT: e 99 MET cc_start: 0.3806 (tmm) cc_final: 0.3487 (tpp) REVERT: g 41 MET cc_start: 0.3848 (mtt) cc_final: 0.3387 (ptp) REVERT: k 25 VAL cc_start: -0.0567 (OUTLIER) cc_final: -0.0863 (m) REVERT: k 36 MET cc_start: 0.0008 (OUTLIER) cc_final: -0.0339 (tmm) outliers start: 102 outliers final: 63 residues processed: 490 average time/residue: 0.2622 time to fit residues: 216.4569 Evaluate side-chains 459 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 386 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 758 LYS Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1037 ILE Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain f residue 20 MET Chi-restraints excluded: chain f residue 42 MET Chi-restraints excluded: chain f residue 63 LEU Chi-restraints excluded: chain g residue 77 ILE Chi-restraints excluded: chain k residue 25 VAL Chi-restraints excluded: chain k residue 36 MET Chi-restraints excluded: chain k residue 43 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 141 optimal weight: 3.9990 chunk 401 optimal weight: 40.0000 chunk 105 optimal weight: 0.8980 chunk 460 optimal weight: 50.0000 chunk 178 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 414 optimal weight: 3.9990 chunk 478 optimal weight: 5.9990 chunk 357 optimal weight: 2.9990 chunk 288 optimal weight: 20.0000 chunk 161 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN A 330 GLN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.197322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.145795 restraints weight = 66962.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.144572 restraints weight = 73351.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.145996 restraints weight = 60399.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.146160 restraints weight = 41076.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.147940 restraints weight = 34760.874| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 45199 Z= 0.209 Angle : 0.697 16.266 62295 Z= 0.323 Chirality : 0.053 0.559 7103 Planarity : 0.004 0.045 7060 Dihedral : 16.344 178.189 8355 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.30 % Allowed : 14.26 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.12), residues: 4687 helix: 0.84 (0.14), residues: 1450 sheet: -1.50 (0.17), residues: 797 loop : -0.67 (0.13), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 51 TYR 0.023 0.002 TYR B 262 PHE 0.022 0.002 PHE A 390 TRP 0.020 0.001 TRP B 236 HIS 0.006 0.001 HIS E 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (45168) covalent geometry : angle 0.68676 / 0.32 (62256) hydrogen bonds : bond 0.03926 / 2.62 ( 1696) hydrogen bonds : angle 4.86872 / 3.43 ( 4588) metal coordination : bond 0.01169 / 0.75 ( 31) metal coordination : angle 4.76209 / 3.17 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 402 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 GLU cc_start: 0.7526 (mp0) cc_final: 0.6517 (mp0) REVERT: A 559 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7002 (mt-10) REVERT: A 593 SER cc_start: 0.8761 (m) cc_final: 0.8552 (p) REVERT: A 828 LEU cc_start: 0.8347 (tp) cc_final: 0.7872 (mp) REVERT: A 1351 ASP cc_start: 0.7084 (m-30) cc_final: 0.6533 (m-30) REVERT: A 1412 MET cc_start: 0.8386 (tmm) cc_final: 0.7888 (tmm) REVERT: A 1423 ASP cc_start: 0.6753 (t0) cc_final: 0.6408 (t0) REVERT: A 1428 MET cc_start: 0.7586 (mtp) cc_final: 0.7345 (mtp) REVERT: B 93 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7751 (tp) REVERT: B 187 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8838 (mm) REVERT: B 456 GLN cc_start: 0.7750 (tt0) cc_final: 0.7371 (tt0) REVERT: B 494 LYS cc_start: 0.8404 (mmtt) cc_final: 0.8036 (tmtt) REVERT: B 554 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: B 864 ASP cc_start: 0.7127 (t0) cc_final: 0.6717 (m-30) REVERT: C 48 ASP cc_start: 0.8241 (t70) cc_final: 0.7894 (t0) REVERT: C 94 CYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7083 (p) REVERT: C 186 TYR cc_start: 0.8774 (p90) cc_final: 0.8512 (p90) REVERT: C 246 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8880 (mm) REVERT: E 98 ASN cc_start: 0.7050 (t0) cc_final: 0.6807 (t0) REVERT: F 115 TYR cc_start: 0.7674 (p90) cc_final: 0.7303 (p90) REVERT: G 104 MET cc_start: 0.2603 (mmp) cc_final: 0.2136 (mmp) REVERT: I 23 MET cc_start: 0.7680 (ptm) cc_final: 0.7434 (ttp) REVERT: b 67 MET cc_start: 0.4674 (ptm) cc_final: 0.4078 (ptt) REVERT: b 155 ARG cc_start: 0.7887 (tmt-80) cc_final: 0.7647 (tpt-90) REVERT: c 82 MET cc_start: 0.0460 (mmt) cc_final: 0.0206 (mmt) REVERT: e 99 MET cc_start: 0.3972 (tmm) cc_final: 0.3667 (tpp) REVERT: g 41 MET cc_start: 0.3673 (mtt) cc_final: 0.3281 (ptp) REVERT: k 25 VAL cc_start: -0.0534 (OUTLIER) cc_final: -0.0807 (m) REVERT: k 36 MET cc_start: 0.0242 (ptt) cc_final: -0.0460 (tmm) outliers start: 97 outliers final: 65 residues processed: 470 average time/residue: 0.2567 time to fit residues: 204.3453 Evaluate side-chains 452 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 381 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 758 LYS Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain f residue 20 MET Chi-restraints excluded: chain f residue 42 MET Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 77 ILE Chi-restraints excluded: chain k residue 25 VAL Chi-restraints excluded: chain k residue 43 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 289 optimal weight: 0.0270 chunk 425 optimal weight: 6.9990 chunk 284 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 292 optimal weight: 10.0000 chunk 374 optimal weight: 0.7980 chunk 220 optimal weight: 0.6980 chunk 275 optimal weight: 0.0270 chunk 311 optimal weight: 0.9980 chunk 397 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 601 ASN A 685 HIS ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1040 GLN C 5 ASN H 126 GLN K 29 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.201153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.150718 restraints weight = 66353.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.147617 restraints weight = 76136.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.149997 restraints weight = 65568.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.149877 restraints weight = 39719.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.150260 restraints weight = 40096.283| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 45199 Z= 0.118 Angle : 0.647 13.595 62295 Z= 0.300 Chirality : 0.051 0.500 7103 Planarity : 0.004 0.066 7060 Dihedral : 16.292 177.408 8355 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.76 % Allowed : 15.23 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.12), residues: 4687 helix: 1.05 (0.14), residues: 1451 sheet: -1.40 (0.17), residues: 806 loop : -0.55 (0.13), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG k 61 TYR 0.021 0.001 TYR E 182 PHE 0.020 0.001 PHE J 8 TRP 0.016 0.001 TRP C 49 HIS 0.005 0.001 HIS I 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (45168) covalent geometry : angle 0.63981 / 0.30 (62256) hydrogen bonds : bond 0.03588 / 2.37 ( 1696) hydrogen bonds : angle 4.68190 / 3.29 ( 4588) metal coordination : bond 0.00626 / 0.41 ( 31) metal coordination : angle 3.87282 / 2.55 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 425 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 GLU cc_start: 0.7418 (mp0) cc_final: 0.6443 (mp0) REVERT: A 559 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6941 (mt-10) REVERT: A 593 SER cc_start: 0.8580 (m) cc_final: 0.8337 (p) REVERT: A 828 LEU cc_start: 0.8104 (tp) cc_final: 0.7679 (mp) REVERT: A 899 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: A 1086 MET cc_start: 0.8405 (mmm) cc_final: 0.8155 (mmm) REVERT: A 1351 ASP cc_start: 0.7143 (m-30) cc_final: 0.6598 (m-30) REVERT: A 1412 MET cc_start: 0.8415 (tmm) cc_final: 0.7889 (tmm) REVERT: A 1428 MET cc_start: 0.7647 (mtp) cc_final: 0.7377 (mtp) REVERT: B 93 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7655 (tp) REVERT: B 187 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8798 (mm) REVERT: B 456 GLN cc_start: 0.7616 (tt0) cc_final: 0.7180 (tt0) REVERT: B 494 LYS cc_start: 0.8443 (mmtt) cc_final: 0.7999 (tmtt) REVERT: B 554 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: C 48 ASP cc_start: 0.8096 (t70) cc_final: 0.7746 (t0) REVERT: C 94 CYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7140 (p) REVERT: C 186 TYR cc_start: 0.8712 (p90) cc_final: 0.8488 (p90) REVERT: E 98 ASN cc_start: 0.7154 (t0) cc_final: 