Starting phenix.real_space_refine on Tue Sep 15 10:02:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5xon_6747/09_2026/5xon_6747.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xon_6747/09_2026/5xon_6747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5xon_6747/09_2026/5xon_6747.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5xon_6747/09_2026/5xon_6747.cif" model { file = "/net/cci-nas-00/data/ceres_data/5xon_6747/09_2026/5xon_6747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xon_6747/09_2026/5xon_6747.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5xon_6747/09_2026/5xon_6747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xon_6747/09_2026/5xon_6747.map" } resolution = 3.83 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= 0.002 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 107 5.49 5 Mg 1 5.21 5 S 208 5.16 5 C 23841 2.51 5 N 6728 2.21 5 O 7474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.17s 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: 38369 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 11239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1427, 11239 Classifications: {'peptide': 1427} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 65, 'TRANS': 1357} Chain breaks: 4 Chain: "B" Number of atoms: 9261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1161, 9261 Classifications: {'peptide': 1161} Link IDs: {'PTRANS': 52, 'TRANS': 1108} Chain breaks: 4 Chain: "C" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2098 Classifications: {'peptide': 263} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 249} Chain: "D" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1314 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 4, 'TRANS': 163} Chain breaks: 2 Chain: "E" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1740 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "F" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "G" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1324 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1052 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 917 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 545 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 932 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "P" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 338 Classifications: {'RNAv2': 16} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, 'rna3p': 13} Chain: "T" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 975 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "N" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 889 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "U" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1239 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 149} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 792 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "W" Number of atoms: 2667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2667 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 12, 'TRANS': 316} Chain breaks: 5 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 527 SG CYS A 67 80.410 61.201 76.534 1.00 96.27 S ATOM 549 SG CYS A 70 83.867 59.658 77.018 1.00 92.27 S ATOM 594 SG CYS A 77 83.086 63.189 77.186 1.00 87.28 S ATOM 829 SG CYS A 107 82.591 83.799 33.369 1.00128.59 S ATOM 851 SG CYS A 110 83.995 80.340 31.519 1.00104.25 S ATOM 1157 SG CYS A 148 85.156 83.832 31.032 1.00104.36 S ATOM 1245 SG CYS A 168 81.199 82.990 30.090 1.00143.63 S ATOM 20032 SG CYS B1163 94.895 60.778 63.902 1.00 79.07 S ATOM 20050 SG CYS B1166 92.571 63.771 62.899 1.00 85.86 S ATOM 20173 SG CYS B1182 90.996 60.691 64.262 1.00 76.40 S ATOM 21141 SG CYS C 85 93.199 75.796 144.430 1.00 94.97 S ATOM 21154 SG CYS C 87 90.165 74.712 142.740 1.00 98.92 S ATOM 21189 SG CYS C 91 90.242 76.401 146.039 1.00109.39 S ATOM 21212 SG CYS C 94 90.464 79.058 143.453 1.00104.83 S ATOM 29298 SG CYS I 75 84.818 166.472 81.659 1.00 88.60 S ATOM 29320 SG CYS I 78 82.301 168.843 84.547 1.00112.45 S ATOM 29536 SG CYS I 103 82.522 164.951 84.808 1.00129.01 S ATOM 29558 SG CYS I 106 81.314 166.542 81.673 1.00 70.72 S ATOM 28750 SG CYS I 7 61.598 150.189 43.924 1.00101.68 S ATOM 28936 SG CYS I 29 63.383 146.876 42.249 1.00122.68 S ATOM 29677 SG CYS J 7 92.923 109.681 132.173 1.00 67.29 S ATOM 29700 SG CYS J 10 95.842 109.481 134.982 1.00 66.74 S ATOM 29976 SG CYS J 44 95.865 112.740 132.535 1.00 70.85 S ATOM 29982 SG CYS J 45 93.385 111.976 135.502 1.00 71.30 S ATOM 31159 SG CYS L 36 50.638 92.162 124.785 1.00106.03 S ATOM 31269 SG CYS L 50 50.356 88.675 123.749 1.00 86.39 S ATOM 34593 SG CYS U 247 123.840 121.662 85.440 1.00120.95 S ATOM 34612 SG CYS U 250 126.829 124.734 84.663 1.00127.79 S ATOM 34836 SG CYS U 278 124.406 123.064 81.984 1.00106.34 S ATOM 34930 SG CYS V 12 24.941 81.107 54.513 1.00 34.75 S ATOM 34952 SG CYS V 15 26.070 84.179 52.532 1.00 22.76 S ATOM 35054 SG CYS V 29 23.236 84.664 54.485 1.00 18.00 S ATOM 35075 SG CYS V 32 22.930 82.370 51.366 1.00 25.35 S Time building chain proxies: 7.59, per 1000 atoms: 0.20 Number of scatterers: 38369 At special positions: 0 Unit cell: (180.894, 190.092, 170.163, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 10 29.99 S 208 16.00 P 107 15.00 Mg 1 11.99 O 7474 8.00 N 6728 7.00 C 23841 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: 3.32 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 70 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 168 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 110 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 87 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 85 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 91 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 78 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 50 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb=" ZN U 301 " pdb="ZN ZN U 301 " - pdb=" SG CYS U 247 " pdb="ZN ZN U 301 " - pdb=" SG CYS U 278 " pdb="ZN ZN U 301 " - pdb=" SG CYS U 250 " pdb=" ZN V 300 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 12 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 15 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 29 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 32 " Number of angles added : 33 8950 Ramachandran restraints generated. 4475 Oldfield, 0 Emsley, 4475 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8514 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 51 sheets defined 34.0% alpha, 17.2% beta 38 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 4.75 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 106 removed outlier: 3.519A pdb=" N ILE A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 130 through 140 Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 261 through 281 removed outlier: 3.777A pdb=" N HIS A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 279 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 303 removed outlier: 3.529A pdb=" N VAL A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 removed outlier: 3.930A pdb=" N ARG A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 325 through 331' Processing helix chain 'A' and resid 368 through 375 Processing helix chain 'A' and resid 385 through 395 Processing helix chain 'A' and resid 472 through 476 Processing helix chain 'A' and resid 495 through 506 removed outlier: 3.606A pdb=" N ARG A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 511 Processing helix chain 'A' and resid 526 through 536 Processing helix chain 'A' and resid 543 through 553 removed outlier: 4.041A pdb=" N ASN A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 581 removed outlier: 4.194A pdb=" N LEU A 578 " --> pdb=" O THR A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 636 Processing helix chain 'A' and resid 639 through 660 removed outlier: 3.905A pdb=" N CYS A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.691A pdb=" N ILE A 671 " --> pdb=" O GLY A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 700 removed outlier: 3.655A pdb=" N MET A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 738 removed outlier: 3.723A pdb=" N LEU A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 750 removed outlier: 3.756A pdb=" N GLN A 746 " --> pdb=" O ASN A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 764 removed outlier: 4.077A pdb=" N ILE A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'A' and resid 810 through 846 removed outlier: 4.178A pdb=" N THR A 832 " --> pdb=" O THR A 828 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 910 through 914 removed outlier: 3.804A pdb=" N VAL A 913 " --> pdb=" O LYS A 910 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 914 " --> pdb=" O PRO A 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 910 through 914' Processing helix chain 'A' and resid 923 through 947 removed outlier: 3.898A pdb=" N GLN A 927 " --> pdb=" O ASP A 923 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU A 929 " --> pdb=" O GLU A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 973 removed outlier: 3.600A pdb=" N ILE A 965 " --> pdb=" O ASN A 961 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 973 " --> pdb=" O ALA A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 996 Processing helix chain 'A' and resid 1006 through 1017 removed outlier: 4.053A pdb=" N THR A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1028 Processing helix chain 'A' and resid 1030 through 1035 Processing helix chain 'A' and resid 1041 through 1058 Processing helix chain 'A' and resid 1065 through 1076 removed outlier: 3.674A pdb=" N ILE A1069 " --> pdb=" O MET A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1081 removed outlier: 3.969A pdb=" N GLN A1080 " --> pdb=" O PRO A1077 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET A1081 " --> pdb=" O ALA A1078 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1077 through 1081' Processing helix chain 'A' and resid 1098 through 1108 removed outlier: 3.791A pdb=" N ARG A1102 " --> pdb=" O LEU A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 removed outlier: 4.069A pdb=" N LEU A1128 " --> pdb=" O ARG A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1141 removed outlier: 3.744A pdb=" N ILE A1140 " --> pdb=" O ILE A1136 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU A1141 " --> pdb=" O GLN A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1173 Processing helix chain 'A' and resid 1200 through 1207 Processing helix chain 'A' and resid 1210 through 1222 removed outlier: 3.707A pdb=" N VAL A1214 " --> pdb=" O THR A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1273 Processing helix chain 'A' and resid 1315 through 1320 Processing helix chain 'A' and resid 1334 through 1343 removed outlier: 3.574A pdb=" N GLY A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1361 Processing helix chain 'A' and resid 1367 through 1379 removed outlier: 4.399A pdb=" N MET A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A1379 " --> pdb=" O VAL A1375 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1394 removed outlier: 3.854A pdb=" N ARG A1394 " --> pdb=" O HIS A1390 