Starting phenix.real_space_refine on Sat May 24 13:17:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eot_28467/05_2025/8eot_28467.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eot_28467/05_2025/8eot_28467.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eot_28467/05_2025/8eot_28467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eot_28467/05_2025/8eot_28467.map" model { file = "/net/cci-nas-00/data/ceres_data/8eot_28467/05_2025/8eot_28467.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eot_28467/05_2025/8eot_28467.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.070 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 2 6.06 5 P 77 5.49 5 Mg 1 5.21 5 S 87 5.16 5 C 15609 2.51 5 N 4508 2.21 5 O 5015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.90s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25299 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1765 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "D" Number of atoms: 9919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1269, 9919 Classifications: {'peptide': 1269} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1208} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "T" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 672 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "N" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain breaks: 1 Chain: "R" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 288 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna2p': 4, 'rna3p': 8} Chain: "G" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 968 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "C" Number of atoms: 8677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 8677 Classifications: {'peptide': 1122} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1060} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "D" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10540 SG CYS D 891 76.145 24.372 88.191 1.00 58.35 S ATOM 11107 SG CYS D 968 74.969 27.728 89.600 1.00 26.26 S ATOM 11149 SG CYS D 975 76.339 27.527 86.092 1.00 36.11 S ATOM 11167 SG CYS D 978 72.995 25.982 86.830 1.00 41.48 S ATOM 3978 SG CYS D 60 109.270 80.364 114.882 1.00 82.75 S ATOM 3996 SG CYS D 62 109.748 82.390 118.089 1.00 94.55 S ATOM 4105 SG CYS D 75 111.916 79.241 117.328 1.00 85.07 S ATOM 4131 SG CYS D 78 108.257 78.947 118.220 1.00 86.04 S Time building chain proxies: 14.35, per 1000 atoms: 0.57 Number of scatterers: 25299 At special positions: 0 Unit cell: (127.02, 133.98, 200.1, 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 2 29.99 S 87 16.00 P 77 15.00 Mg 1 11.99 O 5015 8.00 N 4508 7.00 C 15609 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.03 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 891 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 62 " Number of angles added : 12 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5624 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 43 sheets defined 37.6% alpha, 16.4% beta 29 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 8.56 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 removed outlier: 3.690A pdb=" N SER A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 203 through 224 removed outlier: 3.852A pdb=" N LEU A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 44 removed outlier: 4.121A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 211 Processing helix chain 'B' and resid 215 through 224 removed outlier: 4.596A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 7 removed outlier: 3.723A pdb=" N PHE D 7 " --> pdb=" O VAL D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.676A pdb=" N SER D 24 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 removed outlier: 3.547A pdb=" N LYS D 71 " --> pdb=" O VAL D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 90 removed outlier: 3.725A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU D 90 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 107 Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.674A pdb=" N TYR D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 146 removed outlier: 4.006A pdb=" N ARG D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 182 removed outlier: 3.511A pdb=" N GLN D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 227 removed outlier: 3.706A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP D 199 " --> pdb=" O ARG D 195 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG D 209 " --> pdb=" O MET D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 248 Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.571A pdb=" N LYS D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.771A pdb=" N LEU D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 removed outlier: 3.664A pdb=" N LEU D 324 " --> pdb=" O PRO D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 359 removed outlier: 3.615A pdb=" N VAL D 347 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.917A pdb=" N LEU D 406 " --> pdb=" O SER D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 