0.6917 (t0) REVERT: F 115 TYR cc_start: 0.7650 (p90) cc_final: 0.7374 (p90) REVERT: G 104 MET cc_start: 0.2709 (mmp) cc_final: 0.2259 (mmp) REVERT: I 23 MET cc_start: 0.7752 (ptm) cc_final: 0.7531 (ttp) REVERT: K 37 LYS cc_start: 0.8747 (ptpt) cc_final: 0.8456 (pttt) REVERT: b 49 GLU cc_start: 0.6181 (tt0) cc_final: 0.5969 (pm20) REVERT: b 67 MET cc_start: 0.4730 (ptm) cc_final: 0.4145 (ptt) REVERT: b 155 ARG cc_start: 0.7938 (tmt-80) cc_final: 0.7699 (tpt-90) REVERT: c 82 MET cc_start: 0.0613 (mmt) cc_final: 0.0335 (mmt) REVERT: f 14 LEU cc_start: -0.4133 (OUTLIER) cc_final: -0.4361 (tp) REVERT: g 41 MET cc_start: 0.3688 (mtt) cc_final: 0.3277 (ptp) REVERT: h 38 MET cc_start: 0.3678 (ppp) cc_final: 0.3355 (ppp) REVERT: k 25 VAL cc_start: -0.0671 (OUTLIER) cc_final: -0.0948 (m) REVERT: k 36 MET cc_start: 0.0189 (OUTLIER) cc_final: -0.0370 (tmm) outliers start: 74 outliers final: 42 residues processed: 476 average time/residue: 0.2589 time to fit residues: 207.1460 Evaluate side-chains 439 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 389 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 758 LYS Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 837 CYS Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain f residue 14 LEU Chi-restraints excluded: chain f residue 20 MET Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain k residue 25 VAL Chi-restraints excluded: chain k residue 36 MET Chi-restraints excluded: chain k residue 43 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 149 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 352 optimal weight: 6.9990 chunk 220 optimal weight: 0.7980 chunk 347 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 448 optimal weight: 20.0000 chunk 363 optimal weight: 0.1980 chunk 237 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN K 29 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.200442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.148830 restraints weight = 66980.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.147823 restraints weight = 74883.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.149511 restraints weight = 56064.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.149431 restraints weight = 43015.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.150202 restraints weight = 35112.623| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 45199 Z= 0.130 Angle : 0.651 12.603 62295 Z= 0.302 Chirality : 0.051 0.447 7103 Planarity : 0.004 0.044 7060 Dihedral : 16.260 177.005 8355 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.69 % Allowed : 15.75 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.12), residues: 4687 helix: 1.14 (0.14), residues: 1451 sheet: -1.34 (0.17), residues: 796 loop : -0.48 (0.13), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 438 TYR 0.022 0.001 TYR E 26 PHE 0.026 0.001 PHE A 458 TRP 0.012 0.001 TRP B 22 HIS 0.005 0.001 HIS I 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (45168) covalent geometry : angle 0.64406 / 0.30 (62256) hydrogen bonds : bond 0.03539 / 2.34 ( 1696) hydrogen bonds : angle 4.63716 / 3.26 ( 4588) metal coordination : bond 0.00775 / 0.52 ( 31) metal coordination : angle 3.90723 / 2.55 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 407 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 GLU cc_start: 0.7414 (mp0) cc_final: 0.6367 (mp0) REVERT: A 559 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6914 (mt-10) REVERT: A 593 SER cc_start: 0.8629 (m) cc_final: 0.8339 (p) REVERT: A 899 GLU cc_start: 0.7644 (mp0) cc_final: 0.7236 (mp0) REVERT: A 936 GLU cc_start: 0.6800 (pm20) cc_final: 0.6433 (pm20) REVERT: A 1086 MET cc_start: 0.8383 (mmm) cc_final: 0.8117 (mmm) REVERT: A 1351 ASP cc_start: 0.7108 (m-30) cc_final: 0.6570 (m-30) REVERT: A 1412 MET cc_start: 0.8409 (tmm) cc_final: 0.7908 (tmm) REVERT: A 1428 MET cc_start: 0.7669 (mtp) cc_final: 0.7410 (mtp) REVERT: B 93 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7692 (tp) REVERT: B 187 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8778 (mm) REVERT: B 438 ARG cc_start: 0.7274 (ttp-110) cc_final: 0.6969 (ptm160) REVERT: B 456 GLN cc_start: 0.7567 (tt0) cc_final: 0.7154 (tt0) REVERT: B 494 LYS cc_start: 0.8451 (mmtt) cc_final: 