Starting phenix.real_space_refine on Mon Sep 14 19:56:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6exv_3981/09_2026/6exv_3981_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6exv_3981/09_2026/6exv_3981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6exv_3981/09_2026/6exv_3981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6exv_3981/09_2026/6exv_3981.map" model { file = "/net/cci-nas-00/data/ceres_data/6exv_3981/09_2026/6exv_3981_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6exv_3981/09_2026/6exv_3981_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 75 5.49 5 Mg 1 5.21 5 S 198 5.16 5 C 20415 2.51 5 N 5741 2.21 5 O 6279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s 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: 32717 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1428, 11317 Classifications: {'peptide': 1428} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 68, 'TRANS': 1357} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 9062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1134, 9062 Classifications: {'peptide': 1134} Link IDs: {'PTRANS': 53, 'TRANS': 1080} Chain breaks: 2 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1005 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1334 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 64 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ILX:plan-1': 1, 'TRX:plan-2': 1, 'CSX:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 516 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "P" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 301 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 5} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 735 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 38.847 79.318 106.425 1.00 46.90 S ATOM 486 SG CYS A 74 39.588 84.008 106.933 1.00 45.60 S ATOM 533 SG CYS A 81 40.493 82.266 103.879 1.00 40.48 S ATOM 768 SG CYS A 111 85.660 74.861 121.372 1.00 62.21 S ATOM 796 SG CYS A 114 83.602 76.125 125.393 1.00 63.39 S ATOM 1109 SG CYS A 154 87.890 76.877 123.396 1.00 79.56 S ATOM 19949 SG CYS B1119 50.272 92.971 114.828 1.00 41.50 S ATOM 19971 SG CYS B1122 53.286 90.175 114.329 1.00 44.44 S ATOM 21086 SG CYS C 90 7.666 94.273 47.343 1.00 89.17 S ATOM 21121 SG CYS C 94 7.713 93.531 43.872 1.00 72.28 S ATOM 28949 SG CYS I 86 113.084 63.272 33.301 1.00 50.23 S ATOM 28973 SG CYS I 89 111.906 60.705 30.947 1.00 47.04 S ATOM 29177 SG CYS I 114 109.064 61.928 33.056 1.00 35.97 S ATOM 29212 SG CYS I 119 112.031 59.124 34.218 1.00 56.27 S ATOM 29346 SG CYS J 10 39.833 92.625 29.744 1.00 28.61 S ATOM 29610 SG CYS J 44 43.220 91.743 29.910 1.00 27.15 S ATOM 29616 SG CYS J 45 39.743 88.835 28.240 1.00 27.63 S ATOM 30762 SG CYS L 19 27.685 51.436 54.616 1.00 39.64 S ATOM 30781 SG CYS L 22 25.775 49.259 51.422 1.00 42.62 S ATOM 30898 SG CYS L 36 24.598 49.251 55.501 1.00 56.26 S ATOM 30924 SG CYS L 39 27.603 47.584 54.190 1.00 58.02 S Time building chain proxies: 6.40, per 1000 atoms: 0.20 Number of scatterers: 32717 At special positions: 0 Unit cell: (156.22, 172.27, 171.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 198 16.00 P 75 15.00 Mg 1 11.99 O 6279 8.00 N 5741 7.00 C 20415 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " Number of angles added : 15 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7348 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 49 sheets defined 32.6% alpha, 16.1% beta 26 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 3.72 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 removed outlier: 3.709A pdb=" N SER A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 136 through 148 removed outlier: 3.529A pdb=" N ARG A 140 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 147 " --> pdb=" O HIS A 143 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS A 148 " --> pdb=" O VAL A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 231 through 237 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 276 through 296 removed outlier: 3.965A pdb=" N ASP A 282 " --> pdb=" O HIS A 278 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 292 " --> pdb=" O ASN A 288 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN A 293 " --> pdb=" O GLN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 316 removed outlier: 4.051A pdb=" N LEU A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 398 through 408 Processing helix chain 'A' and resid 465 through 469 removed outlier: 3.840A pdb=" N MET A 469 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.886A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 517 removed outlier: 3.590A pdb=" N ARG A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 525 removed outlier: 3.575A pdb=" N MET A 524 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 521 through 525' Processing helix chain 'A' and resid 539 through 549 removed outlier: 3.664A pdb=" N THR A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 549 " --> pdb=" O VAL A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 587 through 593 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 662 through 684 removed outlier: 3.921A pdb=" N LEU A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 693 removed outlier: 4.100A pdb=" N ILE A 693 " --> pdb=" O GLY A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 722 removed outlier: 3.936A pdb=" N ASP A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN A 722 " --> pdb=" O GLU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 748 Processing helix chain 'A' and resid 749 through 758 Processing helix chain 'A' and resid 766 through 771 Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.724A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 868 removed outlier: 4.688A pdb=" N PHE A 838 " --> pdb=" O THR A 834 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR A 850 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 862 " --> pdb=" O GLY A 858 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 920 removed outlier: 3.764A pdb=" N GLU A 917 " --> pdb=" O ASN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 934 Processing helix chain 'A' and resid 935 through 943 removed outlier: 3.668A pdb=" N VAL A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 952 Processing helix chain 'A' and resid 953 through 970 removed outlier: 3.679A pdb=" N GLU A 957 " --> pdb=" O GLU A 953 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 961 " --> pdb=" O GLU A 957 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASP A 962 " --> pdb=" O ARG A 958 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 967 " --> pdb=" O ARG A 963 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 968 " --> pdb=" O GLU A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.862A pdb=" N ALA A 990 " --> pdb=" O MET A 986 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS A 992 " --> pdb=" O TRP A 988 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A 994 " --> pdb=" O ALA A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1019 removed outlier: 3.688A pdb=" N VAL A1009 " --> pdb=" O HIS A1005 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU A1011 " --> pdb=" O ILE A1007 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A1019 " --> pdb=" O GLU A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1038 removed outlier: 3.693A pdb=" N GLU A1035 " --> pdb=" O ARG A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1049 Processing helix chain 'A' and resid 1051 through 1057 Processing helix chain 'A' and resid 1062 through 1077 removed outlier: 3.615A pdb=" N ASP A1066 " --> pdb=" O GLY A1062 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP A1067 " --> pdb=" O GLU A1063 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU A1068 " --> pdb=" O ALA A1064 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER A1074 " --> pdb=" O GLY A1070 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A1077 " --> pdb=" O GLU A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1091 Processing helix chain 'A' and resid 1097 through 1102 removed outlier: 3.600A pdb=" N THR A1100 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A1102 " --> pdb=" O ALA A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1128 removed outlier: 3.632A pdb=" N LEU A1124 " --> pdb=" O GLY A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.540A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1168 Processing helix chain 'A' and resid 1191 through 1199 removed outlier: 4.264A pdb=" N MET A1199 " --> pdb=" O VAL A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1223 Processing helix chain 'A' and resid 1227 through 1235 Processing helix chain 'A' and resid 1263 through 1266 Processing helix chain 'A' and resid 1280 through 1293 Processing helix chain 'A' and resid 1342 through 1348 removed outlier: 3.656A pdb=" N VAL A1346 " --> pdb=" O SER A1342 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1371 through 1387 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 4.066A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A1406 " --> pdb=" O CYS A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 removed outlier: 3.735A pdb=" N VAL A1419 " --> pdb=" O THR