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1404 Processing helix chain 'A' and resid 1408 through 1417 Processing helix chain 'A' and resid 1426 through 1432 removed outlier: 3.793A pdb=" N ASN A1430 " --> pdb=" O GLY A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1442 Processing helix chain 'A' and resid 1452 through 1456 Processing helix chain 'A' and resid 1457 through 1461 removed outlier: 3.729A pdb=" N ALA A1461 " --> pdb=" O ALA A1458 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 28 Processing helix chain 'B' and resid 31 through 44 removed outlier: 4.153A pdb=" N LEU B 35 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 37 " --> pdb=" O GLN B 33 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 52 Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.590A pdb=" N CYS B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 313 removed outlier: 3.554A pdb=" N LYS B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 318 through 328 removed outlier: 4.038A pdb=" N ALA B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 352 removed outlier: 4.161A pdb=" N GLN B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 383 removed outlier: 3.862A pdb=" N LYS B 367 " --> pdb=" O PHE B 363 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 402 through 431 removed outlier: 4.033A pdb=" N LEU B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN B 408 " --> pdb=" O PRO B 404 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 457 removed outlier: 3.812A pdb=" N THR B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 486 removed outlier: 3.946A pdb=" N LEU B 485 " --> pdb=" O TYR B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 512 removed outlier: 3.735A pdb=" N TRP B 512 " --> pdb=" O ASN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 555 removed outlier: 4.011A pdb=" N TRP B 554 " --> pdb=" O PHE B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 599 Processing helix chain 'B' and resid 648 through 658 removed outlier: 3.555A pdb=" N ILE B 652 " --> pdb=" O THR B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 684 Processing helix chain 'B' and resid 692 through 696 removed outlier: 4.007A pdb=" N GLU B 696 " --> pdb=" O GLY B 692 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 692 through 696' Processing helix chain 'B' and resid 703 through 708 removed outlier: 3.765A pdb=" N LEU B 707 " --> pdb=" O THR B 703 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN B 708 " --> pdb=" O PRO B 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 703 through 708' Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.623A pdb=" N ILE B 748 " --> pdb=" O PRO B 745 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 774 removed outlier: 3.610A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 812 Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1013 through 1017 Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 4.120A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1062 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1151 Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'C' and resid 26 through 39 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 239 through 265 Processing helix chain 'D' and resid 52 through 72 Processing helix chain 'D' and resid 85 through 91 Processing helix chain 'D' and resid 96 through 111 Processing helix chain 'D' and resid 117 through 129 removed outlier: 4.136A pdb=" N HIS D 129 " --> pdb=" O ASP D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 146 Processing helix chain 'D' and resid 152 through 159 removed outlier: 3.777A pdb=" N ALA D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 164 removed outlier: 3.502A pdb=" N LEU D 163 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA D 164 " --> pdb=" O PRO D 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 160 through 164' Processing helix chain 'D' and resid 171 through 181 Processing helix chain 'E' and resid 3 through 25 removed outlier: 3.573A pdb=" N ILE E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 35 Processing helix chain 'E' and resid 37 through 46 removed outlier: 3.690A pdb=" N PHE E 41 " --> pdb=" O SER E 37 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS E 46 " --> pdb=" O ARG E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 64 through 71 Processing helix chain 'E' and resid 88 through 103 removed outlier: 3.752A pdb=" N MET E 92 " --> pdb=" O GLY E 88 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS E 102 " --> pdb=" O ARG E 98 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN E 103 " --> pdb=" O ILE E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 121 Processing helix chain 'E' and resid 156 through 168 removed outlier: 3.905A pdb=" N LYS E 160 " --> pdb=" O SER E 156 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER E 161 " --> pdb=" O ASP E 157 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR E 167 " --> pdb=" O LEU E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 186 removed outlier: 3.570A pdb=" N ARG E 185 " --> pdb=" O ASP E 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 removed outlier: 3.767A pdb=" N MET F 103 " --> pdb=" O LEU F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 128 removed outlier: 3.710A pdb=" N GLN F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 34 removed outlier: 3.569A pdb=" N TYR G 25 " --> pdb=" O GLN G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.804A pdb=" N ASP H 91 " --> pdb=" O LEU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 removed outlier: 3.582A pdb=" N LEU H 131 " --> pdb=" O GLY H 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 27 Processing helix chain 'J' and resid 30 through 37 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.627A pdb=" N VAL J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR J 51 " --> pdb=" O ARG J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 removed outlier: 4.146A pdb=" N ARG J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 51 removed outlier: 4.008A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 removed outlier: 3.600A pdb=" N ALA K 86 " --> pdb=" O ARG K 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 137 removed outlier: 4.602A pdb=" N ILE U 130 " --> pdb=" O ARG U 126 " (cutoff:3.500A) Processing helix chain 'U' and resid 147 through 163 removed outlier: 3.548A pdb=" N VAL U 163 " --> pdb=" O CYS U 159 " (cutoff:3.500A) Processing helix chain 'U' and resid 170 through 183 removed outlier: 3.725A pdb=" N LYS U 174 " --> pdb=" O THR U 170 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU U 175 " --> pdb=" O TYR U 171 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG U 176 " --> pdb=" O ARG U 172 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER U 177 " --> pdb=" O ASN U 173 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU U 182 " --> pdb=" O LEU U 178 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 193 removed outlier: 4.262A pdb=" N ARG U 191 " --> pdb=" O ASN U 187 " (cutoff:3.500A) Processing helix chain 'U' and resid 214 through 231 removed outlier: 3.523A pdb=" N TYR U 225 " --> pdb=" O MET U 221 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS U 226 " --> pdb=" O GLU U 222 " (cutoff:3.500A) Processing helix chain 'V' and resid 20 through 27 removed outlier: 3.726A pdb=" N PHE V 24 " --> pdb=" O PRO V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 32 through 37 Processing helix chain 'V' and resid 42 through 49 Processing helix chain 'V' and resid 66 through 72 Processing helix chain 'V' and resid 91 through 101 Processing helix chain 'W' and resid 213 through 218 removed outlier: 3.885A pdb=" N ILE W 218 " --> pdb=" O ARG W 215 " (cutoff:3.500A) Processing helix chain 'W' and resid 235 through 251 Processing helix chain 'W' and resid 278 through 287 removed outlier: 3.806A pdb=" N ILE W 282 " --> pdb=" O LYS W 278 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 304 No H-bonds generated for 'chain 'W' and resid 302 through 304' Processing helix chain 'W' and resid 305 through 310 removed outlier: 3.616A pdb=" N LEU W 309 " --> pdb=" O GLU W 305 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU W 310 " --> pdb=" O TYR W 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 305 through 310' Processing helix chain 'W' and resid 384 through 388 Processing helix chain 'W' and resid 395 through 403 Processing helix chain 'W' and resid 443 through 450 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 21 Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 35 removed outlier: 3.507A pdb=" N ILE A 35 " --> pdb=" O HIS A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 178 Processing sheet with id=AA4, first strand: chain 'A' and resid 364 through 367 Processing sheet with id=AA5, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.989A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N HIS A 436 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ALA A 403 " --> pdb=" O HIS A 436 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 513 through 514 removed outlier: 3.753A pdb=" N LYS A 519 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 566 through 568 removed outlier: 5.995A pdb=" N ILE A 566 " --> pdb=" O PHE H 97 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE H 97 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 568 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL H 95 " --> pdb=" O LYS A 568 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL H 12 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR H 14 " --> pdb=" O ILE H 27 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LYS H 112 " --> pdb=" O PHE H 103 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE H 103 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR H 114 " --> pdb=" O TYR H 101 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 588 through 591 removed outlier: 3.729A pdb=" N PHE A 615 " --> pdb=" O LEU A 607 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL A 609 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL A 613 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 857 through 858 removed outlier: 3.852A pdb=" N GLN A 866 " --> pdb=" O THR A 857 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 879 through 883 Processing sheet with id=AB2, first strand: chain 'A' and resid 1117 through 1120 removed outlier: 4.320A pdb=" N LYS A1284 " --> pdb=" O ASP A1312 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1143 through 1144 removed outlier: 7.277A pdb=" N THR A1143 " --> pdb=" O LEU A1276 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1226 through 1230 removed outlier: 6.743A pdb=" N LEU A1194 " --> pdb=" O ILE A1154 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE A1154 " --> pdb=" O LEU A1194 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ARG A1196 " --> pdb=" O THR A1152 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N THR A1152 " --> pdb=" O ARG A1196 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLU A1198 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR I 44 " --> pdb=" O ILE A1154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 143 through 147 removed outlier: 4.849A