478 Processing helix chain 'D' and resid 483 through 491 removed outlier: 3.547A pdb=" N GLU D 488 " --> pdb=" O TRP D 484 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE D 491 " --> pdb=" O LEU D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.566A pdb=" N ASN D 564 " --> pdb=" O SER D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 589 removed outlier: 3.566A pdb=" N THR D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR D 589 " --> pdb=" O LEU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 624 removed outlier: 3.576A pdb=" N ARG D 624 " --> pdb=" O MET D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 667 through 675 removed outlier: 3.564A pdb=" N VAL D 671 " --> pdb=" O THR D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 725 removed outlier: 3.986A pdb=" N VAL D 709 " --> pdb=" O PRO D 705 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA D 710 " --> pdb=" O MET D 706 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP D 714 " --> pdb=" O ALA D 710 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 736 Processing helix chain 'D' and resid 742 through 762 removed outlier: 3.635A pdb=" N GLU D 751 " --> pdb=" O ASP D 747 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA D 753 " --> pdb=" O TYR D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 791 removed outlier: 3.927A pdb=" N GLU D 780 " --> pdb=" O GLU D 776 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA D 781 " --> pdb=" O ILE D 777 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR D 782 " --> pdb=" O TRP D 778 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP D 783 " --> pdb=" O LYS D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 805 removed outlier: 4.007A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER D 805 " --> pdb=" O THR D 801 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 819 removed outlier: 4.068A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 853 removed outlier: 3.667A pdb=" N THR D 853 " --> pdb=" O TYR D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 881 removed outlier: 3.586A pdb=" N ARG D 857 " --> pdb=" O THR D 853 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS D 858 " --> pdb=" O HIS D 854 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY D 859 " --> pdb=" O GLY D 855 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU D 860 " --> pdb=" O ALA D 856 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU D 865 " --> pdb=" O ALA D 861 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR D 867 " --> pdb=" O THR D 863 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ALA D 868 " --> pdb=" O ALA D 864 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP D 869 " --> pdb=" O LEU D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 921 removed outlier: 3.556A pdb=" N TYR D 921 " --> pdb=" O GLU D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 954 Processing helix chain 'D' and resid 964 through 968 removed outlier: 3.722A pdb=" N CYS D 968 " --> pdb=" O VAL D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1005 removed outlier: 4.149A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA D 999 " --> pdb=" O VAL D 995 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA D1000 " --> pdb=" O GLY D 996 " (cutoff:3.500A) Processing helix chain 'D' and resid 1006 through 1008 No H-bonds generated for 'chain 'D' and resid 1006 through 1008' Processing helix chain 'D' and resid 1027 through 1035 Processing helix chain 'D' and resid 1117 through 1145 removed outlier: 3.506A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Proline residue: D1127 - end of helix removed outlier: 3.819A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1162 removed outlier: 3.828A pdb=" N VAL D1156 " --> pdb=" O LYS D1152 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN D1160 " --> pdb=" O VAL D1156 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D1162 " --> pdb=" O VAL D1158 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1194 Processing helix chain 'D' and resid 1219 through 1227 removed outlier: 3.718A pdb=" N GLN D1227 " --> pdb=" O ALA D1223 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1247 through 1255 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 removed outlier: 3.570A pdb=" N ASN D1269 " --> pdb=" O ASN D1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.530A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN E 37 " --> pdb=" O GLY E 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 33 through 37' Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 70 removed outlier: 3.795A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN E 70 " --> pdb=" O ASP E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'G' and resid 33 through 45 Processing helix chain 'G' and resid 58 through 74 Processing helix chain 'G' and resid 116 through 125 Processing helix chain 'G' and resid 143 through 150 removed outlier: 3.548A pdb=" N PHE G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.369A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 