A1415 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1430 removed outlier: 3.738A pdb=" N LYS A1429 " --> pdb=" O GLY A1425 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS A1430 " --> pdb=" O PRO A1426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1425 through 1430' Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.766A pdb=" N ALA B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 61 removed outlier: 3.612A pdb=" N MET B 53 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 248 through 253 Processing helix chain 'B' and resid 269 through 275 Processing helix chain 'B' and resid 280 through 288 Processing helix chain 'B' and resid 294 through 300 removed outlier: 4.045A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 removed outlier: 4.165A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 332 through 346 Processing helix chain 'B' and resid 358 through 377 Processing helix chain 'B' and resid 396 through 422 removed outlier: 4.550A pdb=" N PHE B 402 " --> pdb=" O PRO B 398 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 411 " --> pdb=" O MET B 407 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 removed outlier: 3.893A pdb=" N SER B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.745A pdb=" N TRP B 506 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 520 removed outlier: 3.814A pdb=" N ALA B 519 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL B 520 " --> pdb=" O GLY B 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 520' Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.838A pdb=" N GLU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.954A pdb=" N ILE B 561 " --> pdb=" O PRO B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.518A pdb=" N LEU B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 652 through 658 Processing helix chain 'B' and resid 668 through 672 removed outlier: 3.561A pdb=" N THR B 672 " --> pdb=" O GLU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.579A pdb=" N HIS B 716 " --> pdb=" O PHE B 713 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 713 through 717' Processing helix chain 'B' and resid 718 through 726 removed outlier: 3.553A pdb=" N ASN B 722 " --> pdb=" O GLN B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 844 through 848 removed outlier: 4.055A pdb=" N LYS B 847 " --> pdb=" O ILE B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.618A pdb=" N ASP B 953 " --> pdb=" O ARG B 950 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET B 954 " --> pdb=" O GLN B 951 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 950 through 954' Processing helix chain 'B' and resid 969 through 972 Processing helix chain 'B' and resid 978 through 994 removed outlier: 3.781A pdb=" N ILE B 982 " --> pdb=" O ILE B 978 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS B 988 " --> pdb=" O CYS B 984 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1016 Processing helix chain 'B' and resid 1091 through 1096 Processing helix chain 'B' and resid 1100 through 1108 Processing helix chain 'B' and resid 1152 through 1164 removed outlier: 3.646A pdb=" N LYS B1156 " --> pdb=" O PRO B1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 60 through 68 removed outlier: 3.585A pdb=" N ILE C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 120 removed outlier: 3.534A pdb=" N ASP C 119 " --> pdb=" O THR C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 269 Processing helix chain 'D' and resid 33 through 46 Processing helix chain 'D' and resid 59 through 71 removed outlier: 3.752A pdb=" N PHE D 71 " --> pdb=" O TYR D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.503A pdb=" N ILE D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 101 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 123 through 138 removed outlier: 3.941A pdb=" N LEU D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 removed outlier: 3.664A pdb=" N GLY E 25 " --> pdb=" O CYS E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 33 removed outlier: 3.632A pdb=" N GLU E 32 " --> pdb=" O THR E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 84 through 98 Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 138 through 142 removed outlier: 3.588A pdb=" N GLU E 141 " --> pdb=" O ASN E 138 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS E 142 " --> pdb=" O ILE E 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 142' Processing helix chain 'E' and resid 152 through 162 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 98 Processing helix chain 'G' and resid 24 through 33 removed outlier: 4.043A pdb=" N GLU G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 67 removed outlier: 3.744A pdb=" N THR I 66 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.552A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 28 removed outlier: 3.738A pdb=" N ALA J 27 " --> pdb=" O GLY J 23 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU J 28 " --> pdb=" O LEU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 37 Processing helix chain 'J' and resid 42 through 45 Processing helix chain 'J' and resid 46 through 51 Processing helix chain 'K' and resid 39 through 51 removed outlier: 4.180A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 removed outlier: 3.706A pdb=" N GLN K 113 " --> pdb=" O ILE K 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 95 removed outlier: 3.707A pdb=" N GLY A 86 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.537A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 193 through 194 removed outlier: 4.295A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 266 removed outlier: 3.757A pdb=" N MET A 266 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 331 removed outlier: 4.351A pdb=" N LYS A 331 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 358 through 359 Processing sheet with id=AA7, first strand: chain 'A' and resid 457 through 459 removed outlier: 3.840A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.291A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.468A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE H 56 " --> pdb=" O PHE H 10 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE H 9 " --> pdb=" O GLU H 33 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER H 113 " --> pdb=" O GLU H 100 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 603 removed outlier: 6.922A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 789 through 790 removed outlier: 3.507A pdb=" N GLY A 789 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB4, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB5, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB6, first strand: chain 'A' and resid 1140 through 1141 Processing sheet with id=AB7, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.478A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ALA A1171 " --> pdb=" O LYS I 57 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LYS I 57 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR A1173 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL I 55 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A1175 " --> pdb=" O ILE I 53 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AB9, first strand: chain 'D' and resid 30 through 31 removed outlier: 4.678A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP A1472 " --> pdb=" O ARG F 107 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.514A pdb=" N LYS G 71 " --> pdb=" O ASN G 53 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN G 53 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LYS G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE G 51 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N ILE G 75 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N THR G 49 " --> pdb=" O ILE G 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 93 removed outlier: 5.729A pdb=" N TYR B 84 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE B 133 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 93 removed outlier: 5.729A pdb=" N TYR B 84 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE B 133 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AC5, first strand: chain 'B' and resid 192 through 193 Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AC7, first strand: chain 'B' and resid 206 through 207 Processing sheet with id=AC8, first strand: chain 'B' and resid 222 through 223 Processing sheet with id=AC9, first strand: chain 'B' and resid 257 through 258 Processing sheet with id=AD1, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD2, first strand: chain 'B' and resid 572 through 577 removed outlier: 5.603A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 611 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 606 " --> pdb=" O GLU B 611 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 675 through 676 Processing sheet with id=AD4, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.551A pdb=" N GLU B 816 " --> pdb=" O CYS B 919 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.551A pdb=" N GLU B 816 " --> pdb=" O CYS B 919 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD7, first strand: chain 'B' and resid 943 through 944 removed outlier: 