pdb=" N VAL A1446 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY G 59 " --> pdb=" O ILE A1448 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AB7, first strand: chain 'B' and resid 82 through 84 removed outlier: 5.890A pdb=" N SER B 113 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS B 160 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL B 115 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AB9, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC1, first strand: chain 'B' and resid 206 through 209 Processing sheet with id=AC2, first strand: chain 'B' and resid 215 through 218 removed outlier: 3.776A pdb=" N HIS B 227 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN B 246 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 490 through 491 Processing sheet with id=AC4, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC5, first strand: chain 'B' and resid 537 through 538 removed outlier: 4.165A pdb=" N CYS B 741 " --> pdb=" O PHE B 631 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 557 through 558 removed outlier: 5.372A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG B 572 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE B 619 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE B 574 " --> pdb=" O ILE B 619 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 794 through 796 removed outlier: 6.053A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 794 through 796 removed outlier: 6.053A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL B 952 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS L 60 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE L 58 " --> pdb=" O LEU B 954 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD1, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 3.543A pdb=" N VAL B1085 " --> pdb=" O GLU B1070 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA B 826 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 882 through 883 removed outlier: 7.192A pdb=" N LEU B 883 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.770A pdb=" N ILE B 911 " --> pdb=" O THR B 939 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N THR B 939 " --> pdb=" O ILE B 911 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AD5, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD6, first strand: chain 'C' and resid 6 through 12 removed outlier: 3.673A pdb=" N LYS C 6 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 22 " --> pdb=" O LYS C 6 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN C 8 " --> pdb=" O MET C 20 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLU C 18 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ALA C 12 " --> pdb=" O GLU C 16 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLU C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 119 through 122 removed outlier: 5.707A pdb=" N LYS C 120 " --> pdb=" O GLU C 99 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLU C 99 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 122 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN C 154 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS C 160 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY C 162 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU C 43 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 48 " --> pdb=" O PHE L 69 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ILE L 67 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AD9, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AE1, first strand: chain 'E' and resid 59 through 61 removed outlier: 3.608A pdb=" N ILE E 110 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY E 107 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE E 134 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE E 109 " --> pdb=" O PHE E 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.705A pdb=" N LYS E 151 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE E 198 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 5 through 13 removed outlier: 4.451A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 85 through 95 removed outlier: 5.200A pdb=" N VAL G 91 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASP G 102 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN G 93 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU G 106 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ASN G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA G 159 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY G 161 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N SER G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TYR G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR G 150 " --> pdb=" O TYR G 158 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER G 162 " --> pdb=" O LYS G 146 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS G 146 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.669A pdb=" N ALA G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU G 135 " --> pdb=" O SER G 132 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AE7, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AE8, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE9, first strand: chain 'U' and resid 255 through 260 Processing sheet with id=AF1, first strand: chain 'V' and resid 18 through 19 Processing sheet with id=AF2, first strand: chain 'V' and resid 80 through 86 removed outlier: 7.010A pdb=" N GLY V 56 " --> pdb=" O VAL V 84 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL V 86 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N PHE V 54 " --> pdb=" O VAL V 86 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU V 57 " --> pdb=" O GLN W 264 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER W 261 " --> pdb=" O GLU W 275 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'W' and resid 407 through 410 removed outlier: 6.542A pdb=" N PHE W 413 " --> pdb=" O ASP W 409 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU W 420 " --> pdb=" O TYR W 427 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LYS W 353 " --> pdb=" O VAL W 340 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL W 340 " --> pdb=" O LYS W 353 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'W' and resid 664 through 666 Processing sheet with id=AF5, first strand: chain 'W' and resid 675 through 676 Processing sheet with id=AF6, first strand: chain 'W' and resid 788 through 792 removed outlier: 6.755A pdb=" N ARG W 779 " --> pdb=" O LYS W 771 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N THR W 755 " --> pdb=" O GLU W 799 " (cutoff:3.500A) 1349 hydrogen bonds defined for protein. 3744 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 94 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 11.63 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9471 1.33 - 1.45: 7829 1.45 - 1.58: 21440 1.58 - 1.70: 210 1.70 - 1.82: 332 Bond restraints: 39282 Sorted by residual: bond pdb=" C CYS V 29 " pdb=" N PRO V 30 " ideal model delta sigma weight residual 1.335 1.433 -0.098 1.19e-02 7.06e+03 6.78e+01 bond pdb=" C LYS G 164 " pdb=" N GLU G 165 " ideal model delta sigma weight residual 1.332 1.224 0.109 1.40e-02 5.10e+03 6.01e+01 bond pdb=" CA ILE W 440 " pdb=" C ILE W 440 " ideal model delta sigma weight residual 1.521 1.432 0.089 1.21e-02 6.83e+03 5.38e+01 bond pdb=" N LEU D 53 " pdb=" CA LEU D 53 " ideal model delta sigma weight residual 1.459 1.372 0.087 1.20e-02 6.94e+03 5.28e+01 bond pdb=" C1' DT N 2 " pdb=" N1 DT N 2 " ideal model delta sigma weight residual 1.468 1.566 -0.098 1.40e-02 5.10e+03 4.90e+01 ... (remaining 39277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.61: 53247 6.61 - 13.23: 167 13.23 - 19.84: 43 19.84 - 26.46: 18 26.46 - 33.07: 5 Bond angle restraints: 53480 Sorted by residual: angle pdb=" N ALA A 310 " pdb=" CA ALA A 310 " pdb=" C ALA A 310 " ideal model delta sigma weight residual 110.55 82.03 28.52 1.35e+00 5.49e-01 4.46e+02 angle pdb=" N THR A1030 " pdb=" CA THR A1030 " pdb=" C THR A1030 " ideal model delta sigma weight residual 111.11 133.16 -22.05 1.20e+00 6.94e-01 3.38e+02 angle pdb=" N TYR A1368 " pdb=" CA TYR A1368 " pdb=" C TYR A1368 " ideal model delta sigma weight residual 111.82 132.71 -20.89 1.16e+00 7.43e-01 3.24e+02 angle pdb=" N LYS B 351 " pdb=" CA LYS B 351 " pdb=" C LYS B 351 " ideal model delta sigma weight residual 111.03 130.62 -19.59 1.11e+00 8.12e-01 3.12e+02 angle pdb=" N LEU D 53 " pdb=" CA LEU D 53 " pdb=" C LEU D 53 " ideal model delta sigma weight residual 111.11 130.93 -19.82 1.20e+00 6.94e-01 2.73e+02 ... (remaining 53475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 23159 35.30 - 70.59: 553 70.59 - 105.89: 24 105.89 - 141.19: 1 141.19 - 176.48: 5 Dihedral angle restraints: 23742 sinusoidal: 10573 harmonic: 13169 Sorted by residual: dihedral pdb=" C4' U P -5 " pdb=" C3' U P -5 " pdb=" C2' U P -5 " pdb=" C1' U P -5 " ideal model delta sinusoidal sigma weight residual 36.34 -42.41 78.76 1 3.10e+00 1.04e-01 8.04e+02 dihedral pdb=" C4' U P 0 " pdb=" C3' U P 0 " pdb=" C2' U P 0 " pdb=" C1' U P 0 " ideal model delta sinusoidal sigma weight residual 36.34 -40.71 77.05 1 3.10e+00 1.04e-01 7.75e+02 dihedral pdb=" O4' U P -5 " pdb=" C4' U P -5 " pdb=" C3' U P -5 " pdb=" C2' U P -5 " ideal model delta sinusoidal sigma weight residual -35.15 30.55 -65.70 1 4.00e+00 6.25e-02 3.53e+02 ... (remaining 23739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.291: 5904 0.291 - 0.582: 45 0.582 - 0.874: 11 0.874 - 1.165: 7 1.165 - 1.456: 3 Chirality restraints: 5970 Sorted by residual: chirality pdb=" CA THR A1441 " pdb=" N THR A1441 " pdb=" C THR A1441 " pdb=" CB THR A1441 " both_signs ideal model delta sigma weight residual False 2.53 1.07 1.46 2.00e-01 2.50e+01 5.30e+01 chirality pdb=" CA GLU U 198 " pdb=" N GLU U 198 " pdb=" C GLU U 198 " pdb=" CB GLU U 198 " both_signs ideal model delta sigma weight residual False 2.51 1.06 1.45 2.00e-01 2.50e+01 5.23e+01 chirality pdb=" CA ARG A 327 " pdb=" N ARG A 327 " pdb=" C ARG A 327 " pdb=" CB ARG A 327 " both_signs ideal model delta sigma weight residual False 2.51 1.32 1.19 2.00e-01 2.50e+01 3.52e+01 ... (remaining 5967 not shown) Planarity restraints: 6560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 47 " 0.130 5.00e-02 4.00e+02 2.06e-01 6.77e+01 pdb=" N PRO A 48 " -0.355 5.00e-02 4.00e+02 pdb=" CA PRO A 48 " 0.136 5.00e-02 4.00e+02 pdb=" CD PRO A 48 " 0.090 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 700 " -0.026 2.00e-02 2.50e+03 4.74e-02 3.36e+01 pdb=" CG HIS A 700 " 0.092 2.00e-02 2.50e+03 pdb=" ND1 HIS A 700 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 HIS A 700 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS A 700 " 0.028 2.00e-02 2.50e+03 pdb=" NE2 HIS A 700 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC T -6 " 0.049 2.00e-02 2.50e+03 3.22e-02 2.34e+01 pdb=" N1 DC T -6 " -0.080 2.00e-02 2.50e+03 pdb=" C2 DC T -6 " 0.020 2.00e-02 2.50e+03 pdb=" O2 DC T -6 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DC T -6 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC T -6 " 0.004 2.00e-02 2.50e+03 pdb=" N4 DC T -6 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DC T -6 