0.8001 (tmtt) REVERT: B 554 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: C 48 ASP cc_start: 0.8089 (t70) cc_final: 0.7748 (t0) REVERT: C 94 CYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7076 (p) REVERT: C 186 TYR cc_start: 0.8717 (p90) cc_final: 0.8382 (p90) REVERT: F 115 TYR cc_start: 0.7655 (p90) cc_final: 0.7385 (p90) REVERT: G 104 MET cc_start: 0.2736 (mmp) cc_final: 0.2245 (mmp) REVERT: I 25 TYR cc_start: 0.8241 (m-80) cc_final: 0.7734 (m-80) REVERT: K 1 MET cc_start: 0.0081 (tpp) cc_final: -0.0314 (tpp) REVERT: K 37 LYS cc_start: 0.8736 (ptpt) cc_final: 0.8479 (pttt) REVERT: b 49 GLU cc_start: 0.6201 (tt0) cc_final: 0.5978 (pm20) REVERT: b 67 MET cc_start: 0.4836 (ptm) cc_final: 0.4243 (ptt) REVERT: b 155 ARG cc_start: 0.7939 (tmt-80) cc_final: 0.7674 (tpt-90) REVERT: c 82 MET cc_start: 0.0465 (mmt) cc_final: 0.0148 (mmt) REVERT: e 99 MET cc_start: 0.2336 (tpp) cc_final: 0.1825 (tpp) REVERT: f 14 LEU cc_start: -0.4195 (OUTLIER) cc_final: -0.4412 (tp) REVERT: f 42 MET cc_start: 0.3181 (OUTLIER) cc_final: 0.2334 (pmm) REVERT: g 41 MET cc_start: 0.3682 (mtt) cc_final: 0.3266 (ptp) REVERT: k 25 VAL cc_start: -0.0668 (OUTLIER) cc_final: -0.0955 (m) REVERT: k 36 MET cc_start: 0.0089 (OUTLIER) cc_final: -0.0434 (tmm) REVERT: k 45 MET cc_start: 0.1482 (ptm) cc_final: 0.1261 (ptm) outliers start: 71 outliers final: 49 residues processed: 460 average time/residue: 0.2611 time to fit residues: 203.3132 Evaluate side-chains 449 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 392 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 758 LYS Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 837 CYS Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain f residue 14 LEU Chi-restraints excluded: chain f residue 20 MET Chi-restraints excluded: chain f residue 42 MET Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain k residue 25 VAL Chi-restraints excluded: chain k residue 36 MET Chi-restraints excluded: chain k residue 43 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 47 optimal weight: 4.9990 chunk 390 optimal weight: 30.0000 chunk 422 optimal weight: 6.9990 chunk 349 optimal weight: 0.9980 chunk 484 optimal weight: 50.0000 chunk 381 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 323 optimal weight: 10.0000 chunk 238 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN K 2 ASN K 29 ASN b 92 HIS j 22 GLN k 64 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.194578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.141796 restraints weight = 67042.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.139262 restraints weight = 77610.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.141129 restraints weight = 63610.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.141258 restraints weight = 42835.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.144545 restraints weight = 36505.050| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 45199 Z= 0.289 Angle : 0.757 17.595 62295 Z= 0.356 Chirality : 0.054 0.347 7103 Planarity : 0.005 0.055 7060 Dihedral : 16.307 177.543 8355 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.00 % Allowed : 15.68 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.12), residues: 4687 helix: 0.80 (0.14), residues: 1448 sheet: -1.52 (0.17), residues: 805 loop : -0.61 (0.13), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 51 TYR 0.021 0.002 TYR E 182 PHE 0.023 0.002 PHE C 21 TRP 0.016 0.002 TRP B 236 HIS 0.009 0.001 HIS B 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.29 (45168) covalent geometry : angle 0.74477 / 0.36 (62256) hydrogen bonds : bond 0.04099 / 2.73 ( 1696) hydrogen bonds : angle 4.91286 / 3.46 ( 4588) metal coordination : bond 0.01576 / 0.96 ( 31) metal coordination : angle 5.53764 / 3.72 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 389 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 GLU cc_start: 0.7515 (mp0) cc_final: 0.6563 (mp0) REVERT: A 559 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6952 (mt-10) REVERT: A 593 SER cc_start: 0.8826 (m) cc_final: 0.8545 (p) REVERT: A 828 LEU cc_start: 0.8468 (tp) cc_final: 0.7923 (mp) REVERT: A 869 GLU cc_start: 0.6687 (pt0) cc_final: 0.6451 (pt0) REVERT: A 899 GLU cc_start: 0.7694 (mp0) cc_final: 