4.352A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N ILE B 965 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE B 779 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ILE B 967 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ALA B 781 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE B 947 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR B 949 " --> pdb=" O MET B 796 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 943 through 944 Processing sheet with id=AD9, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AE1, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AE2, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.617A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE C 21 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.891A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TRP C 49 " --> pdb=" O TYR C 164 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.891A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL C 50 " --> pdb=" O PHE L 55 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 113 through 115 removed outlier: 3.640A pdb=" N VAL C 151 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 60 through 63 removed outlier: 3.516A pdb=" N VAL E 60 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE8, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.668A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AF1, first strand: chain 'G' and resid 143 through 145 removed outlier: 3.839A pdb=" N LEU G 145 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL G 85 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 25 through 28 removed outlier: 3.825A pdb=" N LEU I 36 " --> pdb=" O LYS I 27 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF4, first strand: chain 'K' and resid 21 through 23 removed outlier: 3.820A pdb=" N ASN K 22 " --> pdb=" O LEU K 32 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU K 32 " --> pdb=" O ASN K 22 " (cutoff:3.500A) 1040 hydrogen bonds defined for protein. 2880 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 8.48 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5409 1.31 - 1.44: 8831 1.44 - 1.57: 18789 1.57 - 1.70: 147 1.70 - 1.83: 313 Bond restraints: 33489 Sorted by residual: bond pdb=" C3' DC T 23 " pdb=" O3' DC T 23 " ideal model delta sigma weight residual 1.435 1.387 0.048 1.30e-02 5.92e+03 1.38e+01 bond pdb=" C1' DT T 31 " pdb=" N1 DT T 31 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.22e+01 bond pdb=" C3' DA N 35 " pdb=" C2' DA N 35 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DC N 37 " pdb=" C2' DC N 37 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.68e+00 bond pdb=" N1 DC T 23 " pdb=" C6 DC T 23 " ideal model delta sigma weight residual 1.367 1.349 0.018 6.00e-03 2.78e+04 8.85e+00 ... (remaining 33484 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 44721 3.25 - 6.51: 729 6.51 - 9.76: 97 9.76 - 13.01: 16 13.01 - 16.27: 3 Bond angle restraints: 45566 Sorted by residual: angle pdb=" O4' DC T 23 " pdb=" C4' DC T 23 " pdb=" C3' DC T 23 " ideal model delta sigma weight residual 106.00 101.57 4.43 6.00e-01 2.78e+00 5.46e+01 angle pdb=" C LYS A 812 " pdb=" N ASP A 813 " pdb=" CA ASP A 813 " ideal model delta sigma weight residual 122.82 130.95 -8.13 1.42e+00 4.96e-01 3.28e+01 angle pdb=" N GLY B1087 " pdb=" CA GLY B1087 " pdb=" C GLY B1087 " ideal model delta sigma weight residual 113.18 126.24 -13.06 2.37e+00 1.78e-01 3.04e+01 angle pdb=" C3' A P 12 " pdb=" O3' A P 12 " pdb=" P G P 13 " ideal model delta sigma weight residual 119.70 125.95 -6.25 1.20e+00 6.94e-01 2.71e+01 angle pdb=" O4' DC T 22 " pdb=" C4' DC T 22 " pdb=" C3' DC T 22 " ideal model delta sigma weight residual 106.00 102.92 3.08 6.00e-01 2.78e+00 2.64e+01 ... (remaining 45561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.63: 19950 34.63 - 69.25: 412 69.25 - 103.88: 18 103.88 - 138.50: 0 138.50 - 173.13: 3 Dihedral angle restraints: 20383 sinusoidal: 9023 harmonic: 11360 Sorted by residual: dihedral pdb=" CA ARG E 54 " pdb=" C ARG E 54 " pdb=" N ARG E 55 " pdb=" CA ARG E 55 " ideal model delta harmonic sigma weight residual -180.00 -149.39 -30.61 0 5.00e+00 4.00e-02 3.75e+01 dihedral pdb=" CA VAL A 538 " pdb=" C VAL A 538 " pdb=" N GLN A 539 " pdb=" CA GLN A 539 " ideal model delta harmonic sigma weight residual 180.00 149.75 30.25 0 5.00e+00 4.00e-02 3.66e+01 dihedral pdb=" CA GLU B1088 " pdb=" C GLU B1088 " pdb=" N MET B1089 " pdb=" CA MET B1089 " ideal model delta harmonic sigma weight residual 180.00 150.90 29.10 0 5.00e+00 4.00e-02 3.39e+01 ... (remaining 20380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 4123 0.080 - 0.159: 876 0.159 - 0.239: 92 0.239 - 0.318: 9 0.318 - 0.398: 2 Chirality restraints: 5102 Sorted by residual: chirality pdb=" CB ILE G 101 " pdb=" CA ILE G 101 " pdb=" CG1 ILE G 101 " pdb=" CG2 ILE G 101 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CA HYP M 8 " pdb=" N HYP M 8 " pdb=" C HYP M 8 " pdb=" CB HYP M 8 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C3' A P 12 " pdb=" C4' A P 12 " pdb=" O3' A P 12 " pdb=" C2' A P 12 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 5099 not shown) Planarity restraints: 5645 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 573 " 0.019 2.00e-02 2.50e+03 2.14e-02 1.15e+01 pdb=" CG TRP B 573 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP B 573 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 573 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 573 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 573 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 573 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 573 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 573 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 573 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1029 " 0.020 2.00e-02 2.50e+03 2.11e-02 8.91e+00 pdb=" CG TYR B1029 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR B1029 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B1029 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B1029 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B1029 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B1029 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B1029 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1048 " 0.022 2.00e-02 2.50e+03 2.09e-02 8.74e+00 pdb=" CG TYR B1048 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR B1048 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR B1048 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B1048 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B1048 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B1048 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B1048 " 0.002 2.00e-02 2.50e+03 ... (remaining 5642 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 216 2.60 - 3.17: 25155 3.17 - 3.75: 46840 3.75 - 4.32: 66361 4.32 - 4.90: 110915 Nonbonded interactions: 249487 Sorted by model distance: nonbonded pdb=" NH2 ARG B 591 " pdb=" OE2 GLU B 663 " model vdw 2.022 3.120 nonbonded pdb=" O3' C P 20 " pdb="MG MG A2003 " model vdw 2.054 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2003 " model vdw 2.065 2.170 nonbonded pdb=" OD2 ASP H 71 " pdb=" OH TYR H 142 " model vdw 2.075 3.040 nonbonded pdb=" O ASN I 22 " pdb="ZN ZN I 201 " model vdw 2.110 2.230 ... (remaining 249482 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: 1.120 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: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 36.740 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.855 33513 Z= 0.440 Angle : 1.135 34.029 45581 Z= 0.630 Chirality : 0.065 0.398 5102 Planarity : 0.007 0.069 5645 Dihedral : 13.300 173.126 13035 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.86 % Favored : 91.09 % Rotamer: Outliers : 0.29 % Allowed : 3.58 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -4.63 (0.11), residues: 3860 helix: -3.83 (0.09), residues: 1187 sheet: -1.82 (0.21), residues: 535 loop : -3.02 (0.11), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 797 TYR 0.051 0.004 TYR B1048 PHE 0.034 0.004 PHE A 112 TRP 0.056 0.004 TRP B 573 HIS 0.012 0.003 HIS A 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00840 / 0.38 (33489) covalent geometry : angle 1.10705 / 0.63 (45566) hydrogen bonds : bond 0.17808 / 11.61 ( 1059) hydrogen bonds : angle 9.40894 / 6.65 ( 2998) metal coordination : bond 0.30311 / 16.57 ( 22) metal coordination : angle 13.93430 / 8.51 ( 15) Misc. bond : bond 0.03302 / 1.70 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 610 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 LYS cc_start: 0.7557 (mtpp) cc_final: 0.6874 (mmtm) REVERT: A 393 ILE cc_start: 0.6960 (pp) cc_final: 0.6615 (mt) REVERT: A 428 ASP cc_start: 0.7282 (p0) cc_final: 0.6907 (p0) REVERT: A 444 TYR cc_start: 0.6842 (m-10) cc_final: 0.5605 (m-10) REVERT: A 493 ASN cc_start: 0.8194 (t0) cc_final: 0.7867 (t0) REVERT: A 561 MET cc_start: 0.8417 (mmt) cc_final: 0.8127 (mmm) REVERT: A 652 LEU cc_start: 0.8797 (tp) cc_final: 0.8544 (mp) REVERT: A 715 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6668 (mt-10) REVERT: A 794 GLU cc_start: 0.6293 (tt0) cc_final: 