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DC T -6 " -0.001 2.00e-02 2.50e+03 ... (remaining 6557 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 38 2.11 - 2.81: 10516 2.81 - 3.51: 47803 3.51 - 4.20: 85302 4.20 - 4.90: 146429 Nonbonded interactions: 290088 Sorted by model distance: nonbonded pdb=" O4 DT T -18 " pdb=" N1 DA N 19 " model vdw 1.414 2.496 nonbonded pdb=" NZ LYS A 790 " pdb=" OG1 THR I 67 " model vdw 1.429 3.120 nonbonded pdb=" CG2 THR A1082 " pdb=" CD LYS U 260 " model vdw 1.610 3.860 nonbonded pdb=" CE MET A 709 " pdb=" CG2 VAL A1091 " model vdw 1.624 3.880 nonbonded pdb=" CB ARG G 151 " pdb=" CZ PHE W 667 " model vdw 1.628 3.740 ... (remaining 290083 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 45.180 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 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 : 0.010 0.688 39316 Z= 0.458 Angle : 1.291 33.071 53513 Z= 0.806 Chirality : 0.085 1.456 5970 Planarity : 0.006 0.206 6560 Dihedral : 13.353 176.483 15228 Min Nonbonded Distance : 1.414 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.76 % Allowed : 11.84 % Favored : 87.40 % Rotamer: Outliers : 1.25 % Allowed : 2.03 % Favored : 96.72 % Cbeta Deviations : 1.57 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.05 % 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: -3.90 (0.11), residues: 4475 helix: -2.30 (0.11), residues: 1325 sheet: -1.90 (0.17), residues: 716 loop : -3.05 (0.11), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG V 73 TYR 0.029 0.002 TYR W 416 PHE 0.019 0.002 PHE G 70 TRP 0.024 0.002 TRP C 170 HIS 0.065 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.36 (39282) covalent geometry : angle 1.23804 / 0.80 (53480) hydrogen bonds : bond 0.17160 / 10.96 ( 1423) hydrogen bonds : angle 9.28099 / 6.49 ( 3928) metal coordination : bond 0.27860 / 17.26 ( 34) metal coordination : angle 14.73130 / 9.69 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8950 Ramachandran restraints generated. 4475 Oldfield, 0 Emsley, 4475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8950 Ramachandran restraints generated. 4475 Oldfield, 0 Emsley, 4475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 906 time to evaluate : 1.424 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 16 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7575 (tt0) REVERT: A 72 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7540 (mp0) REVERT: A 135 PHE cc_start: 0.8614 (t80) cc_final: 0.8171 (t80) REVERT: A 139 TRP cc_start: 0.8701 (t60) cc_final: 0.8434 (t60) REVERT: A 178 ASP cc_start: 0.7831 (t0) cc_final: 0.6618 (p0) REVERT: A 235 MET cc_start: 0.8383 (mtm) cc_final: 0.8176 (mtp) REVERT: A 262 ASP cc_start: 0.8077 (m-30) cc_final: 0.7603 (m-30) REVERT: A 295 GLN cc_start: 0.7766 (tt0) cc_final: 0.7537 (tm-30) REVERT: A 539 ASP cc_start: 0.8926 (p0) cc_final: 0.8565 (p0) REVERT: A 614 MET cc_start: 0.8464 (mmp) cc_final: 0.8204 (mmm) REVERT: A 637 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7365 (mm-30) REVERT: A 732 ARG cc_start: 0.8539 (ttt-90) cc_final: 0.8047 (ttp-170) REVERT: A 735 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8345 (tm-30) REVERT: A 782 ASP cc_start: 0.8233 (m-30) cc_final: 0.7617 (t0) REVERT: A 827 ASP cc_start: 0.7674 (t70) cc_final: 0.7425 (t70) REVERT: A 899 TYR cc_start: 0.7196 (t80) cc_final: 0.6522 (t80) REVERT: A 994 ASP cc_start: 0.7929 (m-30) cc_final: 0.7630 (t0) REVERT: A 1113 ILE cc_start: 0.8284 (pt) cc_final: 0.8042 (pt) REVERT: A 1286 TYR cc_start: 0.7169 (m-80) cc_final: 0.6550 (m-10) REVERT: A 1291 LYS cc_start: 0.8475 (mttp) cc_final: 0.8139 (mttm) REVERT: A 1318 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8236 (mp0) REVERT: A 1410 GLU cc_start: 0.8234 (mp0) cc_final: 0.7748 (pt0) REVERT: A 1420 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8490 (tt0) REVERT: A 1447 MET cc_start: 0.7577 (mmp) cc_final: 0.6771 (mmt) REVERT: B 156 VAL cc_start: 0.8267 (t) cc_final: 0.7962 (t) REVERT: B 190 MET cc_start: 0.8197 (pmm) cc_final: 0.7848 (mmt) REVERT: B 216 VAL cc_start: 0.9215 (t) cc_final: 0.8862 (p) REVERT: B 262 LYS cc_start: 0.6759 (mttp) cc_final: 0.6425 (mtpp) REVERT: B 524 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7781 (mp10) REVERT: B 702 MET cc_start: 0.8941 (tpp) cc_final: 0.8659 (tpt) REVERT: B 705 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8075 (tm-30) REVERT: B 792 MET cc_start: 0.7958 (mtm) cc_final: 0.7684 (mtp) REVERT: B 999 MET cc_start: 0.9051 (mmm) cc_final: 0.8757 (mmt) REVERT: B 1072 MET cc_start: 0.8353 (mtp) cc_final: 0.8110 (mtm) REVERT: B 1174 ASN cc_start: 0.7625 (t0) cc_final: 0.6586 (t0) REVERT: B 1192 TYR cc_start: 0.7607 (m-80) cc_final: 0.7262 (m-10) REVERT: C 75 ASP cc_start: 0.7809 (m-30) cc_final: 0.7535 (m-30) REVERT: C 77 GLU cc_start: 0.8531 (mt-10) cc_final: 0.7893 (tm-30) REVERT: C 80 LYS cc_start: 0.7816 (mtmm) cc_final: 0.7607 (ttmm) REVERT: C 148 ARG cc_start: 0.7377 (ttt180) cc_final: 0.7051 (ttt-90) REVERT: C 213 PRO cc_start: 0.8220 (Cg_endo) cc_final: 0.7820 (Cg_exo) REVERT: E 73 ASP cc_start: 0.8546 (p0) cc_final: 0.8202 (p0) REVERT: E 113 ASN cc_start: 0.8458 (m-40) cc_final: 0.8103 (m-40) REVERT: E 130 ILE cc_start: 0.8094 (mt) cc_final: 0.7722 (mm) REVERT: E 133 THR cc_start: 0.9025 (p) cc_final: 0.8773 (t) REVERT: F 104 ASN cc_start: 0.8164 (t0) cc_final: 0.7954 (t0) REVERT: F 108 LEU cc_start: 0.8856 (mp) cc_final: 0.8624 (mp) REVERT: F 114 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6669 (pm20) REVERT: F 151 LEU cc_start: 0.9186 (mt) cc_final: 0.8897 (mm) REVERT: H 36 ILE cc_start: 0.8618 (mt) cc_final: 0.8010 (tt) REVERT: H 46 MET cc_start: 0.9146 (mmm) cc_final: 0.8797 (mmm) REVERT: H 77 SER cc_start: 0.9107 (t) cc_final: 0.8605 (p) REVERT: H 105 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8289 (mt-10) REVERT: H 110 LYS cc_start: 0.7510 (mmtp) cc_final: 0.7052 (mmmt) REVERT: J 1 MET cc_start: 0.7577 (ttt) cc_final: 0.7226 (ttt) REVERT: J 27 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8267 (mp0) REVERT: J 54 ASP cc_start: 0.8025 (t70) cc_final: 0.7162 (p0) REVERT: K 76 GLN cc_start: 0.7668 (tt0) cc_final: 0.7437 (tt0) REVERT: K 111 ILE cc_start: 0.6818 (mt) cc_final: 0.6540 (mt) REVERT: U 221 MET cc_start: 0.7384 (mtm) cc_final: 0.6995 (mtp) REVERT: U 264 SER cc_start: 0.3283 (OUTLIER) cc_final: 0.3020 (m) REVERT: U 284 PHE cc_start: 0.1140 (OUTLIER) cc_final: -0.0225 (t80) REVERT: W 755 THR cc_start: 0.8796 (m) cc_final: 0.8361 (p) REVERT: W 771 LYS cc_start: 0.7796 (tttt) cc_final: 0.7428 (tppt) REVERT: W 793 CYS cc_start: 0.4888 (OUTLIER) cc_final: 0.4684 (p) outliers start: 50 outliers final: 6 residues processed: 947 average time/residue: 0.2782 time to fit residues: 410.4160 Evaluate side-chains 470 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 460 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain U residue 147 LYS Chi-restraints excluded: chain U residue 194 ILE Chi-restraints excluded: chain U residue 264 SER Chi-restraints excluded: chain U residue 284 PHE Chi-restraints excluded: chain W residue 672 ARG Chi-restraints excluded: chain W residue 793 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 6.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 170 ASN A 312 GLN A 398 ASN ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 ASN A 961 ASN A1087 HIS A1190 GLN A1435 GLN B 63 GLN B 97 HIS B 157 HIS B 356 HIS B 531 ASN B 651 HIS B 887 HIS ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN C 150 HIS C 252 GLN D 38 GLN D 46 HIS E 4 ASN E 100 GLN E 120 ASN E 145 HIS F 119 GLN G 125 ASN H 44 ASN I 23 GLN I 31 ASN K 29 ASN L 55 HIS U 184 ASN U 187 ASN W 264 GLN W 339 GLN W 434 ASN ** W 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.193247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.153529 restraints weight = 58361.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.144692 restraints weight = 115482.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.141887 restraints weight = 91797.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.140771 restraints weight = 88192.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.141346 restraints weight = 66619.787| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 39316 Z= 0.278 Angle : 0.888 25.153 53513 Z= 0.450 Chirality : 0.060 1.619 5970 Planarity : 0.006 0.101 6560 Dihedral : 15.521 178.863 6157 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.08 % Favored : 92.60 % Rotamer: Outliers : 2.18 % Allowed : 7.78 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.05 % 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: -2.77 (0.11), residues: 4475 helix: -0.84 (0.13), residues: 1369 sheet: -1.53 (0.18), residues: 737 loop : -2.62 (0.12), residues: 2369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 151 TYR 0.019 0.002 TYR H 94 PHE 0.039 0.003 PHE W 667 TRP 0.027 0.002 TRP W 227 HIS 0.010 0.002 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.28 (39282) covalent geometry : angle 0.87423 / 0.45 (53480) hydrogen bonds : bond 0.06904 / 4.46 ( 1423) hydrogen bonds : angle 5.99110 / 4.20 ( 3928) metal coordination : bond 0.01702 / 0.97 ( 34) metal coordination : angle 6.29951 / 4.11 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8950 Ramachandran restraints generated. 4475 Oldfield, 0 Emsley, 4475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8950 Ramachandran restraints generated. 4475 Oldfield, 0 Emsley, 4475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 494 time to evaluate : 1.426 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 132 LYS cc_start: 0.8020 (mttp) cc_final: 0.7693 (mtmt) REVERT: A 178 ASP cc_start: 0.7848 (t0) cc_final: 0.6603 (p0) REVERT: A 201 LYS cc_start: 0.7176 (ptmt) cc_final: 0.6722 (mttt) REVERT: A 530 CYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8130 (m) REVERT: A 614 MET cc_start: 0.8488 (mmp) cc_final: 0.8047 (mmm) REVERT: A 712 ARG cc_start: 0.6630 (mtt180) cc_final: 0.6227 (mmt-90) REVERT: A 721 ARG cc_start: 0.7459 (ttp-110) cc_final: 0.7250 (ttp-110) REVERT: A 735 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: A 827 ASP cc_start: 0.8322 (t70) cc_final: 0.8111 (t70) REVERT: A 899 TYR cc_start: 0.7325 (t80) cc_final: 0.7063 (t80) REVERT: A 1153 GLU cc_start: 0.5394 (mt-10) cc_final: 0.4970 (pt0) REVERT: A 1229 MET cc_start: 0.8282 (ttm) cc_final: 0.7800 (tmm) REVERT: A 1286 TYR cc_start: 0.7391 (m-80) cc_final: 0.6982 (m-80) REVERT: A 1291 LYS cc_start: 0.8384 (mttp) cc_final: 0.8040 (mttm) REVERT: B 235 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7817 (pt) REVERT: B 466 MET cc_start: 0.6006 (mpt) cc_final: 0.5738 (mpt) REVERT: B 613 ARG cc_start: 0.8346 (mmm160) cc_final: 0.7902 (tpp-160) REVERT: B 702 MET cc_start: 0.8830 (tpp) cc_final: 0.8417 (tpt) REVERT: B 792 MET cc_start: 0.7858 (mtm) cc_final: 0.7602 (mtp) REVERT: B 1072 MET cc_start: 0.8528 (mtp) cc_final: 0.8185 (mtm) REVERT: B 1082 MET cc_start: 0.8656 (mmm) cc_final: 0.8403 (mtp) REVERT: B 1174 ASN cc_start: 0.7805 (t0) cc_final: 0.7381 (t0) REVERT: B 1192 TYR cc_start: 0.7726 (m-80) cc_final: 0.7245 (m-10) REVERT: E 5 ASN cc_start: 0.8014 (m-40) cc_final: 0.7638 (m-40) REVERT: E 62 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7955 (m-40) REVERT: E 73 ASP cc_start: 0.7820 (p0) cc_final: 0.7519 (p0) REVERT: E 122 MET cc_start: 0.5183 (OUTLIER) cc_final: 0.4556 (mmt) REVERT: E 130 ILE cc_start: 0.8269 (mt) cc_final: 0.8067 (mm) REVERT: F 104 ASN cc_start: 0.8166 (t0) cc_final: 0.7763 (t0) REVERT: G 22 MET cc_start: 0.6510 (pmm) cc_final: 0.5802 (pmm) REVERT: H 36 ILE cc_start: 0.8573 (mt) cc_final: 0.8274 (tt) REVERT: H 77 SER cc_start: 0.9140 (t) cc_final: 0.8704 (p) REVERT: H 125 GLU cc_start: 0.6743 (mt-10) cc_final: 0.6430 (mt-10) REVERT: I 34 TYR cc_start: 0.7758 (t80) cc_final: 0.7355 (t80) REVERT: J 48 MET cc_start: 0.8155 (tpp) cc_final: 0.7850 (tpp) REVERT: J 62 TYR cc_start: 0.8982 (m-80) cc_final: 0.8040 (m-80) REVERT: K 108 GLU cc_start: 0.7744 (tp30) cc_final: 0.7456 (tp30) REVERT: L 38 HIS cc_start: 0.7415 (t-170) cc_final: 0.7048 (t-170) REVERT: U 157 LYS cc_start: 0.6506 (pttt) cc_final: 0.6228 (tppt) REVERT: U 218 LYS cc_start: 0.7659 (ptpp) cc_final: 0.7426 (ptpt) REVERT: U 284 PHE cc_start: 0.1844 (OUTLIER) cc_final: -0.0283 (t80) REVERT: W 754 LYS cc_start: 0.7235 (mmtm) cc_final: 0.7033 (tptp) REVERT: W 777 ARG cc_start: 0.4646 (ptp-170) cc_final: 0.3449 (ptt180) REVERT: W 781 GLU cc_start: 0.7737 (tt0) cc_final: 0.7168 (mt-10) outliers start: 87 outliers final: 52 residues processed: 554 average time/residue: 0.2347 time to fit residues: 211.1236 Evaluate side-chains 453 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 395 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 979 LYS Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1111 LYS Chi-restraints excluded: chain A residue 1136 ILE Chi-restraints excluded: chain A residue 1144 THR Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1424 CYS Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 526 CYS Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1032 SER Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain U residue 194 ILE Chi-restraints excluded: chain U residue 284 PHE Chi-restraints excluded: chain W residue 304 VAL Chi-restraints excluded: chain W residue 313 VAL Chi-restraints excluded: chain W residue 672 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 158 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 447 optimal weight: 40.0000 chunk 88 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 444 optimal weight: 30.0000 chunk 67 optimal weight: 3.9990 chunk 315 optimal weight: 6.9990 chunk 344 optimal weight: 20.0000 chunk 173 optimal weight: 1.9990 chunk 435 optimal weight: 40.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 HIS ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 ASN B 157 HIS B 438 ASN B 932 HIS C 252 GLN D 17 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.189873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.149308 restraints weight = 58051.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.139429 restraints weight = 112497.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.134701 restraints weight = 93583.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.133950 restraints weight = 91121.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.134467 restraints weight = 67346.408| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 39316 Z= 0.248 Angle : 0.769 19.886 53513 Z= 0.394 Chirality : 0.054 1.631 5970 Planarity : 0.005 0.078 6560 Dihedral : 15.294 172.805 6149 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.16 % Favored : 91.62 % Rotamer: Outliers : 2.60 % Allowed : 9.39 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.05 % 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: -2.14 (0.12), residues: 4475 helix: -0.10 (0.14), residues: 1378 sheet: -1.34 (0.18), residues: 736 loop : -2.32 (0.12), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 79 TYR 0.020 0.002 TYR J 62 PHE 0.031 0.002 PHE A1222 TRP 0.020 0.002 TRP B 300 HIS 0.007 0.001 HIS B1025 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.25 (39282) covalent geometry : angle 0.76093 / 0.39 (53480) hydrogen bonds : bond 0.06511 / 4.19 ( 1423) hydrogen bonds : angle 5.53102 / 3.87 ( 3928) metal coordination : bond 0.00722 / 0.44 ( 34) metal coordination : angle 4.65662 / 2.97 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8950 Ramachandran restraints generated. 4475 Oldfield, 0 Emsley, 4475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8950 Ramachandran restraints generated. 4475 Oldfield, 0 Emsley, 4475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 417 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.8447 (mp) cc_final: 0.8160 (mt) REVERT: A 88 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.7242 (ttmm) REVERT: A 178 ASP cc_start: 0.7980 (t0) cc_final: 0.7767 (t0) REVERT: A 201 LYS cc_start: 0.7459 (ptmt) cc_final: 0.6783 (mttp) REVERT: A 614 MET cc_start: 0.8594 (mmp) cc_final: 0.8130 (mmm) REVERT: A 735 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: A 741 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8890 (pp) REVERT: A 899 TYR cc_start: 0.7452 (t80) cc_final: 0.7179 (t80) REVERT: A 1076 GLU cc_start: 0.8687 (tm-30) cc_final: 0.7997 (tm-30) REVERT: A 1153 GLU cc_start: 0.6253 (mt-10) cc_final: 0.5739 (pt0) REVERT: A 1229 MET cc_start: 0.8330 (ttm) cc_final: 0.7801 (tmm) REVERT: A 1286 TYR cc_start: 0.7213 (m-80) cc_final: 0.6961 (m-80) REVERT: A 1291 LYS cc_start: 0.8257 (mttp) cc_final: 0.7978 (mttm) REVERT: A 1378 MET cc_start: 0.8050 (mtp) cc_final: 0.7723 (mtp) REVERT: B 466 MET cc_start: 0.6000 (mpt) cc_final: 0.5752 (mpt) REVERT: B 613 ARG cc_start: 0.8158 (mmm160) cc_final: 0.7640 (tpp-160) REVERT: B 702 MET cc_start: 0.8924 (tpp) cc_final: 0.8577 (tpt) REVERT: B 1072 MET cc_start: 0.8472 (mtp) cc_final: 0.8146 (mtm) REVERT: B 1174 ASN cc_start: 0.7892 (t0) cc_final: 0.7446 (t0) REVERT: E 73 ASP cc_start: 0.7915 (p0) cc_final: 0.7591 (p0) REVERT: F 104 ASN cc_start: 0.8254 (t0) cc_final: 0.7791 (t0) REVERT: G 22 MET cc_start: 0.6464 (pmm) cc_final: 0.5540 (pmm) REVERT: H 36 ILE cc_start: 0.8713 (mt) cc_final: 0.8435 (tt) REVERT: J 48 MET cc_start: 0.8547 (tpp) cc_final: 0.8102 (tpp) REVERT: J 54 ASP cc_start: 0.8017 (t0) cc_final: 0.7438 (t0) REVERT: J 62 TYR cc_start: 0.9096 (m-80) cc_final: 0.8457 (m-80) REVERT: U 284 PHE cc_start: 0.1361 (OUTLIER) cc_final: -0.0521 (t80) REVERT: W 269 LYS cc_start: 0.7583 (mmmt) cc_final: 0.7305 (mmtm) REVERT: W 754 LYS cc_start: 0.7580 (mmtm) cc_final: 0.7198 (tptp) REVERT: W 781 GLU cc_start: 0.7839 (tt0) cc_final: 0.7569 (mt-10) outliers start: 104 outliers final: 63 residues processed: 488 average time/residue: 0.2335 time to fit residues: 186.6426 Evaluate side-chains 444 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 377 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 971 GLN Chi-restraints excluded: chain A residue 1085 THR Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1136 ILE Chi-restraints excluded: chain A residue 1144 THR Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 526 CYS Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1032 SER Chi-restraints excluded: chain B residue 1036 SER Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain U residue 194 ILE Chi-restraints excluded: chain U residue 284 PHE Chi-restraints excluded: chain W residue 313 VAL Chi-restraints excluded: chain W residue 672 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 294 optimal weight: 30.0000 chunk 107 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 367 optimal weight: 6.9990 chunk 325 optimal weight: 9.9990 chunk 424 optimal weight: 50.0000 chunk 139 optimal weight: 4.9990 chunk 5 optimal weight: 0.0980 chunk 106 optimal weight: 3.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 GLN B 157 HIS B 887 HIS B 996 HIS E 113 ASN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.190798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.135345 restraints weight = 57809.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.128562 restraints weight = 56575.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.128524 restraints weight = 62586.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.128923 restraints weight = 57409.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.129170 restraints weight = 52857.508| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 39316 Z= 0.165 Angle : 0.665 15.644 53513 Z= 0.342 Chirality : 0.047 0.568 5970 Planarity : 0.005 0.067 6560 Dihedral : 15.127 171.621 6149 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.85 % Favored : 93.92 % Rotamer: Outliers : 2.28 % Allowed : 10.26 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.05 % 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: -1.69 (0.12), residues: 4475 helix: 0.40 (0.14), residues: 1377 sheet: -1.13 (0.18), residues: 727 loop : -2.12 (0.12), residues: 2371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 93 TYR 0.021 0.001 TYR A 544 PHE 0.020 0.002 PHE K 71 TRP 0.014 0.001 TRP B 300 HIS 0.008 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (39282) covalent geometry : angle 0.65744 / 0.34 (53480) hydrogen bonds : bond 0.05443 / 3.49 ( 1423) hydrogen bonds : angle 5.12432 / 3.58 ( 3928) metal coordination : bond 0.00603 / 0.38 ( 34) metal coordination : angle 4.01115 / 2.60 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8950 Ramachandran restraints generated. 4475 Oldfield, 0 Emsley, 4475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8950 Ramachandran restraints generated. 4475 Oldfield, 0 Emsley, 4475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 412 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.8481 (mp) cc_final: 0.8145 (mt) REVERT: A 178 ASP cc_start: 0.7971 (t0) cc_final: 0.7755 (t0) REVERT: A 201 LYS cc_start: 0.7156 (ptmt) cc_final: 0.6567 (mttt) REVERT: A 614 MET cc_start: 0.8651 (mmp) cc_final: 0.8403 (mmm) REVERT: A 691 VAL cc_start: 0.8448 (t) cc_final: 0.8192 (t) REVERT: A 718 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6531 (tm-30) REVERT: A 735 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: A 899 TYR cc_start: 0.7523 (t80) cc_final: 0.7248 (t80) REVERT: A 906 LYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6763 (ptmm) REVERT: A 1076 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8057 (tm-30) REVERT: A 1153 GLU cc_start: 0.6587 (mt-10) cc_final: 0.6110 (pt0) REVERT: A 1286 TYR cc_start: 0.7228 (m-80) cc_final: 0.7027 (m-80) REVERT: A 1291 LYS cc_start: 0.8352 (mttp) cc_final: 0.8019 (mttm) REVERT: B 337 ARG cc_start: 0.5963 (mtm-85) cc_final: 0.5552 (mtm110) REVERT: B 466 MET cc_start: 0.5977 (mpt) cc_final: 0.5713 (mpt) REVERT: B 613 ARG cc_start: 0.8254 (mmm160) cc_final: 0.7732 (tpp-160) REVERT: B 702 MET cc_start: 0.8852 (tpp) cc_final: 0.8525 (tpt) REVERT: B 1009 ASP cc_start: 0.8939 (OUTLIER) cc_final: 0.8601 (t0) REVERT: B 1072 MET cc_start: 0.8237 (mtp) cc_final: 0.7990 (mtm) REVERT: B 1174 ASN cc_start: 0.7754 (t0) cc_final: 0.7340 (t0) REVERT: B 1179 GLN cc_start: 0.8250 (mt0) cc_final: 0.7749 (tt0) REVERT: E 73 ASP cc_start: 0.7983 (p0) cc_final: 0.7656 (p0) REVERT: F 104 ASN cc_start: 0.8258 (t0) cc_final: 0.7788 (t0) REVERT: G 22 MET cc_start: 0.6547 (pmm) cc_final: 0.5512 (pmm) REVERT: H 36 ILE cc_start: 0.8688 (mt) cc_final: 0.8428 (tt) REVERT: H 44 ASN cc_start: 0.7490 (m-40) cc_final: 0.7185 (m-40) REVERT: J 54 ASP cc_start: 0.7927 (t0) cc_final: 0.7442 (t0) REVERT: J 62 TYR cc_start: 0.9061 (m-80) cc_final: 0.8500 (m-80) REVERT: U 221 MET cc_start: 0.6253 (mtt) cc_final: 0.5917 (mmt) REVERT: U 284 PHE cc_start: 0.1184 (OUTLIER) cc_final: -0.0785 (t80) REVERT: W 269 LYS cc_start: 0.7772 (mmmt) cc_final: 0.7513 (mmtm) REVERT: W 754 LYS cc_start: 0.7349 (mmtm) cc_final: 0.7028 (mmtt) REVERT: W 781 GLU cc_start: 0.7833 (tt0) cc_final: 0.7559 (mt-10) outliers start: 91 outliers final: 65 residues processed: 475 average time/residue: 0.2251 time to fit residues: 175.5062 Evaluate side-chains 443 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 374 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 971 GLN Chi-restraints excluded: chain A residue 1085 THR Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1111 LYS Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1136 ILE Chi-restraints excluded: chain A residue 1144 THR Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1032 SER Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain U residue 194 ILE Chi-restraints excluded: chain U residue 284 PHE Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 313 VAL Chi-restraints excluded: chain W residue 672 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 320 optimal weight: 7.9990 chunk 224 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 399 optimal weight: 50.0000 chunk 309 optimal weight: 9.9990 chunk 290 optimal weight: 20.0000 chunk 353 optimal weight: 0.0030 chunk 24 optimal weight: 1.9990 chunk 288 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 GLN ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 ASN B 157 HIS F 119 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.188861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.150198 restraints weight = 57884.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.142316 restraints weight = 100596.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.138930 restraints weight = 100933.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138607 restraints weight = 90971.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.137556 restraints weight = 70520.239| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 39316 Z= 0.197 Angle : 0.676 15.739 53513 Z= 0.348 Chirality : 0.046 0.317 5970 Planarity : 0.005 0.065 6560 Dihedral : 15.033 171.021 6149 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.06 % Favored : 92.72 % Rotamer: Outliers : 2.63 % Allowed : 10.86 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.05 % 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: -1.54 (0.12), residues: 4475 helix: 0.53 (0.14), residues: 1391 sheet: -1.10 (0.18), residues: 725 loop : -2.02 (0.12), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG W 759 TYR 0.020 0.002 TYR J 62 PHE 0.020 0.002 PHE K 71 TRP 0.017 0.002 TRP B 579 HIS 0.008 0.001 HIS L 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (39282) covalent geometry : angle 0.66906 / 0.35 (53480) hydrogen bonds : bond 0.05685 / 3.66 ( 1423) hydrogen bonds : angle 4.96078 / 3.47 ( 3928) metal coordination : bond 0.00567 / 0.37 ( 34) metal coordination : angle 3.93248 / 2.54 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8950 Ramachandran restraints generated. 4475 Oldfield, 0 Emsley, 4475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8950 Ramachandran restraints generated. 4475 Oldfield, 0 Emsley, 4475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 397 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.8792 (ptmm) cc_final: 0.8450 (ptmm) REVERT: A 201 LYS cc_start: 0.7556 (ptmt) cc_final: 0.6914 (mttp) REVERT: A 337 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8997 (mp) REVERT: A 614 MET cc_start: 0.8813 (mmp) cc_final: 0.8582 (mmm) REVERT: A 718 GLU cc_start: 0.6712 (tm-30) cc_final: 0.6014 (tm-30) REVERT: A 735 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: A 741 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8963 (pp) REVERT: A 906 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6811 (ptmm) REVERT: A 1076 GLU cc_start: 0.8547 (tm-30) cc_final: 0.7964 (tm-30) REVERT: A 1153 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6461 (pt0) REVERT: A 1291 LYS cc_start: 0.8251 (mttp) cc_final: 0.7983 (mttm) REVERT: B 702 MET cc_start: 0.8833 (tpp) cc_final: 0.8468 (tpt) REVERT: B 1174 ASN cc_start: 0.7979 (t0) cc_final: 0.7284 (t0) REVERT: B 1179 GLN cc_start: 0.8264 (mt0) cc_final: 0.7740 (tt0) REVERT: E 62 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7853 (m-40) REVERT: E 73 ASP cc_start: 0.7866 (p0) cc_final: 0.7529 (p0) REVERT: F 104 ASN cc_start: 0.8296 (t0) cc_final: 0.7832 (t0) REVERT: H 44 ASN cc_start: 0.7588 (m-40) cc_final: 0.7238 (m-40) REVERT: J 54 ASP cc_start: 0.7962 (t0) cc_final: 0.7578 (t0) REVERT: J 57 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7139 (mm-30) REVERT: J 62 TYR cc_start: 0.9087 (m-80) cc_final: 0.8800 (m-80) REVERT: U 229 LEU cc_start: 0.6736 (tp) cc_final: 0.6497 (tp) REVERT: W 774 ASN cc_start: 0.6448 (m-40) cc_final: 0.6124 (m-40) REVERT: W 781 GLU cc_start: 0.7928 (tt0) cc_final: 0.7702 (mt-10) outliers start: 105 outliers final: 80 residues processed: 471 average time/residue: 0.2319 time to fit residues: 179.2574 Evaluate side-chains 453 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 368 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 971 GLN Chi-restraints excluded: chain A residue 979 LYS Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1085 THR Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1111 LYS Chi-restraints excluded: chain A residue 1144 THR Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 526 CYS Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1032 SER Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain U residue 194 ILE Chi-restraints excluded: chain U residue 204 LEU Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 313 VAL Chi-restraints excluded: chain W residue 672 ARG Chi-restraints excluded: chain W residue 782 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 451 optimal weight: 50.0000 chunk 82 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 chunk 354 optimal weight: 0.5980 chunk 191 optimal weight: 6.9990 chunk 241 optimal weight: 1.9990 chunk 283 optimal weight: 4.9990 chunk 410 optimal weight: 0.0670 chunk 173 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 ASN A 312 GLN ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS B 292 HIS B 761 HIS B 887 HIS ** B1174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 ASN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 784 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.192440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.143301 restraints weight = 58651.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.132680 restraints weight = 81805.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.129367 restraints weight = 72217.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.129794 restraints weight = 65198.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.129791 restraints weight = 56176.374| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39316 Z= 0.119 Angle : 0.602 16.293 53513 Z= 0.311 Chirality : 0.044 0.303 5970 Planarity : 0.004 0.067 6560 Dihedral : 14.902 171.178 6143 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.69 % Favored : 95.08 % Rotamer: Outliers : 1.80 % Allowed : 11.96 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.05 % 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: -1.16 (0.13), residues: 4475 helix: 0.89 (0.15), residues: 1389 sheet: -0.84 (0.18), residues: 730 loop : -1.83 (0.12), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 93 TYR 0.014 0.001 TYR A 899 PHE 0.018 0.001 PHE K 71 TRP 0.012 0.001 TRP A 956 HIS 0.007 0.001 HIS L 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (39282) covalent geometry : angle 0.59596 / 0.31 (53480) hydrogen bonds : bond 0.04608 / 2.94 ( 1423) hydrogen bonds : angle 4.68987 / 3.29 ( 3928) metal coordination : bond 0.00490 / 0.30 ( 34) metal coordination : angle 3.58289 / 2.24 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8950 Ramachandran restraints generated. 4475 Oldfield, 0 Emsley, 4475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8950 Ramachandran restraints generated. 4475 Oldfield, 0 Emsley, 4475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 396 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7125 (ptmt) cc_final: 0.6526 (mttt) REVERT: A 539 ASP cc_start: 0.8654 (p0) cc_final: 0.8438 (p0) REVERT: A 718 GLU cc_start: 0.6579 (tm-30) cc_final: 0.5888 (tm-30) REVERT: A 735 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7796 (tm-30) REVERT: A 741 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8999 (pp) REVERT: A 742 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8491 (m110) REVERT: A 906 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6832 (ptmm) REVERT: A 1014 GLN cc_start: 0.8272 (tp40) cc_final: 0.7930 (tm-30) REVERT: A 1076 GLU cc_start: 0.8455 (tm-30) cc_final: 0.7858 (tm-30) REVERT: A 1153 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6492 (pt0) REVERT: A 1291 LYS cc_start: 0.8434 (mttp) cc_final: 0.8080 (mttm) REVERT: B 13 THR cc_start: 0.7079 (p) cc_final: 0.6786 (t) REVERT: B 702 MET cc_start: 0.8762 (tpp) cc_final: 0.8436 (tpt) REVERT: B 766 ARG cc_start: 0.8720 (mmt180) cc_final: 0.8408 (mmt180) REVERT: B 1009 ASP cc_start: 0.9065 (OUTLIER) cc_final: 0.8738 (t0) REVERT: C 20 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8697 (ttm) REVERT: E 21 MET cc_start: 0.8791 (ttp) cc_final: 0.8500 (ptm) REVERT: E 62 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7812 (m-40) REVERT: E 73 ASP cc_start: 0.8203 (p0) cc_final: 0.7892 (p0) REVERT: F 90 ARG cc_start: 0.8282 (ttp80) cc_final: 0.8009 (ttt90) REVERT: F 104 ASN cc_start: 0.8303 (t0) cc_final: 0.7813 (t0) REVERT: H 44 ASN cc_start: 0.7607 (m-40) cc_final: 0.7221 (m110) REVERT: J 54 ASP cc_start: 0.7857 (t0) cc_final: 0.7519 (t0) REVERT: J 62 TYR cc_start: 0.9108 (m-80) cc_final: 0.8757 (m-80) REVERT: U 157 LYS cc_start: 0.6995 (tppt) cc_final: 0.6273 (pttm) REVERT: W 772 GLU cc_start: 0.7853 (tm-30) cc_final: 0.6742 (tm-30) REVERT: W 774 ASN cc_start: 0.6036 (m-40) cc_final: 0.5271 (m-40) outliers start: 72 outliers final: 45 residues processed: 449 average time/residue: 0.2235 time to fit residues: 166.6339 Evaluate side-chains 417 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 365 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 1085 THR Chi-restraints excluded: chain A residue 1144 THR Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain U residue 194 ILE Chi-restraints excluded: chain W residue 672 ARG Chi-restraints excluded: chain W residue 752 LEU Chi-restraints excluded: chain W residue 784 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 274 optimal weight: 2.9990 chunk 371 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 334 optimal weight: 0.0670 chunk 34 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 HIS A 312 GLN ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS B 350 GLN ** B1174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.192321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.144599 restraints weight = 58457.