0.7254 (mp0) REVERT: A 936 GLU cc_start: 0.6776 (pm20) cc_final: 0.6413 (pm20) REVERT: A 1095 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8394 (mt) REVERT: A 1351 ASP cc_start: 0.7159 (m-30) cc_final: 0.6637 (m-30) REVERT: A 1412 MET cc_start: 0.8425 (tmm) cc_final: 0.7895 (tmm) REVERT: B 93 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7840 (tp) REVERT: B 456 GLN cc_start: 0.7858 (tt0) cc_final: 0.7388 (tt0) REVERT: B 494 LYS cc_start: 0.8422 (mmtt) cc_final: 0.8053 (tmtt) REVERT: B 554 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: C 48 ASP cc_start: 0.8285 (t70) cc_final: 0.7876 (t0) REVERT: C 186 TYR cc_start: 0.8792 (p90) cc_final: 0.8470 (p90) REVERT: F 115 TYR cc_start: 0.7617 (p90) cc_final: 0.7306 (p90) REVERT: K 37 LYS cc_start: 0.8695 (ptpt) cc_final: 0.8406 (pttm) REVERT: K 81 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.8272 (t80) REVERT: b 67 MET cc_start: 0.4943 (ptm) cc_final: 0.4341 (ptt) REVERT: c 82 MET cc_start: 0.0423 (mmt) cc_final: 0.0081 (mmt) REVERT: e 99 MET cc_start: 0.2111 (tpp) cc_final: 0.1455 (tpp) REVERT: f 14 LEU cc_start: -0.4325 (OUTLIER) cc_final: -0.4560 (tp) REVERT: g 41 MET cc_start: 0.3591 (mtt) cc_final: 0.3178 (ptp) REVERT: k 25 VAL cc_start: -0.0812 (OUTLIER) cc_final: -0.1088 (m) REVERT: k 36 MET cc_start: -0.0123 (ptt) cc_final: -0.0412 (tmm) outliers start: 84 outliers final: 62 residues processed: 450 average time/residue: 0.2654 time to fit residues: 200.6786 Evaluate side-chains 441 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 373 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 758 LYS Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 837 CYS Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1037 ILE Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain f residue 14 LEU Chi-restraints excluded: chain f residue 20 MET Chi-restraints excluded: chain f residue 42 MET Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain k residue 25 VAL Chi-restraints excluded: chain k residue 43 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 78 optimal weight: 0.9980 chunk 295 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 233 optimal weight: 0.0070 chunk 429 optimal weight: 10.0000 chunk 301 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 250 optimal weight: 0.9980 chunk 377 optimal weight: 0.8980 chunk 400 optimal weight: 30.0000 chunk 47 optimal weight: 0.5980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN A 783 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1145 GLN C 260 GLN ** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.195230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.143135 restraints weight = 67105.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.142629 restraints weight = 70252.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.143349 restraints weight = 63827.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.143613 restraints weight = 39934.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.146041 restraints weight = 34470.485| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.146 45199 Z= 0.222 Angle : 0.814 59.139 62295 Z= 0.399 Chirality : 0.053 0.823 7103 Planarity : 0.004 0.051 7060 Dihedral : 16.316 177.543 8355 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.74 % Favored : 95.24 % Rotamer: Outliers : 1.78 % Allowed : 15.87 % Favored : 82.35 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.12), residues: 4687 helix: 0.84 (0.14), residues: 1446 sheet: -1.53 (0.17), residues: 805 loop : -0.61 (0.13), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 40 TYR 0.022 0.002 TYR i 28 PHE 0.018 0.002 PHE K 105 TRP 0.014 0.002 TRP B 236 HIS 0.006 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 (45168) covalent geometry : angle 0.80239 / 0.40 (62256) hydrogen bonds : bond 0.04030 / 2.69 ( 1696) hydrogen bonds : angle 4.90453 / 3.45 ( 4588) metal coordination : bond 0.01315 / 0.79 ( 31) metal coordination : angle 5.58002 / 3.75 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 372 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 556 GLU cc_start: 0.7469 (mp0) cc_final: 0.6537 (mp0) REVERT: A 559 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6883 (mt-10) REVERT: A 593 