0.6010 (tt0) REVERT: A 1086 MET cc_start: 0.8279 (mmm) cc_final: 0.7995 (mmm) REVERT: A 1244 ASN cc_start: 0.6807 (m-40) cc_final: 0.6456 (t0) REVERT: A 1344 MET cc_start: 0.8249 (tpt) cc_final: 0.8048 (tpp) REVERT: A 1423 ASP cc_start: 0.7340 (t70) cc_final: 0.7126 (t0) REVERT: A 1484 MET cc_start: 0.3091 (ppp) cc_final: 0.2415 (ptp) REVERT: B 53 MET cc_start: 0.7718 (mmp) cc_final: 0.7463 (mmt) REVERT: B 187 ILE cc_start: 0.8890 (mp) cc_final: 0.8673 (mt) REVERT: B 294 ASP cc_start: 0.8384 (t70) cc_final: 0.8102 (t0) REVERT: B 297 MET cc_start: 0.7158 (ptp) cc_final: 0.6708 (ttp) REVERT: B 815 LYS cc_start: 0.8338 (mtmt) cc_final: 0.7895 (mptt) REVERT: B 826 GLU cc_start: 0.6658 (pp20) cc_final: 0.6374 (pm20) REVERT: B 917 LYS cc_start: 0.8361 (ttmm) cc_final: 0.8082 (ttmt) REVERT: B 942 LYS cc_start: 0.8243 (ptpt) cc_final: 0.7923 (ptpp) REVERT: B 1048 TYR cc_start: 0.8852 (m-10) cc_final: 0.8632 (m-80) REVERT: B 1171 MET cc_start: 0.8479 (mtm) cc_final: 0.8266 (mtm) REVERT: C 25 ASN cc_start: 0.8611 (t0) cc_final: 0.8362 (m110) REVERT: C 96 GLU cc_start: 0.6826 (tp30) cc_final: 0.6529 (tt0) REVERT: C 160 ARG cc_start: 0.7763 (ptt180) cc_final: 0.7494 (ptt-90) REVERT: C 216 SER cc_start: 0.8339 (m) cc_final: 0.8049 (p) REVERT: F 95 LYS cc_start: 0.7035 (ptpt) cc_final: 0.6702 (ptmt) REVERT: G 14 HIS cc_start: 0.7182 (t-90) cc_final: 0.6975 (t70) REVERT: H 110 THR cc_start: 0.6182 (m) cc_final: 0.5934 (m) REVERT: H 111 ARG cc_start: 0.6259 (ttt90) cc_final: 0.5758 (ttt-90) REVERT: H 146 LYS cc_start: 0.8162 (ptmm) cc_final: 0.7662 (pttp) REVERT: I 92 LYS cc_start: 0.6808 (mttp) cc_final: 0.6164 (mmtm) REVERT: J 26 GLN cc_start: 0.7633 (tp-100) cc_final: 0.7307 (tp40) REVERT: K 29 ASN cc_start: 0.7103 (m-40) cc_final: 0.6822 (m110) REVERT: K 110 LYS cc_start: 0.7415 (ttmp) cc_final: 0.7097 (ttmt) outliers start: 10 outliers final: 2 residues processed: 619 average time/residue: 0.2385 time to fit residues: 228.2712 Evaluate side-chains 433 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 431 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain L residue 54 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 576 GLN A 671 ASN A 673 GLN A 678 ASN A 790 GLN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1230 GLN A1420 ASN B 518 HIS ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN B 639 HIS B 649 ASN B 741 HIS B 749 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN B 970 HIS B 992 ASN B1120 ASN C 66 HIS C 190 ASN G 139 GLN H 46 GLN I 22 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.175189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.137566 restraints weight = 34576.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.134256 restraints weight = 37972.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.133987 restraints weight = 43004.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.134663 restraints weight = 32740.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.134790 restraints weight = 27646.217| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33513 Z= 0.150 Angle : 0.683 12.442 45581 Z= 0.359 Chirality : 0.047 0.257 5102 Planarity : 0.005 0.058 5645 Dihedral : 14.344 173.308 5174 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.28 % Allowed : 8.68 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.12), residues: 3860 helix: -2.35 (0.12), residues: 1218 sheet: -1.33 (0.21), residues: 536 loop : -2.70 (0.12), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 358 TYR 0.021 0.002 TYR B1048 PHE 0.022 0.002 PHE A1202 TRP 0.023 0.002 TRP A 988 HIS 0.006 0.001 HIS A1005 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (33489) covalent geometry : angle 0.67977 / 0.36 (45566) hydrogen bonds : bond 0.05538 / 3.73 ( 1059) hydrogen bonds : angle 5.89612 / 4.15 ( 2998) metal coordination : bond 0.01603 / 1.05 ( 22) metal coordination : angle 3.51166 / 1.81 ( 15) Misc. bond : bond 0.01036 / 0.53 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 469 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: A 213 LYS cc_start: 0.7627 (mtpp) cc_final: 0.7266 (mmtm) REVERT: A 289 GLN cc_start: 0.8353 (tm-30) cc_final: 0.8123 (tm-30) REVERT: A 393 ILE cc_start: 0.7254 (pp) cc_final: 0.6937 (mt) REVERT: A 428 ASP cc_start: 0.7314 (p0) cc_final: 0.7112 (p0) REVERT: A 444 TYR cc_start: 0.7022 (m-10) cc_final: 0.5973 (m-10) REVERT: A 461 GLN cc_start: 0.8794 (mp10) cc_final: 0.8475 (mp10) REVERT: A 493 ASN cc_start: 0.8314 (t0) cc_final: 0.8007 (t0) REVERT: A 715 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6888 (mt-10) REVERT: A 794 GLU cc_start: 0.6388 (tt0) cc_final: 0.6133 (tt0) REVERT: A 941 ASP cc_start: 0.7701 (t0) cc_final: 0.7445 (t0) REVERT: A 1262 MET cc_start: 0.3342 (tpt) cc_final: 0.2750 (ptm) REVERT: A 1451 MET cc_start: 0.7361 (mmp) cc_final: 0.7105 (mmp) REVERT: A 1484 MET cc_start: 0.3439 (ppp) cc_final: 0.2388 (ptp) REVERT: B 53 MET cc_start: 0.7602 (mmp) cc_final: 0.7247 (mmt) REVERT: B 109 MET cc_start: 0.7232 (mmm) cc_final: 0.6927 (mmt) REVERT: B 112 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6514 (tt0) REVERT: B 187 ILE cc_start: 0.9023 (mp) cc_final: 0.8730 (mm) REVERT: B 674 MET cc_start: 0.8222 (tpt) cc_final: 0.7784 (tpt) REVERT: B 917 LYS cc_start: 0.8414 (ttmm) cc_final: 0.8161 (ttmt) REVERT: C 216 SER cc_start: 0.8438 (m) cc_final: 0.8099 (p) REVERT: D 42 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5495 (mt-10) REVERT: E 108 GLN cc_start: 0.8401 (tm-30) cc_final: 0.7963 (tt0) REVERT: F 95 LYS cc_start: 0.7342 (ptpt) cc_final: 0.7085 (ptmt) REVERT: F 101 LYS cc_start: 0.6940 (mmmt) cc_final: 0.6580 (mmtp) REVERT: H 146 LYS cc_start: 0.8171 (ptmm) cc_final: 0.7903 (pttp) REVERT: I 92 LYS cc_start: 0.6482 (mttp) cc_final: 0.6107 (mmtm) REVERT: I 108 MET cc_start: 0.8173 (mtp) cc_final: 0.7938 (mtp) REVERT: K 110 LYS cc_start: 0.7451 (ttmp) cc_final: 0.6951 (ttmt) REVERT: L 50 LYS cc_start: 0.8406 (mttt) cc_final: 0.8132 (mtmt) outliers start: 44 outliers final: 24 residues processed: 499 average time/residue: 0.2175 time to fit residues: 174.2922 Evaluate side-chains 439 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 414 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 1054 MET Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1287 CYS Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain L residue 54 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 27 optimal weight: 5.9990 chunk 379 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 210 optimal weight: 0.5980 chunk 347 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 268 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 330 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 642 GLN B 741 HIS B 825 GLN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.172188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.135806 restraints weight = 34749.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.133211 restraints weight = 43026.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.133101 restraints weight = 39982.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.133519 restraints weight = 31235.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.133558 restraints weight = 28425.249| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 33513 Z= 0.179 Angle : 0.667 11.370 45581 Z= 0.348 Chirality : 0.048 0.224 5102 Planarity : 0.005 0.055 5645 Dihedral : 14.076 174.417 5174 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.98 % Allowed : 9.75 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.12), residues: 3860 helix: -1.58 (0.14), residues: 1222 sheet: -1.07 (0.22), residues: 527 loop : -2.50 (0.12), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 358 TYR 0.020 0.002 TYR F 60 PHE 0.019 0.002 PHE C 21 TRP 0.022 0.002 TRP A 988 HIS 0.008 0.001 HIS A1005 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (33489) covalent geometry : angle 0.66551 / 0.35 (45566) hydrogen bonds : bond 0.05302 / 3.55 ( 1059) hydrogen bonds : angle 5.25287 / 3.70 ( 2998) metal coordination : bond 0.00938 / 0.56 ( 22) metal coordination : angle 2.88305 / 1.48 ( 15) Misc. bond : bond 0.00051 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 429 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 213 LYS cc_start: 0.7567 (mtpp) cc_final: 0.7255 (mmtm) REVERT: A 289 GLN cc_start: 0.8457 (tm-30) cc_final: 0.7713 (tt0) REVERT: A 393 ILE cc_start: 0.7337 (pp) cc_final: 0.7002 (mt) REVERT: A 444 TYR cc_start: 0.7062 (m-10) cc_final: 0.6164 (m-10) REVERT: A 493 ASN cc_start: 0.8219 (t0) cc_final: 0.7842 (t0) REVERT: A 715 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6936 (mt-10) REVERT: A 743 ARG cc_start: 0.7341 (tpm170) cc_final: 0.7122 (tpp80) REVERT: A 941 ASP cc_start: 0.7692 (t0) cc_final: 0.7491 (t0) REVERT: A 1262 MET cc_start: 0.3080 (tpt) cc_final: 0.2499 (ptm) REVERT: A 1484 MET cc_start: 0.3338 (ppp) cc_final: 0.2393 (ptp) REVERT: B 53 MET cc_start: 0.7579 (mmp) cc_final: 0.7291 (mmt) REVERT: B 109 MET cc_start: 0.7464 (mmm) cc_final: 0.7169 (mmt) REVERT: B 112 GLU cc_start: 0.7498 (mt-10) cc_final: 0.6430 (tt0) REVERT: B 187 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8839 (mm) REVERT: B 199 LYS cc_start: 0.8598 (ttpp) cc_final: 0.8302 (ttpp) REVERT: B 859 ARG cc_start: 0.8308 (ptp-110) cc_final: 0.8078 (ttm110) REVERT: B 1171 MET cc_start: 0.8369 (mtm) cc_final: 0.8136 (mtm) REVERT: C 216 SER cc_start: 0.8492 (m) cc_final: 0.8120 (p) REVERT: D 39 MET cc_start: 0.6435 (ttm) cc_final: 0.5916 (ttm) REVERT: D 42 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.5725 (mt-10) REVERT: E 108 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8008 (tt0) REVERT: E 158 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6695 (mp0) REVERT: F 80 MET cc_start: 0.5980 (OUTLIER) cc_final: 0.4790 (mmt) REVERT: F 95 LYS cc_start: 0.7424 (ptpt) cc_final: 0.7179 (ptmt) REVERT: H 16 ASP cc_start: 0.5327 (p0) cc_final: 0.5108 (p0) REVERT: H 111 ARG cc_start: 0.6173 (ttt90) cc_final: 0.5767 (ttt-90) REVERT: H 146 LYS cc_start: 0.8136 (ptmm) cc_final: 0.7794 (pttp) REVERT: I 92 LYS cc_start: 0.6650 (mttp) cc_final: 0.6171 (mmtm) REVERT: J 26 GLN cc_start: 0.7550 (tp-100) cc_final: 0.7260 (tp40) REVERT: K 11 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7275 (mp) REVERT: K 111 ASP cc_start: 0.7333 (t0) cc_final: 0.7104 (t0) REVERT: L 50 LYS cc_start: 0.8411 (mttt) cc_final: 0.8132 (mtmt) outliers start: 68 outliers final: 30 residues processed: 478 average time/residue: 0.2201 time to fit residues: 168.6986 Evaluate side-chains 446 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 411 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain L residue 54 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 209 optimal weight: 0.0570 chunk 231 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 292 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 324 optimal weight: 50.0000 chunk 134 optimal weight: 6.9990 chunk 323 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 330 optimal weight: 1.9990 overall best weight: 1.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1005 HIS B 741 HIS ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.174242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.135669 restraints weight = 34419.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.130300 restraints weight = 38334.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.130566 restraints weight = 40734.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.131130 restraints weight = 30414.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.131127 restraints weight = 28117.493| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33513 Z= 0.132 Angle : 0.607 11.597 45581 Z= 0.317 Chirality : 0.046 0.283 5102 Planarity : 0.004 0.051 5645 Dihedral : 13.889 176.359 5174 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.21 % Allowed : 10.92 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.13), residues: 3860 helix: -0.98 (0.14), residues: 1215 sheet: -0.86 (0.22), residues: 524 loop : -2.31 (0.12), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 358 TYR 0.019 0.001 TYR E 182 PHE 0.015 0.001 PHE C 21 TRP 0.016 0.001 TRP A 988 HIS 0.008 0.001 HIS A1005 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (33489) covalent geometry : angle 0.60642 / 0.32 (45566) hydrogen bonds : bond 0.04583 / 3.09 ( 1059) hydrogen bonds : angle 4.83573 / 3.40 ( 2998) metal coordination : bond 0.00544 / 0.39 ( 22) metal coordination : angle 1.97248 / 1.01 ( 15) Misc. bond : bond 0.00069 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 438 time to evaluate : 1.276 Fit side-chains revert: symmetry clash REVERT: A 213 LYS cc_start: 0.7689 (mtpp) cc_final: 0.7164 (mmtm) REVERT: A 289 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7566 (tt0) REVERT: A 336 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7451 (tp) REVERT: A 393 ILE cc_start: 0.7293 (pp) cc_final: 0.7025 (mt) REVERT: A 444 TYR cc_start: 0.7023 (m-10) cc_final: 0.6041 (m-10) REVERT: A 467 MET cc_start: 0.7764 (mmt) cc_final: 0.7457 (mmt) REVERT: A 493 ASN cc_start: 0.8188 (t0) cc_final: 0.7814 (t0) REVERT: A 517 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6448 (mp0) REVERT: A 715 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6731 (mt-10) REVERT: A 718 GLU cc_start: 0.7211 (tp30) cc_final: 0.7006 (tp30) REVERT: A 733 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7507 (tp) REVERT: A 743 ARG cc_start: 0.7278 (tpm170) cc_final: 0.7018 (tpp80) REVERT: A 794 GLU cc_start: 0.6605 (tt0) cc_final: 0.6367 (tt0) REVERT: A 941 ASP cc_start: 0.7586 (t0) cc_final: 0.7377 (t0) REVERT: A 1262 MET cc_start: 0.3220 (tpt) cc_final: 0.2466 (ptm) REVERT: A 1484 MET cc_start: 0.3357 (ppp) cc_final: 0.2201 (ptp) REVERT: B 53 MET cc_start: 0.7662 (mmp) cc_final: 0.7091 (mmm) REVERT: B 109 MET cc_start: 0.7461 (mmm) cc_final: 0.7170 (mmt) REVERT: B 112 GLU cc_start: 0.7595 (mt-10) cc_final: 0.6402 (tt0) REVERT: B 199 LYS cc_start: 0.8554 (ttpp) cc_final: 0.8290 (ttpp) REVERT: B 674 MET cc_start: 0.8295 (tpt) cc_final: 0.7776 (tpt) REVERT: B 784 SER cc_start: 0.8575 (t) cc_final: 0.8336 (p) REVERT: B 859 ARG cc_start: 0.8170 (ptp-110) cc_final: 0.7923 (ttm110) REVERT: B 861 SER cc_start: 0.8752 (t) cc_final: 0.8485 (p) REVERT: B 1157 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8089 (tt) REVERT: B 1171 MET cc_start: 0.8493 (mtm) cc_final: 0.8282 (mtm) REVERT: C 216 SER cc_start: 0.8491 (m) cc_final: 0.8154 (p) REVERT: D 39 MET cc_start: 0.5827 (ttm) cc_final: 0.5316 (ttm) REVERT: D 42 GLU cc_start: 0.6039 (OUTLIER) cc_final: 0.5175 (mt-10) REVERT: D 65 LEU cc_start: 0.1097 (OUTLIER) cc_final: -0.0037 (mt) REVERT: E 108 GLN cc_start: 0.8373 (tm-30) cc_final: 0.7919 (tt0) REVERT: E 116 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7190 (mp10) REVERT: E 158 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: F 80 MET cc_start: 0.5699 (OUTLIER) cc_final: 0.4751 (mmt) REVERT: F 95 LYS cc_start: 0.7265 (ptpt) cc_final: 0.7026 (ptmt) REVERT: F 101 LYS cc_start: 0.7163 (mmmt) cc_final: 0.6776 (mmtp) REVERT: H 16 ASP cc_start: 0.5333 (p0) cc_final: 0.5068 (p0) REVERT: H 146 LYS cc_start: 0.8178 (ptmm) cc_final: 0.7676 (pttp) REVERT: I 92 LYS cc_start: 0.6824 (mttp) cc_final: 0.6255 (mmtm) REVERT: J 26 GLN cc_start: 0.7619 (tp-100) cc_final: 0.7265 (tp40) REVERT: L 50 LYS cc_start: 0.8503 (mttt) cc_final: 0.8156 (mttt) outliers start: 76 outliers final: 36 residues processed: 497 average time/residue: 0.2133 time to fit residues: 170.3142 Evaluate side-chains 459 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 414 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 849 ASP Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain L residue 54 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 138 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 361 optimal weight: 10.0000 chunk 373 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 chunk 323 optimal weight: 8.9990 chunk 197 optimal weight: 6.9990 chunk 350 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN B1021 HIS D 34 ASN E 210 GLN ** G 14 HIS ** 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 = 0.3893 r_free = 0.3893 target = 0.174319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.135098 restraints weight = 34818.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.132314 restraints weight = 46562.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.132441 restraints weight = 42356.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.132861 restraints weight = 31853.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.132880 restraints weight = 29976.844| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.156 33513 Z= 0.286 Angle : 0.752 12.687 45581 Z= 0.390 Chirality : 0.052 0.246 5102 Planarity : 0.006 0.063 5645 Dihedral : 14.019 174.741 5174 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.32 % Favored : 91.66 % Rotamer: Outliers : 2.79 % Allowed : 11.70 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.13), residues: 3860 helix: -1.19 (0.14), residues: 1223 sheet: -0.99 (0.22), residues: 550 loop : -2.37 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 358 TYR 0.026 0.002 TYR B 811 PHE 0.029 0.002 PHE A 548 TRP 0.018 0.002 TRP A 988 HIS 0.010 0.002 HIS A 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00715 / 0.29 (33489) covalent geometry : angle 0.75142 / 0.39 (45566) hydrogen bonds : bond 0.05886 / 3.95 ( 1059) hydrogen bonds : angle 5.02599 / 3.53 ( 2998) metal coordination : bond 0.01021 / 0.63 ( 22) metal coordination : angle 2.21267 / 1.07 ( 15) Misc. bond : bond 0.00026 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 423 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 LYS cc_start: 0.7669 (mtpp) cc_final: 0.7276 (mmtm) REVERT: A 289 GLN cc_start: 0.8614 (tm-30) cc_final: 0.7857 (tt0) REVERT: A 444 TYR cc_start: 0.7027 (m-10) cc_final: 0.6273 (m-10) REVERT: A 493 ASN cc_start: 0.8204 (t0) cc_final: 0.7870 (t0) REVERT: A 517 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6583 (mp0) REVERT: A 715 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6996 (mt-10) REVERT: A 1262 MET cc_start: 0.3684 (tpt) cc_final: 0.2688 (ptm) REVERT: A 1484 MET cc_start: 0.3466 (ppp) cc_final: 0.2507 (ptp) REVERT: B 109 MET cc_start: 0.7536 (mmm) cc_final: 0.7274 (mmt) REVERT: B 112 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6403 (tt0) REVERT: B 187 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8972 (mm) REVERT: B 199 LYS cc_start: 0.8615 (ttpp) cc_final: 0.8414 (ttpp) REVERT: B 407 MET cc_start: 0.7824 (mtm) cc_final: 0.7351 (ptp) REVERT: B 431 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6667 (tp) REVERT: B 456 GLN cc_start: 0.5956 (tp-100) cc_final: 0.5488 (tm-30) REVERT: B 674 MET cc_start: 0.8383 (tpt) cc_final: 0.7909 (tpt) REVERT: C 6 GLN cc_start: 0.7760 (mp-120) cc_final: 0.7415 (mp10) REVERT: C 216 SER cc_start: 0.8459 (m) cc_final: 0.8075 (p) REVERT: D 42 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.5643 (mt-10) REVERT: D 65 LEU cc_start: 0.1172 (OUTLIER) cc_final: -0.0174 (mt) REVERT: E 158 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: F 95 LYS cc_start: 0.7594 (ptpt) cc_final: 0.7274 (ptmt) REVERT: H 16 ASP cc_start: 0.5838 (p0) cc_final: 0.5636 (p0) REVERT: H 111 ARG cc_start: 0.6405 (ttt90) cc_final: 0.5972 (ttt-90) REVERT: H 146 LYS cc_start: 0.8149 (ptmm) cc_final: 0.7873 (ptpt) REVERT: I 92 LYS cc_start: 0.6818 (mttp) cc_final: 0.6308 (mmtm) REVERT: J 26 GLN cc_start: 0.7502 (tp-100) cc_final: 0.7212 (tp40) REVERT: K 84 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7793 (mp10) REVERT: K 102 GLU cc_start: 0.7445 (tt0) cc_final: 0.7201 (tt0) REVERT: L 50 LYS cc_start: 0.8495 (mttt) cc_final: 0.8165 (mttp) outliers start: 96 outliers final: 59 residues processed: 493 average time/residue: 0.2107 time to fit residues: 167.0326 Evaluate side-chains 474 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 408 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 84 GLN Chi-restraints excluded: chain L residue 54 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 122 optimal weight: 10.0000 chunk 334 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 294 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 chunk 193 optimal weight: 0.6980 chunk 361 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 346 optimal weight: 0.6980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 649 ASN ** G 14 HIS ** 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 = 0.3867 r_free = 0.3867 target = 0.171820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.134669 restraints weight = 34632.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.131948 restraints weight = 46649.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.132162 restraints weight = 36842.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.132514 restraints weight = 29310.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.132469 restraints weight = 29793.505| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33513 Z= 0.145 Angle : 0.621 11.422 45581 Z= 0.323 Chirality : 0.047 0.231 5102 Planarity : 0.004 0.052 5645 Dihedral : 13.903 176.907 5174 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.39 % Allowed : 12.78 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.13), residues: 3860 helix: -0.78 (0.15), residues: 1222 sheet: -0.81 (0.23), residues: 517 loop : -2.25 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 358 TYR 0.018 0.001 TYR E 182 PHE 0.013 0.001 PHE C 21 TRP 0.012 0.001 TRP C 176 HIS 0.005 0.001 HIS A 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (33489) covalent geometry : angle 0.61996 / 0.32 (45566) hydrogen bonds : bond 0.04741 / 3.20 ( 1059) hydrogen bonds : angle 4.69649 / 3.30 ( 2998) metal coordination : bond 0.00596 / 0.39 ( 22) metal coordination : angle 1.82197 / 0.90 ( 15) Misc. bond : bond 0.00040 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 415 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: A 38 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6093 (pm20) REVERT: A 213 LYS cc_start: 0.7625 (mtpp) cc_final: 0.7163 (mmtm) REVERT: A 234 PHE cc_start: 0.8027 (t80) cc_final: 0.7114 (t80) REVERT: A 289 GLN cc_start: 0.8519 (tm-30) cc_final: 0.7768 (tt0) REVERT: A 336 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7199 (mp) REVERT: A 341 GLN cc_start: 0.6858 (OUTLIER) cc_final: 0.6516 (pt0) REVERT: A 444 TYR cc_start: 0.7027 (m-10) cc_final: 0.6251 (m-10) REVERT: A 493 ASN cc_start: 0.8166 (t0) cc_final: 0.7807 (t0) REVERT: A 517 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6465 (mp0) REVERT: A 715 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6859 (mt-10) REVERT: A 733 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7764 (tp) REVERT: A 1262 MET cc_start: 0.3398 (tpt) cc_final: 0.2681 (ptm) REVERT: A 1364 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7504 (tp30) REVERT: A 1484 MET cc_start: 0.3382 (ppp) cc_final: 0.2288 (ptp) REVERT: B 28 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8277 (tt) REVERT: B 112 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6400 (tt0) REVERT: B 187 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8837 (mm) REVERT: B 199 LYS cc_start: 0.8566 (ttpp) cc_final: 0.8268 (ttpp) REVERT: B 649 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.7950 (t0) REVERT: B 674 MET cc_start: 0.8323 (tpt) cc_final: 0.7761 (tpt) REVERT: B 1171 MET cc_start: 0.8521 (mtm) cc_final: 0.8222 (mtm) REVERT: C 6 GLN cc_start: 0.7657 (mp-120) cc_final: 0.7309 (mp10) REVERT: C 216 SER cc_start: 0.8429 (m) cc_final: 0.8062 (p) REVERT: D 42 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.5734 (mt-10) REVERT: D 65 LEU cc_start: 0.1149 (OUTLIER) cc_final: -0.0086 (mt) REVERT: E 158 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: F 80 MET cc_start: 0.6017 (OUTLIER) cc_final: 0.4850 (mmt) REVERT: F 95 LYS cc_start: 0.7575 (ptpt) cc_final: 0.7279 (ptmt) REVERT: F 101 LYS cc_start: 0.7171 (mmmt) cc_final: 0.6858 (mmtp) REVERT: H 146 LYS cc_start: 0.8085 (ptmm) cc_final: 0.7824 (ptpt) REVERT: I 92 LYS cc_start: 0.6799 (mttp) cc_final: 0.6367 (mmtm) REVERT: J 26 GLN cc_start: 0.7540 (tp-100) cc_final: 0.7309 (tp40) REVERT: L 50 LYS cc_start: 0.8425 (mttt) cc_final: 0.8118 (mttp) outliers start: 82 outliers final: 47 residues processed: 480 average time/residue: 0.2219 time to fit residues: 170.0424 Evaluate side-chains 463 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 404 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 983 GLU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 54 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 157 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 195 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 chunk 289 optimal weight: 30.0000 chunk 167 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 260 GLN ** G 14 HIS ** 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 = 0.3872 r_free = 0.3872 target = 0.172393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.133436 restraints weight = 34655.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.128845 restraints weight = 38766.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.128849 restraints weight = 46066.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.129725 restraints weight = 35092.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.129830 restraints weight = 28066.831| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33513 Z= 0.129 Angle : 0.595 11.235 45581 Z= 0.311 Chirality : 0.046 0.202 5102 Planarity : 0.004 0.047 5645 Dihedral : 13.830 178.115 5174 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.36 % Allowed : 13.60 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.13), residues: 3860 helix: -0.54 (0.15), residues: 1221 sheet: -0.69 (0.22), residues: 536 loop : -2.15 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1031 TYR 0.018 0.001 TYR E 182 PHE 0.013 0.001 PHE B1108 TRP 0.010 0.001 TRP A 988 HIS 0.005 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (33489) covalent geometry : angle 0.59396 / 0.31 (45566) hydrogen bonds : bond 0.04482 / 3.03 ( 1059) hydrogen bonds : angle 4.53679 / 3.19 ( 2998) metal coordination : bond 0.00475 / 0.33 ( 22) metal coordination : angle 1.69369 / 0.85 ( 15) Misc. bond : bond 0.00037 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 409 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 38 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6078 (pm20) REVERT: A 213 LYS cc_start: 0.7578 (mtpp) cc_final: 0.7004 (mmtm) REVERT: A 234 PHE cc_start: 0.8053 (t80) cc_final: 0.7126 (t80) REVERT: A 289 GLN cc_start: 0.8472 (tm-30) cc_final: 0.7742 (tt0) REVERT: A 341 GLN cc_start: 0.6820 (OUTLIER) cc_final: 0.6476 (pt0) REVERT: A 444 TYR cc_start: 0.7082 (m-10) cc_final: 0.6308 (m-10) REVERT: A 493 ASN cc_start: 0.8186 (t0) cc_final: 0.7827 (t0) REVERT: A 501 MET cc_start: 0.8482 (mtp) cc_final: 0.8164 (mtp) REVERT: A 517 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6528 (mp0) REVERT: A 715 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6966 (mt-10) REVERT: A 733 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7653 (tp) REVERT: A 743 ARG cc_start: 0.7630 (tpp80) cc_final: 0.7180 (tpp80) REVERT: A 950 ASN cc_start: 0.8094 (m-40) cc_final: 0.7391 (t0) REVERT: A 1262 MET cc_start: 0.3494 (tpt) cc_final: 0.2500 (ptm) REVERT: A 1341 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8525 (t) REVERT: A 1364 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7505 (tp30) REVERT: A 1484 MET cc_start: 0.3412 (ppp) cc_final: 0.2290 (ptp) REVERT: B 28 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8257 (tt) REVERT: B 53 MET cc_start: 0.7745 (mmm) cc_final: 0.7198 (mmm) REVERT: B 112 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6394 (tt0) REVERT: B 187 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8801 (mm) REVERT: B 199 LYS cc_start: 0.8521 (ttpp) cc_final: 0.8262 (ttpp) REVERT: B 407 MET cc_start: 0.7732 (mtm) cc_final: 0.7194 (ptp) REVERT: B 456 GLN cc_start: 0.5568 (tp-100) cc_final: 0.5306 (tm-30) REVERT: B 674 MET cc_start: 0.8330 (tpt) cc_final: 0.7778 (tpt) REVERT: B 771 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6925 (mt-10) REVERT: B 1171 MET cc_start: 0.8561 (mtm) cc_final: 0.8277 (mtm) REVERT: C 6 GLN cc_start: 0.7615 (mp-120) cc_final: 0.7299 (mp10) REVERT: C 216 SER cc_start: 0.8503 (m) cc_final: 0.8129 (p) REVERT: D 42 GLU cc_start: 0.6196 (OUTLIER) cc_final: 0.5306 (mt-10) REVERT: E 116 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.6899 (mp10) REVERT: E 158 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: F 80 MET cc_start: 0.5825 (OUTLIER) cc_final: 0.4765 (mmt) REVERT: F 95 LYS cc_start: 0.7466 (ptpt) cc_final: 0.7161 (ptmt) REVERT: H 146 LYS cc_start: 0.8089 (ptmm) cc_final: 0.7801 (ptpt) REVERT: I 92 LYS cc_start: 0.6817 (mttp) cc_final: 0.6309 (mmtm) REVERT: J 26 GLN cc_start: 0.7533 (tp-100) cc_final: 0.7261 (tp40) REVERT: L 50 LYS cc_start: 0.8483 (mttt) cc_final: 0.8133 (mttp) outliers start: 81 outliers final: 54 residues processed: 473 average time/residue: 0.2142 time to fit residues: 162.4924 Evaluate side-chains 464 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 398 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 983 GLU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 54 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 143 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 289 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 341 optimal weight: 0.0070 chunk 210 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 385 optimal weight: 30.0000 chunk 254 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 299 optimal weight: 4.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.172482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.136645 restraints weight = 34444.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.133884 restraints weight = 38616.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.133742 restraints weight = 38658.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.134112 restraints weight = 28879.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.134114 restraints weight = 28310.087| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33513 Z= 0.133 Angle : 0.593 12.603 45581 Z= 0.309 Chirality : 0.046 0.198 5102 Planarity : 0.004 0.052 5645 Dihedral : 13.783 179.833 5174 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.50 % Allowed : 13.83 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.13), residues: 3860 helix: -0.39 (0.15), residues: 1219 sheet: -0.63 (0.23), residues: 526 loop : -2.03 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 107 TYR 0.019 0.001 TYR E 182 PHE 0.014 0.001 PHE A 548 TRP 0.015 0.001 TRP A1192 HIS 0.005 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (33489) covalent geometry : angle 0.59251 / 0.31 (45566) hydrogen bonds : bond 0.04392 / 2.97 ( 1059) hydrogen bonds : angle 4.43757 / 3.12 ( 2998) metal coordination : bond 0.00490 / 0.34 ( 22) metal coordination : angle 1.51700 / 0.75 ( 15) Misc. bond : bond 0.00033 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 403 time to evaluate : 1.159 Fit side-chains revert: symmetry clash REVERT: A 213 LYS cc_start: 0.7460 (mtpp) cc_final: 0.7034 (mmtm) REVERT: A 234 PHE cc_start: 0.7982 (t80) cc_final: 0.7104 (t80) REVERT: A 289 GLN cc_start: 0.8389 (tm-30) cc_final: 0.7663 (tt0) REVERT: A 444 TYR cc_start: 0.7053 (m-10) cc_final: 0.6283 (m-10) REVERT: A 493 ASN cc_start: 0.8176 (t0) cc_final: 0.7802 (t0) REVERT: A 517 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6448 (mp0) REVERT: A 733 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7697 (tp) REVERT: A 950 ASN cc_start: 0.8073 (m-40) cc_final: 0.7401 (t0) REVERT: A 1085 GLU cc_start: 0.7851 (pt0) cc_final: 0.7592 (pt0) REVERT: A 1262 MET cc_start: 0.3434 (tpt) cc_final: 0.2636 (ptm) REVERT: A 1341 VAL cc_start: 0.8769 (OUTLIER) cc_final: 0.8558 (t) REVERT: A 1364 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7459 (tp30) REVERT: A 1484 MET cc_start: 0.3223 (ppp) cc_final: 0.2279 (ptp) REVERT: B 28 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8240 (tt) REVERT: B 53 MET cc_start: 0.7755 (mmm) cc_final: 0.7212 (mmm) REVERT: B 112 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6456 (tt0) REVERT: B 187 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8806 (mm) REVERT: B 199 LYS cc_start: 0.8586 (ttpp) cc_final: 0.8324 (ttpp) REVERT: B 297 MET cc_start: 0.6557 (ttp) cc_final: 0.6228 (ttm) REVERT: B 407 MET cc_start: 0.7722 (mtm) cc_final: 0.7186 (ptp) REVERT: B 431 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6589 (tp) REVERT: B 442 ASP cc_start: 0.6100 (m-30) cc_final: 0.5791 (m-30) REVERT: B 629 GLU cc_start: 0.7732 (tp30) cc_final: 0.7492 (tt0) REVERT: B 649 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7879 (t0) REVERT: B 674 MET cc_start: 0.8333 (tpt) cc_final: 0.7815 (tpt) REVERT: B 771 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6773 (mt-10) REVERT: B 1171 MET cc_start: 0.8578 (mtm) cc_final: 0.8304 (mtm) REVERT: C 6 GLN cc_start: 0.7559 (mp-120) cc_final: 0.7256 (mp10) REVERT: C 216 SER cc_start: 0.8446 (m) cc_final: 0.8080 (p) REVERT: D 42 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.5713 (mt-10) REVERT: D 65 LEU cc_start: 0.1207 (OUTLIER) cc_final: 0.0129 (mt) REVERT: E 116 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7041 (mp10) REVERT: F 80 MET cc_start: 0.6010 (OUTLIER) cc_final: 0.4819 (mmt) REVERT: F 95 LYS cc_start: 0.7600 (ptpt) cc_final: 0.7275 (ptmt) REVERT: F 101 LYS cc_start: 0.7335 (mmmt) cc_final: 0.6805 (mmtp) REVERT: H 146 LYS cc_start: 0.8098 (ptmm) cc_final: 0.7816 (ptpt) REVERT: I 92 LYS cc_start: 0.6802 (mttp) cc_final: 0.6328 (mmtm) REVERT: J 26 GLN cc_start: 0.7503 (tp-100) cc_final: 0.7178 (tp40) REVERT: K 11 LEU cc_start: 0.7587 (mp) cc_final: 0.7317 (mp) REVERT: K 84 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: K 102 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7734 (pt0) REVERT: L 50 LYS cc_start: 0.8454 (mttt) cc_final: 0.8110 (mttp) outliers start: 86 outliers final: 57 residues processed: 469 average time/residue: 0.2179 time to fit residues: 163.7050 Evaluate side-chains 466 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 395 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 983 GLU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 84 GLN Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain L residue 54 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 274 optimal weight: 0.4980 chunk 266 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 196 optimal weight: 0.7980 chunk 178 optimal weight: 4.9990 chunk 372 optimal weight: 1.9990 chunk 329 optimal weight: 50.0000 chunk 142 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 GLN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.169874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.133161 restraints weight = 34667.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.130322 restraints weight = 41956.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.130432 restraints weight = 39971.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.130755 restraints weight = 30603.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.130834 restraints weight = 29567.259| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 33513 Z= 0.207 Angle : 0.659 11.245 45581 Z= 0.343 Chirality : 0.049 0.212 5102 Planarity : 0.005 0.054 5645 Dihedral : 13.829 179.734 5174 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.39 % Allowed : 14.24 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.13), residues: 3860 helix: -0.55 (0.15), residues: 1216 sheet: -0.65 (0.22), residues: 532 loop : -2.10 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 107 TYR 0.020 0.002 TYR B 811 PHE 0.023 0.002 PHE A 548 TRP 0.013 0.002 TRP A 988 HIS 0.007 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.21 (33489) covalent geometry : angle 0.65873 / 0.34 (45566) hydrogen bonds : bond 0.05024 / 3.38 ( 1059) hydrogen bonds : angle 4.56375 / 3.21 ( 2998) metal coordination : bond 0.00711 / 0.46 ( 22) metal coordination : angle 1.65416 / 0.80 ( 15) Misc. bond : bond 0.00022 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 404 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: A 38 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6096 (pm20) REVERT: A 213 LYS cc_start: 0.7440 (mtpp) cc_final: 0.7077 (mmtm) REVERT: A 234 PHE cc_start: 0.8087 (t80) cc_final: 0.7151 (t80) REVERT: A 289 GLN cc_start: 0.8525 (tm-30) cc_final: 0.7808 (tt0) REVERT: A 444 TYR cc_start: 0.7007 (m-10) cc_final: 0.6332 (m-10) REVERT: A 493 ASN cc_start: 0.8130 (t0) cc_final: 0.7777 (t0) REVERT: A 517 