Processing helix chain 'C' and resid 85 through 94 removed outlier: 3.728A pdb=" N VAL C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 234 through 242 Processing helix chain 'C' and resid 244 through 252 removed outlier: 3.932A pdb=" N VAL C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 removed outlier: 4.468A pdb=" N ARG C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS C 264 " --> pdb=" O SER C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 removed outlier: 3.855A pdb=" N LYS C 280 " --> pdb=" O ASP C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.940A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.762A pdb=" N LYS C 318 " --> pdb=" O TYR C 314 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU C 320 " --> pdb=" O VAL C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 404 removed outlier: 3.763A pdb=" N GLN C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG C 398 " --> pdb=" O SER C 394 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL C 399 " --> pdb=" O ARG C 395 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.607A pdb=" N ILE C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.804A pdb=" N LYS C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 537 Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.668A pdb=" N MET C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 removed outlier: 3.593A pdb=" N HIS C 599 " --> pdb=" O PHE C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 632 through 637 removed outlier: 3.532A pdb=" N ILE C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP C 637 " --> pdb=" O ARG C 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 632 through 637' Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 856 through 858 No H-bonds generated for 'chain 'C' and resid 856 through 858' Processing helix chain 'C' and resid 900 through 904 removed outlier: 3.527A pdb=" N ASP C 903 " --> pdb=" O PRO C 900 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET C 904 " --> pdb=" O VAL C 901 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 900 through 904' Processing helix chain 'C' and resid 928 through 943 removed outlier: 3.806A pdb=" N LEU C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 981 through 990 removed outlier: 3.807A pdb=" N SER C 990 " --> pdb=" O GLN C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1080 Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 3.962A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1097 through 1109 removed outlier: 3.679A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.956A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'C' and resid 1156 through 1160 removed outlier: 3.777A pdb=" N ALA C1159 " --> pdb=" O GLU C1156 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA C1160 " --> pdb=" O ARG C1157 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1156 through 1160' Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 6.219A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 189 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.682A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 removed outlier: 3.638A pdb=" N VAL A 147 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 166 " --> pdb=" O VAL A 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 15 removed outlier: 5.569A pdb=" N LEU B 9 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N GLU B 24 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLU B 11 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL B 22 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL B 13 " --> pdb=" O GLN B 20 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLN B 20 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N THR B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL B 183 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE B 189 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 8.015A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'D' and resid 93 through 102 removed outlier: 7.191A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 10.282A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 234 through 235 removed outlier: 3.634A pdb=" N TYR D 134 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 420 through 422 removed outlier: 3.752A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.842A pdb=" N ALA D 521 " --> pdb=" O PRO D 444 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AB7, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AB8, first strand: chain 'D' and resid 897 through 899 removed outlier: 4.804A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 929 through 930 removed outlier: 7.253A pdb=" N ALA D 929 " --> pdb=" O ILE D 937 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 1067 through 1068 removed outlier: 3.503A pdb=" N GLY D1051 " --> pdb=" O VAL D1105 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1061 through 1064 removed outlier: 6.535A pdb=" N TYR D1062 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS D1079 " --> pdb=" O TYR D1062 