SER cc_start: 0.8807 (m) cc_final: 0.8506 (p) REVERT: A 828 LEU cc_start: 0.8422 (tp) cc_final: 0.7880 (mp) REVERT: A 899 GLU cc_start: 0.7641 (mp0) cc_final: 0.7180 (mp0) REVERT: A 1351 ASP cc_start: 0.7138 (m-30) cc_final: 0.6606 (m-30) REVERT: A 1412 MET cc_start: 0.8421 (tmm) cc_final: 0.7903 (tmm) REVERT: B 92 TYR cc_start: 0.7323 (m-80) cc_final: 0.7104 (m-80) REVERT: B 93 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7809 (tp) REVERT: B 456 GLN cc_start: 0.7837 (tt0) cc_final: 0.7418 (tt0) REVERT: B 494 LYS cc_start: 0.8387 (mmtt) cc_final: 0.8103 (tmtt) REVERT: B 554 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: B 744 MET cc_start: 0.8585 (mmm) cc_final: 0.8245 (mmm) REVERT: C 48 ASP cc_start: 0.8252 (t70) cc_final: 0.7848 (t0) REVERT: C 186 TYR cc_start: 0.8744 (p90) cc_final: 0.8428 (p90) REVERT: F 115 TYR cc_start: 0.7586 (p90) cc_final: 0.7288 (p90) REVERT: K 37 LYS cc_start: 0.8660 (ptpt) cc_final: 0.8376 (pttm) REVERT: K 81 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.8266 (t80) REVERT: b 67 MET cc_start: 0.4815 (ptm) cc_final: 0.4231 (ptt) REVERT: c 82 MET cc_start: 0.0516 (mmt) cc_final: 0.0168 (mmt) REVERT: e 99 MET cc_start: 0.2080 (tpp) cc_final: 0.1454 (tpp) REVERT: f 14 LEU cc_start: -0.4293 (OUTLIER) cc_final: -0.4533 (tp) REVERT: g 41 MET cc_start: 0.3642 (mtt) cc_final: 0.3241 (ptp) REVERT: k 25 VAL cc_start: -0.0740 (OUTLIER) cc_final: -0.1007 (m) REVERT: k 36 MET cc_start: -0.0003 (ptt) cc_final: -0.0436 (tmm) outliers start: 75 outliers final: 65 residues processed: 427 average time/residue: 0.2565 time to fit residues: 185.6516 Evaluate side-chains 441 residues out of total 4210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 371 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 758 LYS Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 726 SER Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 837 CYS Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain b residue 49 GLU Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain b residue 149 ILE Chi-restraints excluded: chain f residue 14 LEU Chi-restraints excluded: chain f residue 20 MET Chi-restraints excluded: chain f residue 42 MET Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain k residue 25 VAL Chi-restraints excluded: chain k residue 43 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 293 optimal weight: 0.8980 chunk 305 optimal weight: 0.7980 chunk 309 optimal weight: 1.9990 chunk 367 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 413 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 263 optimal weight: 0.8980 chunk 371 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1145 GLN ** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.195176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.143291 restraints weight = 67346.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.141775 restraints weight = 72546.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.143194 restraints weight = 64647.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.143575 restraints weight = 41816.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.146034 restraints weight = 36734.379| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.146 45199 Z= 0.222 Angle : 0.814 59.138 62295 Z= 0.399 Chirality : 0.053 0.823 7103 Planarity : 0.004 0.051 7060 Dihedral : 16.316 177.543 8355 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.74 % Favored : 95.24 % Rotamer: Outliers : 1.66 % Allowed : 15.94 % Favored : 82.39 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.12), residues: 4687 helix: 0.84 (0.14), residues: 1446 sheet: -1.53 (0.17), residues: 805 loop : -0.61 (0.13), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 40 TYR 0.022 0.002 TYR i 28 PHE 0.018 0.002 PHE K 105 TRP 0.014 0.002 TRP B 236 HIS 0.006 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 (45168) covalent geometry : angle 0.80239 / 0.40 (62256) hydrogen bonds : bond 0.04030 / 2.69 ( 1696) hydrogen bonds : angle 4.90453 / 3.45 ( 4588) metal coordination : bond 0.01315 / 0.79 ( 31) metal coordination : angle 5.58002 / 3.75 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8271.60 seconds wall clock time: 143 minutes 56.63 seconds (8636.63 seconds total)