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.135780 restraints weight = 100663.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.130526 restraints weight = 70476.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.130152 restraints weight = 71372.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.131000 restraints weight = 57389.924| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39316 Z= 0.117 Angle : 0.595 16.440 53513 Z= 0.305 Chirality : 0.043 0.295 5970 Planarity : 0.004 0.064 6560 Dihedral : 14.836 171.258 6143 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.30 % Favored : 94.50 % Rotamer: Outliers : 2.00 % Allowed : 12.19 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.05 % 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: -0.97 (0.13), residues: 4475 helix: 1.03 (0.15), residues: 1388 sheet: -0.75 (0.19), residues: 719 loop : -1.68 (0.12), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 19 TYR 0.013 0.001 TYR J 43 PHE 0.018 0.001 PHE B 435 TRP 0.010 0.001 TRP A 956 HIS 0.009 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (39282) covalent geometry : angle 0.58952 / 0.30 (53480) hydrogen bonds : bond 0.04429 / 2.82 ( 1423) hydrogen bonds : angle 4.56848 / 3.21 ( 3928) metal coordination : bond 0.00469 / 0.28 ( 34) metal coordination : angle 3.24282 / 2.01 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8950 Ramachandran restraints generated. 4475 Oldfield, 0 Emsley, 4475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8950 Ramachandran restraints generated. 4475 Oldfield, 0 Emsley, 4475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 379 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8765 (mttt) cc_final: 0.8399 (mttm) REVERT: A 201 LYS cc_start: 0.7098 (ptmt) cc_final: 0.6540 (mttt) REVERT: A 337 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8872 (mp) REVERT: A 539 ASP cc_start: 0.8676 (p0) cc_final: 0.8460 (p0) REVERT: A 718 GLU cc_start: 0.6525 (tm-30) cc_final: 0.5836 (tm-30) REVERT: A 735 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7909 (tm-30) REVERT: A 741 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8998 (pp) REVERT: A 742 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8447 (m-40) REVERT: A 906 LYS cc_start: 0.6971 (OUTLIER) cc_final: 0.6550 (ptmm) REVERT: A 1014 GLN cc_start: 0.8285 (tp40) cc_final: 0.7945 (tm-30) REVERT: A 1153 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6505 (pt0) REVERT: A 1204 MET cc_start: 0.8286 (tpp) cc_final: 0.7244 (tmm) REVERT: A 1229 MET cc_start: 0.8140 (ttm) cc_final: 0.7432 (tmm) REVERT: A 1291 LYS cc_start: 0.8464 (mttp) cc_final: 0.8108 (mttm) REVERT: A 1439 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.6929 (ppp) REVERT: B 13 THR cc_start: 0.7479 (p) cc_final: 0.7193 (t) REVERT: B 702 MET cc_start: 0.8758 (tpp) cc_final: 0.8444 (tpt) REVERT: B 904 ARG cc_start: 0.8431 (ttt90) cc_final: 0.8169 (ttt90) REVERT: B 1009 ASP cc_start: 0.9034 (OUTLIER) cc_final: 0.8759 (t0) REVERT: C 20 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8616 (ttm) REVERT: E 21 MET cc_start: 0.8787 (ttp) cc_final: 0.8339 (ptm) REVERT: E 73 ASP cc_start: 0.8188 (p0) cc_final: 0.7889 (p0) REVERT: F 90 ARG cc_start: 0.8266 (ttp80) cc_final: 0.7943 (ttt90) REVERT: F 104 ASN cc_start: 0.8294 (t0) cc_final: 0.7793 (t0) REVERT: G 22 MET cc_start: 0.6340 (pmm) cc_final: 0.5227 (pmm) REVERT: H 44 ASN cc_start: 0.7719 (m-40) cc_final: 0.7365 (m110) REVERT: I 28 SER cc_start: 0.8092 (t) cc_final: 0.7797 (p) REVERT: J 57 GLU cc_start: 0.7399 (mm-30) cc_final: 0.6957 (mm-30) REVERT: J 62 TYR cc_start: 0.9134 (m-80) cc_final: 0.8808 (m-80) REVERT: U 157 LYS cc_start: 0.6912 (tppt) cc_final: 0.6223 (pttm) REVERT: U 175 LEU cc_start: 0.6928 (pp) cc_final: 0.6021 (mm) REVERT: W 772 GLU cc_start: 0.7796 (tm-30) cc_final: 0.6617 (tm-30) REVERT: W 774 ASN cc_start: 0.5937 (m-40) cc_final: 0.5464 (m-40) outliers start: 80 outliers final: 61 residues processed: 437 average time/residue: 0.2255 time to fit residues: 162.1116 Evaluate side-chains 432 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 363 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 300 HIS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 1085 THR Chi-restraints excluded: chain A residue 1144 THR Chi-restraints excluded: chain A residue 1432 MET Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain U residue 194 ILE Chi-restraints excluded: chain U residue 204 LEU Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 313 VAL Chi-restraints excluded: chain W residue 672 ARG Chi-restraints excluded: chain W residue 752 LEU Chi-restraints excluded: chain W residue 782 LEU Chi-restraints excluded: chain W residue 784 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 274 optimal weight: 2.9990 chunk 41 optimal weight: 0.0270 chunk 98 optimal weight: 5.9990 chunk 87 optimal weight: 0.2980 chunk 409 optimal weight: 9.9990 chunk 157 optimal weight: 0.9990 chunk 371 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 180 optimal weight: 0.9980 chunk 291 optimal weight: 30.0000 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS B 350 GLN B 887 HIS ** B1174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 784 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.192426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.144979 restraints weight = 57882.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.133304 restraints weight = 89922.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.130292 restraints weight = 66732.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.129247 restraints weight = 62869.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.129949 restraints weight = 55285.126| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 39316 Z= 0.112 Angle : 0.579 14.984 53513 Z= 0.298 Chirality : 0.043 0.295 5970 Planarity : 0.004 0.062 6560 Dihedral : 14.788 171.374 6143 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.03 % Favored : 94.79 % Rotamer: Outliers : 1.73 % Allowed : 12.64 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.05 % 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: -0.82 (0.13), residues: 4475 helix: 1.15 (0.15), residues: 1380 sheet: -0.63 (0.19), residues: 717 loop : -1.59 (0.13), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 19 TYR 0.012 0.001 TYR J 43 PHE 0.019 0.001 PHE A 299 TRP 0.009 0.001 TRP A 956 HIS 0.008 0.001 HIS L 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (39282) covalent geometry : angle 0.57505 / 0.30 (53480) hydrogen bonds : bond 0.04255 / 2.71 ( 1423) hydrogen bonds : angle 4.47145 / 3.15 ( 3928) metal coordination : bond 0.00412 / 0.25 ( 34) metal coordination : angle 2.76313 / 1.75 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8950 Ramachandran restraints generated. 4475 Oldfield, 0 Emsley, 4475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8950 Ramachandran restraints generated. 4475 Oldfield, 0 Emsley, 4475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 385 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8763 (mttt) cc_final: 0.8408 (mttm) REVERT: A 178 ASP cc_start: 0.7838 (t0) cc_final: 0.6634 (p0) REVERT: A 201 LYS cc_start: 0.7109 (ptmt) cc_final: 0.6512 (mttt) REVERT: A 337 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8787 (mp) REVERT: A 539 ASP cc_start: 0.8671 (p0) cc_final: 0.8451 (p0) REVERT: A 718 GLU cc_start: 0.6437 (tm-30) cc_final: 0.5756 (tm-30) REVERT: A 735 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8070 (tm-30) REVERT: A 736 MET cc_start: 0.7976 (ttm) cc_final: 0.7654 (ttp) REVERT: A 741 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8995 (pp) REVERT: A 742 ASN cc_start: 0.9090 (OUTLIER) cc_final: 0.8815 (m110) REVERT: A 906 LYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6539 (ptmm) REVERT: A 1014 GLN cc_start: 0.8202 (tp40) cc_final: 0.7826 (tm-30) REVERT: A 1153 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6468 (pt0) REVERT: A 1291 LYS cc_start: 0.8493 (mttp) cc_final: 0.8118 (mttm) REVERT: A 1439 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.6880 (ppp) REVERT: B 13 THR cc_start: 0.7488 (p) cc_final: 0.7241 (t) REVERT: B 435 PHE cc_start: 0.7211 (p90) cc_final: 0.7003 (p90) REVERT: B 702 MET cc_start: 0.8750 (tpp) cc_final: 0.8434 (tpt) REVERT: B 904 ARG cc_start: 0.8453 (ttt90) cc_final: 0.8207 (ttt90) REVERT: B 1130 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.8221 (t80) REVERT: C 20 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8635 (ttm) REVERT: E 21 MET cc_start: 0.8780 (ttp) cc_final: 0.8280 (ptm) REVERT: E 73 ASP cc_start: 0.8196 (p0) cc_final: 0.7901 (p0) REVERT: F 90 ARG cc_start: 0.8297 (ttp80) cc_final: 0.7894 (ttt90) REVERT: F 104 ASN cc_start: 0.8288 (t0) cc_final: 0.7794 (t0) REVERT: G 22 MET cc_start: 0.6453 (pmm) cc_final: 0.5571 (pmm) REVERT: H 44 ASN cc_start: 0.7733 (m-40) cc_final: 0.7466 (m-40) REVERT: H 112 LYS cc_start: 0.8959 (mttt) cc_final: 0.8756 (mtpt) REVERT: I 28 SER cc_start: 0.8436 (t) cc_final: 0.8161 (p) REVERT: I 30 ARG cc_start: 0.8421 (ttp-170) cc_final: 0.8196 (ttp-170) REVERT: J 57 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6825 (mm-30) REVERT: J 62 TYR cc_start: 0.9123 (m-80) cc_final: 0.8839 (m-80) REVERT: L 49 ARG cc_start: 0.3387 (ptm160) cc_final: 0.2356 (mtp180) REVERT: L 64 LYS cc_start: 0.9004 (mmmt) cc_final: 0.7820 (mtpt) REVERT: U 157 LYS cc_start: 0.6754 (tppt) cc_final: 0.6287 (pttm) REVERT: U 175 LEU cc_start: 0.6962 (pp) cc_final: 0.5924 (mm) REVERT: W 772 GLU cc_start: 0.7798 (tm-30) cc_final: 0.6563 (tm-30) REVERT: W 774 ASN cc_start: 0.5888 (m-40) cc_final: 0.5407 (m-40) outliers start: 69 outliers final: 52 residues processed: 434 average time/residue: 0.2337 time to fit residues: 165.7615 Evaluate side-chains 427 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 367 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 1085 THR Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1144 THR Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1130 PHE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain U residue 194 ILE Chi-restraints excluded: chain U residue 204 LEU Chi-restraints excluded: chain W residue 752 LEU Chi-restraints excluded: chain W residue 782 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 26 optimal weight: 4.9990 chunk 386 optimal weight: 5.9990 chunk 320 optimal weight: 8.9990 chunk 204 optimal weight: 5.9990 chunk 325 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 chunk 118 optimal weight: 20.0000 chunk 351 optimal weight: 0.9980 chunk 289 optimal weight: 30.0000 chunk 363 optimal weight: 0.0030 chunk 152 optimal weight: 10.0000 overall best weight: 2.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 HIS ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 HIS B 157 HIS ** B1174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.190674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.142863 restraints weight = 58562.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.130444 restraints weight = 88688.