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: A 561 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7097 (mmt) REVERT: A 733 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7842 (tp) REVERT: A 950 ASN cc_start: 0.8108 (m-40) cc_final: 0.7425 (t0) REVERT: A 1262 MET cc_start: 0.3909 (tpt) cc_final: 0.2715 (ptm) REVERT: A 1364 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7595 (tp30) REVERT: A 1484 MET cc_start: 0.3508 (ppp) cc_final: 0.2519 (ptp) REVERT: B 53 MET cc_start: 0.7770 (mmm) cc_final: 0.7338 (mmm) REVERT: B 112 GLU cc_start: 0.7446 (mt-10) cc_final: 0.6510 (tt0) REVERT: B 187 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8934 (mm) REVERT: B 199 LYS cc_start: 0.8564 (ttpp) cc_final: 0.8311 (ttpp) REVERT: B 297 MET cc_start: 0.6624 (ttp) cc_final: 0.6293 (ttm) REVERT: B 431 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6719 (tp) REVERT: B 442 ASP cc_start: 0.6118 (m-30) cc_final: 0.5855 (m-30) REVERT: B 674 MET cc_start: 0.8363 (tpt) cc_final: 0.7875 (tpt) REVERT: B 771 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6743 (mt-10) REVERT: C 216 SER cc_start: 0.8455 (m) cc_final: 0.8071 (p) REVERT: D 42 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.5947 (mp0) REVERT: D 65 LEU cc_start: 0.1294 (OUTLIER) cc_final: 0.0138 (mt) REVERT: E 116 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7062 (mp10) REVERT: F 80 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.4900 (mmt) REVERT: F 95 LYS cc_start: 0.7697 (ptpt) cc_final: 0.7337 (ptmt) REVERT: H 111 ARG cc_start: 0.6272 (ttt90) cc_final: 0.5913 (ttt-90) REVERT: H 146 LYS cc_start: 0.8123 (ptmm) cc_final: 0.7845 (ptpt) REVERT: I 92 LYS cc_start: 0.6743 (mttp) cc_final: 0.6289 (mmtm) REVERT: J 26 GLN cc_start: 0.7552 (tp-100) cc_final: 0.7260 (tp40) REVERT: K 29 ASN cc_start: 0.6914 (m110) cc_final: 0.6688 (m-40) REVERT: K 84 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7690 (mp10) REVERT: L 50 LYS cc_start: 0.8429 (mttt) cc_final: 0.8113 (mttp) outliers start: 82 outliers final: 61 residues processed: 470 average time/residue: 0.2138 time to fit residues: 160.2798 Evaluate side-chains 472 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 399 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 983 GLU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 84 GLN Chi-restraints excluded: chain L residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 346 optimal weight: 1.9990 chunk 358 optimal weight: 1.9990 chunk 310 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 316 optimal weight: 8.9990 chunk 20 optimal weight: 0.2980 chunk 105 optimal weight: 0.8980 chunk 161 optimal weight: 9.9990 chunk 312 optimal weight: 0.9980 chunk 186 optimal weight: 0.0980 chunk 144 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.173589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.137266 restraints weight = 34557.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.133369 restraints weight = 41113.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.133420 restraints weight = 43063.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.134263 restraints weight = 31576.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.134198 restraints weight = 27538.691| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 33513 Z= 0.108 Angle : 0.582 11.544 45581 Z= 0.304 Chirality : 0.045 0.200 5102 Planarity : 0.004 0.052 5645 Dihedral : 13.752 178.217 5174 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.60 % Allowed : 14.91 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.13), residues: 3860 helix: -0.15 (0.15), residues: 1202 sheet: -0.52 (0.23), residues: 519 loop : -1.91 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.000 ARG A 342 TYR 0.018 0.001 TYR E 182 PHE 0.013 0.001 PHE B 320 TRP 0.015 0.001 TRP A1192 HIS 0.005 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (33489) covalent geometry : angle 0.58154 / 0.30 (45566) hydrogen bonds : bond 0.04169 / 2.82 ( 1059) hydrogen bonds : angle 4.33314 / 3.05 ( 2998) metal coordination : bond 0.00427 / 0.30 ( 22) metal coordination : angle 1.45128 / 0.74 ( 15) Misc. bond : bond 0.00056 / 0.03 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 415 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: A 38 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6055 (pm20) REVERT: A 213 LYS cc_start: 0.7445 (mtpp) cc_final: 0.7026 (mmtm) REVERT: A 234 PHE cc_start: 0.7868 (t80) cc_final: 0.7016 (t80) REVERT: A 289 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7654 (tt0) REVERT: A 444 TYR cc_start: 0.7011 (m-10) cc_final: 0.6333 (m-10) REVERT: A 493 ASN cc_start: 0.8122 (t0) cc_final: 0.7752 (t0) REVERT: A 501 MET cc_start: 0.8385 (mtp) cc_final: 0.8132 (mtp) REVERT: A 517 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6577 (mp0) REVERT: A 559 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7078 (pt0) REVERT: A 561 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7007 (mmt) REVERT: A 733 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7686 (tp) REVERT: A 743 ARG cc_start: 0.7599 (tpp80) cc_final: 0.7139 (tpp80) REVERT: A 950 ASN cc_start: 0.8017 (m-40) cc_final: 0.7322 (t0) REVERT: A 1085 GLU cc_start: 0.7776 (pt0) cc_final: 0.7479 (pt0) REVERT: A 1262 MET cc_start: 0.3687 (tpt) cc_final: 0.2573 (ptm) REVERT: A 1364 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7457 (tp30) REVERT: A 1484 MET cc_start: 0.3400 (ppp) cc_final: 0.2325 (ptp) REVERT: B 53 MET cc_start: 0.7644 (mmm) cc_final: 0.7208 (mmm) REVERT: B 112 GLU cc_start: 0.7551 (mt-10) cc_final: 0.6624 (tt0) REVERT: B 199 LYS cc_start: 0.8520 (ttpp) cc_final: 0.8290 (ttpp) REVERT: B 555 GLU cc_start: 0.7381 (pp20) cc_final: 0.7064 (pp20) REVERT: B 629 GLU cc_start: 0.7660 (tp30) cc_final: 0.7449 (tt0) REVERT: B 674 MET cc_start: 0.8301 (tpt) cc_final: 0.7782 (tpt) REVERT: B 771 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6904 (mt-10) REVERT: B 816 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7458 (tp30) REVERT: B 942 LYS cc_start: 0.8301 (ptpp) cc_final: 0.7912 (ptpp) REVERT: C 216 SER cc_start: 0.8411 (m) cc_final: 0.8051 (p) REVERT: D 42 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.5842 (mp0) REVERT: E 116 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7243 (mp10) REVERT: F 80 MET cc_start: 0.5984 (OUTLIER) cc_final: 0.4805 (mmt) REVERT: F 95 LYS cc_start: 0.7638 (ptpt) cc_final: 0.7319 (ptmt) REVERT: F 101 LYS cc_start: 0.7363 (mmmt) cc_final: 0.6789 (mmtp) REVERT: H 146 LYS cc_start: 0.8069 (ptmm) cc_final: 0.7809 (ptpt) REVERT: I 92 LYS cc_start: 0.6735 (mttp) cc_final: 0.6340 (mmtm) REVERT: J 26 GLN cc_start: 0.7484 (tp-100) cc_final: 0.7221 (tp40) REVERT: K 102 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7734 (pt0) REVERT: L 50 LYS cc_start: 0.8425 (mttt) cc_final: 0.8195 (mttt) outliers start: 55 outliers final: 44 residues processed: 459 average time/residue: 0.2166 time to fit residues: 158.2321 Evaluate side-chains 451 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 397 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 983 GLU Chi-restraints excluded: chain B residue 1132 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain L residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 170 optimal weight: 5.9990 chunk 285 optimal weight: 8.9990 chunk 281 optimal weight: 0.1980 chunk 366 optimal weight: 0.8980 chunk 336 optimal weight: 50.0000 chunk 283 optimal weight: 4.9990 chunk 257 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 363 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 757 GLN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** 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 = 0.3865 r_free = 0.3865 target = 0.171717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.133946 restraints weight = 34738.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.130270 restraints weight = 37388.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.130279 restraints weight = 40578.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.131483 restraints weight = 31032.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.131198 restraints weight = 26229.353| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 33513 Z= 0.152 Angle : 0.610 11.110 45581 Z= 0.317 Chirality : 0.047 0.197 5102 Planarity : 0.004 0.046 5645 Dihedral : 13.744 177.891 5174 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.04 % Allowed : 14.79 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.13), residues: 3860 helix: -0.24 (0.15), residues: 1210 sheet: -0.51 (0.23), residues: 530 loop : -1.91 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 380 TYR 0.019 0.001 TYR E 182 PHE 0.018 0.001 PHE J 8 TRP 0.014 0.001 TRP A1192 HIS 0.005 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (33489) covalent geometry : angle 0.60968 / 0.32 (45566) hydrogen bonds : bond 0.04458 / 3.01 ( 1059) hydrogen bonds : angle 4.35308 / 3.07 ( 2998) metal coordination : bond 0.00557 / 0.39 ( 22) metal coordination : angle 1.69235 / 0.85 ( 15) Misc. bond : bond 0.00005 / 0.00 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5484.99 seconds wall clock time: 95 minutes 33.43 seconds (5733.43 seconds total)