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 1089 through 1090 Processing sheet with id=AC4, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 7.022A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AC6, first strand: chain 'G' and resid 79 through 83 removed outlier: 3.648A pdb=" N GLN G 81 " --> pdb=" O ARG G 112 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY G 131 " --> pdb=" O HIS G 53 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 86 through 93 Processing sheet with id=AC8, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.587A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.753A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AD2, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.583A pdb=" N SER C 177 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 188 through 191 removed outlier: 4.085A pdb=" N HIS C 200 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL C 224 " --> pdb=" O GLN C 232 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 232 " --> pdb=" O VAL C 224 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 354 through 356 Processing sheet with id=AD5, first strand: chain 'C' and resid 505 through 506 removed outlier: 4.870A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AD7, first strand: chain 'C' and resid 558 through 562 Processing sheet with id=AD8, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.708A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.960A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 648 " --> pdb=" O VAL C 696 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 676 through 677 Processing sheet with id=AE2, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AE3, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 7.167A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU C 917 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA C 722 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR C1024 " --> pdb=" O ILE C 723 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 749 through 760 removed outlier: 3.976A pdb=" N VAL C 869 " --> pdb=" O ILE C 757 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU C 867 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N LYS C 876 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY C 845 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY C 845 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 768 through 769 removed outlier: 3.653A pdb=" N GLU C 768 " --> pdb=" O VAL C 806 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 801 through 803 removed outlier: 7.107A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 944 through 945 891 hydrogen bonds defined for protein. 2493 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 12.48 Time building geometry restraints manager: 7.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6889 1.33 - 1.45: 4269 1.45 - 1.57: 14433 1.57 - 1.69: 150 1.69 - 1.81: 153 Bond restraints: 25894 Sorted by residual: bond pdb=" N VAL B 111 " pdb=" CA VAL B 111 " ideal model delta sigma weight residual 1.461 1.500 -0.039 1.23e-02 6.61e+03 1.00e+01 bond pdb=" N ILE B 110 " pdb=" CA ILE B 110 " ideal model delta sigma weight residual 1.459 1.496 -0.038 1.25e-02 6.40e+03 9.09e+00 bond pdb=" N GLU C 303 " pdb=" CA GLU C 303 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.90e+00 bond pdb=" N ARG C 230 " pdb=" CA ARG C 230 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.19e+00 bond pdb=" N ASP B 109 " pdb=" CA ASP B 109 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.18e-02 7.18e+03 6.83e+00 ... (remaining 25889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 34092 1.45 - 2.91: 1100 2.91 - 4.36: 199 4.36 - 5.81: 26 5.81 - 7.26: 8 Bond angle restraints: 35425 Sorted by residual: angle pdb=" N PRO B 112 " pdb=" CA PRO B 112 " pdb=" C PRO B 112 " ideal model delta sigma weight residual 110.70 117.20 -6.50 1.22e+00 6.72e-01 2.84e+01 angle pdb=" C ARG B 182 " pdb=" CA ARG B 182 " pdb=" CB ARG B 182 " ideal model delta sigma weight residual 110.79 104.83 5.96 1.39e+00 5.18e-01 1.84e+01 angle pdb=" CA PRO B 113 " pdb=" C PRO B 113 " pdb=" O PRO B 113 " ideal model delta sigma weight residual 121.67 117.23 4.44 1.22e+00 6.72e-01 1.32e+01 angle pdb=" N LYS C 304 " pdb=" CA LYS C 304 " pdb=" C LYS C 304 " ideal model delta sigma weight residual 113.55 108.98 4.57 1.26e+00 6.30e-01 1.32e+01 angle pdb=" C VAL C 409 " pdb=" N GLU C 410 " pdb=" CA GLU C 410 " ideal model delta sigma weight residual 121.54 128.34 -6.80 1.91e+00 2.74e-01 1.27e+01 ... (remaining 35420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 15107 35.84 - 71.69: 526 71.69 - 107.53: 14 107.53 - 143.38: 0 143.38 - 179.22: 1 Dihedral angle restraints: 15648 sinusoidal: 6895 harmonic: 8753 Sorted by residual: dihedral pdb=" O4' A R 19 " pdb=" C1' A R 19 " pdb=" N9 A R 19 " pdb=" C4 A R 19 " ideal model delta sinusoidal sigma weight residual -106.00 -171.29 65.29 1 1.70e+01 3.46e-03 1.93e+01 dihedral pdb=" O4' G R 20 " pdb=" C1' G R 20 " pdb=" N9 G R 20 " pdb=" C4 G R 20 " ideal model