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.127321 restraints weight = 77462.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.127962 restraints weight = 65297.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.127953 restraints weight = 52112.208| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 39316 Z= 0.159 Angle : 0.613 15.129 53513 Z= 0.315 Chirality : 0.044 0.286 5970 Planarity : 0.004 0.063 6560 Dihedral : 14.773 171.557 6139 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.85 % Favored : 93.97 % Rotamer: Outliers : 1.73 % Allowed : 12.69 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.05 % 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: -0.81 (0.13), residues: 4475 helix: 1.18 (0.15), residues: 1373 sheet: -0.66 (0.19), residues: 728 loop : -1.59 (0.13), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 19 TYR 0.015 0.001 TYR J 43 PHE 0.017 0.001 PHE K 71 TRP 0.013 0.001 TRP B 579 HIS 0.009 0.001 HIS L 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (39282) covalent geometry : angle 0.60943 / 0.31 (53480) hydrogen bonds : bond 0.04874 / 3.12 ( 1423) hydrogen bonds : angle 4.49091 / 3.16 ( 3928) metal coordination : bond 0.00510 / 0.31 ( 34) metal coordination : angle 2.71876 / 1.74 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8950 Ramachandran restraints generated. 4475 Oldfield, 0 Emsley, 4475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8950 Ramachandran restraints generated. 4475 Oldfield, 0 Emsley, 4475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 370 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8810 (mttt) cc_final: 0.8453 (mttm) REVERT: A 84 MET cc_start: 0.8148 (tpp) cc_final: 0.7919 (tpp) REVERT: A 201 LYS cc_start: 0.7226 (ptmt) cc_final: 0.6565 (mttp) REVERT: A 337 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8777 (mp) REVERT: A 539 ASP cc_start: 0.8697 (p0) cc_final: 0.8482 (p0) REVERT: A 718 GLU cc_start: 0.6556 (tm-30) cc_final: 0.5833 (tm-30) REVERT: A 735 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: A 736 MET cc_start: 0.7999 (ttm) cc_final: 0.7786 (ttm) REVERT: A 741 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8991 (pp) REVERT: A 742 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.8633 (m110) REVERT: A 1065 MET cc_start: 0.7857 (mtt) cc_final: 0.7602 (mtt) REVERT: A 1153 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6536 (pt0) REVERT: A 1291 LYS cc_start: 0.8532 (mttp) cc_final: 0.8155 (mttm) REVERT: A 1439 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.6980 (ppp) REVERT: B 13 THR cc_start: 0.7562 (p) cc_final: 0.7354 (t) REVERT: B 702 MET cc_start: 0.8812 (tpp) cc_final: 0.8488 (tpt) REVERT: B 904 ARG cc_start: 0.8580 (ttt90) cc_final: 0.8313 (ttt90) REVERT: B 1009 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8759 (t0) REVERT: B 1130 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8181 (t80) REVERT: C 20 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8677 (ttm) REVERT: E 21 MET cc_start: 0.8822 (ttp) cc_final: 0.8442 (ptm) REVERT: E 73 ASP cc_start: 0.8173 (p0) cc_final: 0.7852 (p0) REVERT: F 90 ARG cc_start: 0.8437 (ttp80) cc_final: 0.8008 (ttt90) REVERT: F 104 ASN cc_start: 0.8346 (t0) cc_final: 0.7876 (t0) REVERT: G 22 MET cc_start: 0.6448 (pmm) cc_final: 0.5608 (pmm) REVERT: H 44 ASN cc_start: 0.7748 (m-40) cc_final: 0.7474 (m-40) REVERT: I 28 SER cc_start: 0.8414 (t) cc_final: 0.8157 (p) REVERT: I 30 ARG cc_start: 0.8415 (ttp-170) cc_final: 0.8161 (ttp-170) REVERT: L 49 ARG cc_start: 0.3212 (ptm160) cc_final: 0.2784 (ttp-170) REVERT: L 64 LYS cc_start: 0.8984 (mmmt) cc_final: 0.7901 (mtpt) outliers start: 69 outliers final: 57 residues processed: 420 average time/residue: 0.2281 time to fit residues: 158.7539 Evaluate side-chains 421 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 356 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 1085 THR Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1144 THR Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1130 PHE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain U residue 194 ILE Chi-restraints excluded: chain U residue 204 LEU Chi-restraints excluded: chain W residue 313 VAL Chi-restraints excluded: chain W residue 752 LEU Chi-restraints excluded: chain W residue 782 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 179 optimal weight: 0.9990 chunk 287 optimal weight: 50.0000 chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 252 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 426 optimal weight: 8.9990 chunk 438 optimal weight: 50.0000 chunk 208 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 HIS ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 GLN B 157 HIS B1141 HIS ** B1174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.190156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.138461 restraints weight = 58746.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.132055 restraints weight = 91472.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.126944 restraints weight = 62707.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.125836 restraints weight = 67915.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.126720 restraints weight = 58593.510| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 39316 Z= 0.186 Angle : 0.641 14.479 53513 Z= 0.329 Chirality : 0.045 0.297 5970 Planarity : 0.004 0.062 6560 Dihedral : 14.782 171.471 6139 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.94 % Favored : 93.88 % Rotamer: Outliers : 1.73 % Allowed : 12.94 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.05 % 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: -0.85 (0.13), residues: 4475 helix: 1.14 (0.15), residues: 1374 sheet: -0.76 (0.19), residues: 739 loop : -1.58 (0.13), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 19 TYR 0.015 0.001 TYR J 43 PHE 0.021 0.002 PHE B 550 TRP 0.014 0.001 TRP B 300 HIS 0.044 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (39282) covalent geometry : angle 0.63712 / 0.33 (53480) hydrogen bonds : bond 0.05097 / 3.25 ( 1423) hydrogen bonds : angle 4.54538 / 3.20 ( 3928) metal coordination : bond 0.00566 / 0.34 ( 34) metal coordination : angle 2.83947 / 1.82 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8950 Ramachandran restraints generated. 4475 Oldfield, 0 Emsley, 4475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8950 Ramachandran restraints generated. 4475 Oldfield, 0 Emsley, 4475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 364 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8869 (mttt) cc_final: 0.8530 (mttm) REVERT: A 84 MET cc_start: 0.8203 (tpp) cc_final: 0.7978 (tpp) REVERT: A 201 LYS cc_start: 0.7271 (ptmt) cc_final: 0.6563 (mttp) REVERT: A 337 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8810 (mp) REVERT: A 539 ASP cc_start: 0.8669 (p0) cc_final: 0.8449 (p0) REVERT: A 718 GLU cc_start: 0.6645 (tm-30) cc_final: 0.5905 (tm-30) REVERT: A 735 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8106 (tm-30) REVERT: A 741 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9019 (pp) REVERT: A 742 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8676 (m110) REVERT: A 1153 GLU cc_start: 0.6871 (mt-10) cc_final: 0.6452 (pt0) REVERT: A 1291 LYS cc_start: 0.8574 (mttp) cc_final: 0.8199 (mttm) REVERT: A 1439 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7038 (ppp) REVERT: B 13 THR cc_start: 0.7661 (p) cc_final: 0.7435 (t) REVERT: B 702 MET cc_start: 0.8857 (tpp) cc_final: 0.8540 (tpt) REVERT: B 1009 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8615 (t0) REVERT: B 1130 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8203 (t80) REVERT: C 20 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8718 (ttm) REVERT: E 21 MET cc_start: 0.8811 (ttp) cc_final: 0.8384 (ptm) REVERT: E 73 ASP cc_start: 0.8158 (p0) cc_final: 0.7844 (p0) REVERT: F 90 ARG cc_start: 0.8404 (ttp80) cc_final: 0.8076 (ttt90) REVERT: F 104 ASN cc_start: 0.8368 (t0) cc_final: 0.7902 (t0) REVERT: G 22 MET cc_start: 0.6515 (pmm) cc_final: 0.5684 (pmm) REVERT: H 44 ASN cc_start: 0.7751 (m-40) cc_final: 0.7451 (m-40) REVERT: I 28 SER cc_start: 0.8429 (t) cc_final: 0.8173 (p) REVERT: I 30 ARG cc_start: 0.8400 (ttp-170) cc_final: 0.8126 (ttp-170) REVERT: J 57 GLU cc_start: 0.7465 (mm-30) cc_final: 0.6973 (mm-30) REVERT: L 49 ARG cc_start: 0.3149 (ptm160) cc_final: 0.2538 (mtp180) REVERT: L 64 LYS cc_start: 0.8969 (mmmt) cc_final: 0.7887 (mtpt) REVERT: U 180 MET cc_start: 0.6480 (mtm) cc_final: 0.6095 (ttm) outliers start: 69 outliers final: 58 residues processed: 415 average time/residue: 0.2302 time to fit residues: 158.8101 Evaluate side-chains 420 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 354 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 300 HIS Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 1079 THR Chi-restraints excluded: chain A residue 1085 THR Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1144 THR Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1130 PHE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain U residue 194 ILE Chi-restraints excluded: chain U residue 204 LEU Chi-restraints excluded: chain W residue 313 VAL Chi-restraints excluded: chain W residue 752 LEU Chi-restraints excluded: chain W residue 782 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 232 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 401 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 454 optimal weight: 20.0000 chunk 296 optimal weight: 30.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 HIS ** B1174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.189489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.143314 restraints weight = 57341.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.139111 restraints weight = 99105.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.139335 restraints weight = 94719.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.137274 restraints weight = 66865.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.137279 restraints weight = 76456.562| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39316 Z= 0.146 Angle : 0.610 14.135 53513 Z= 0.313 Chirality : 0.044 0.299 5970 Planarity : 0.004 0.063 6560 Dihedral : 14.752 171.598 6139 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.70 % Favored : 94.15 % Rotamer: Outliers : 1.63 % Allowed : 13.12 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.05 % 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: -0.78 (0.13), residues: 4475 helix: 1.22 (0.15), residues: 1373 sheet: -0.71 (0.19), residues: 736 loop : -1.56 (0.13), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 19 TYR 0.015 0.001 TYR J 43 PHE 0.028 0.001 PHE A 299 TRP 0.015 0.001 TRP B 300 HIS 0.015 0.001 HIS A 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (39282) covalent geometry : angle 0.60671 / 0.31 (53480) hydrogen bonds : bond 0.04799 / 3.06 ( 1423) hydrogen bonds : angle 4.47649 / 3.15 ( 3928) metal coordination : bond 0.00489 / 0.30 ( 34) metal coordination : angle 2.72676 / 1.73 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6410.66 seconds wall clock time: 111 minutes 30.67 seconds (6690.67 seconds total)