delta sinusoidal sigma weight residual -106.00 -169.04 63.04 1 1.70e+01 3.46e-03 1.82e+01 dihedral pdb=" CA SER C1093 " pdb=" C SER C1093 " pdb=" N ASP C1094 " pdb=" CA ASP C1094 " ideal model delta harmonic sigma weight residual -180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 15645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3620 0.073 - 0.145: 408 0.145 - 0.218: 10 0.218 - 0.290: 4 0.290 - 0.363: 2 Chirality restraints: 4044 Sorted by residual: chirality pdb=" CB VAL B 111 " pdb=" CA VAL B 111 " pdb=" CG1 VAL B 111 " pdb=" CG2 VAL B 111 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA LEU C 308 " pdb=" N LEU C 308 " pdb=" C LEU C 308 " pdb=" CB LEU C 308 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA TYR C 306 " pdb=" N TYR C 306 " pdb=" C TYR C 306 " pdb=" CB TYR C 306 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 4041 not shown) Planarity restraints: 4394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 657 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO D 658 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 658 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 658 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 444 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.09e+00 pdb=" N PRO C 445 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 445 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 445 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 413 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO C 414 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 414 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 414 " -0.026 5.00e-02 4.00e+02 ... (remaining 4391 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 158 2.59 - 3.17: 19756 3.17 - 3.74: 36375 3.74 - 4.32: 48819 4.32 - 4.90: 84753 Nonbonded interactions: 189861 Sorted by model distance: nonbonded pdb=" OD1 ASP D 539 " pdb="MG MG D2001 " model vdw 2.009 2.170 nonbonded pdb=" O3' A R 30 " pdb="MG MG D2001 " model vdw 2.079 2.170 nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2001 " model vdw 2.216 2.170 nonbonded pdb=" O GLY D1247 " pdb=" ND2 ASN D1251 " model vdw 2.235 3.120 nonbonded pdb=" O SER C 182 " pdb=" OH TYR C 186 " model vdw 2.239 3.040 ... (remaining 189856 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 223 o \ r (resid 224 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 25 through 226)) selection = (chain 'B' and resid 1 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 71.690 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.120 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25902 Z= 0.197 Angle : 0.631 7.264 35437 Z= 0.372 Chirality : 0.045 0.363 4044 Planarity : 0.005 0.063 4394 Dihedral : 15.750 179.223 10024 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.45 % Favored : 94.42 % Rotamer: Outliers : 6.03 % Allowed : 9.74 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.15), residues: 3045 helix: -0.12 (0.16), residues: 1027 sheet: -0.01 (0.27), residues: 405 loop : -1.85 (0.14), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D1220 HIS 0.004 0.001 HIS C 372 PHE 0.017 0.001 PHE C 301 TYR 0.015 0.001 TYR C 731 ARG 0.003 0.000 ARG D 556 Details of bonding type rmsd hydrogen bonds : bond 0.17227 ( 966) hydrogen bonds : angle 5.78155 ( 2647) metal coordination : bond 0.00586 ( 8) metal coordination : angle 1.60570 ( 12) covalent geometry : bond 0.00418 (25894) covalent geometry : angle 0.63023 (35425) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 146 time to evaluate : 2.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 91 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7379 (mtt-85) REVERT: D 460 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8864 (mp) REVERT: C 373 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8500 (t80) REVERT: C 570 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7282 (m-80) REVERT: C 1066 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8592 (mp10) outliers start: 154 outliers final: 62 residues processed: 292 average time/residue: 0.3518 time to fit residues: 162.9531 Evaluate side-chains 171 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 104 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 606 HIS Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 726 ARG Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 981 ARG Chi-restraints excluded: chain D residue 995 VAL Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1089 PHE Chi-restraints excluded: chain D residue 1131 GLN Chi-restraints excluded: chain D residue 1262 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 783 ASP Chi-restraints excluded: chain C residue 833 ARG Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 1066 GLN Chi-restraints excluded: chain C residue 1127 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 7.9990 chunk 234 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 chunk 94 optimal weight: 0.2980 chunk 147 optimal weight: 0.9990 chunk 180 optimal weight: 4.9990 chunk 281 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 36 ASN A 100 GLN D 146 ASN D 262 GLN D 283 ASN D 505 HIS D 552 GLN D 563 ASN D 674 ASN D 685 ASN D 693 GLN ** D 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1032 GLN D1239 ASN C 178 GLN C 435 GLN C 443 ASN C 543 GLN C 610 ASN C 875 GLN C 889 HIS C1055 GLN C1165 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.064369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.041722 restraints weight = 93318.830| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.47 r_work: 0.2646 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25902 Z= 0.146 Angle : 0.544 7.209 35437 Z= 0.291 Chirality : 0.042 0.179 4044 Planarity : 0.004 0.065 4394 Dihedral : 15.815 178.558 4348 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.25 % Favored : 94.68 % Rotamer: Outliers : 3.83 % Allowed : 11.97 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.15), residues: 3045 helix: 0.28 (0.17), residues: 1049 sheet: 0.08 (0.26), residues: 424 loop : -1.65 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 944 HIS 0.005 0.001 HIS C 323 PHE 0.014 0.001 PHE C 153 TYR 0.012 0.001 TYR C 731 ARG 0.006 0.000 ARG G 154 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 966) hydrogen bonds : angle 4.46074 ( 2647) metal coordination : bond 0.00890 ( 8) metal coordination : angle 3.10936 ( 12) covalent geometry : bond 0.00342 (25894) covalent geometry : angle 0.54064 (35425) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 119 time to evaluate : 2.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LYS cc_start: 0.9055 (ttpp) cc_final: 0.8726 (mtpp) REVERT: D 205 MET cc_start: 0.8491 (ppp) cc_final: 0.8234 (ppp) REVERT: D 460 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8748 (mp) REVERT: D 866 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8055 (mtp180) REVERT: D 983 MET cc_start: 0.9106 (mmm) cc_final: 0.8888 (mmm) REVERT: D 1112 MET cc_start: 0.8620 (tpt) cc_final: 0.8322 (tpt) REVERT: E 42 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8472 (mt-10) REVERT: G 102 ARG cc_start: 0.9177 (ttm110) cc_final: 0.8500 (ptp90) REVERT: C 103 MET cc_start: 0.9394 (OUTLIER) cc_final: 0.9052 (ptm) REVERT: C 274 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8649 (mp) REVERT: C 373 PHE cc_start: 0.9434 (OUTLIER) cc_final: 0.8860 (t80) REVERT: C 570 TYR cc_start: 0.9306 (OUTLIER) cc_final: 0.8192 (m-80) outliers start: 98 outliers final: 55 residues processed: 210 average time/residue: 0.3259 time to fit residues: 112.8144 Evaluate side-chains 169 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 108 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 606 HIS Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 866 ARG Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 981 ARG Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1127 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 64 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 chunk 62 optimal weight: 40.0000 chunk 42 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 229 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 193 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 283 ASN D 826 ASN D1109 GLN C 443 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.063600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.040966 restraints weight = 93083.545| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 3.47 r_work: 0.2625 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25902 Z= 0.165 Angle : 0.536 10.717 35437 Z= 0.284 Chirality : 0.043 0.201 4044 Planarity : 0.004 0.066 4394 Dihedral : 15.595 178.367 4301 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.45 % Favored : 94.48 % Rotamer: Outliers : 3.79 % Allowed : 12.64 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 3045 helix: 0.53 (0.17), residues: 1052 sheet: 0.13 (0.26), residues: 424 loop : -1.59 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1220 HIS 0.006 0.001 HIS C 323 PHE 0.014 0.001 PHE C 153 TYR 0.012 0.001 TYR C 731 ARG 0.008 0.000 ARG G 124 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 966) hydrogen bonds : angle 4.26694 ( 2647) metal coordination : bond 0.00838 ( 8) metal coordination : angle 2.52478 ( 12) covalent geometry : bond 0.00393 (25894) covalent geometry : angle 0.53433 (35425) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 111 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8383 (tm-30) REVERT: D 91 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8503 (mtt180) REVERT: D 126 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.8955 (tp30) REVERT: D 205 MET cc_start: 0.8686 (ppp) cc_final: 0.8419 (ppp) REVERT: D 688 MET cc_start: 0.9114 (mmp) cc_final: 0.8829 (mmt) REVERT: D 866 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8108 (mtp180) REVERT: D 983 MET cc_start: 0.9142 (mmm) cc_final: 0.8781 (mmm) REVERT: D 1112 MET cc_start: 0.8592 (tpt) cc_final: 0.8310 (tpt) REVERT: E 42 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8519 (mt-10) REVERT: G 83 GLU cc_start: 0.6772 (mp0) cc_final: 0.6359 (mp0) REVERT: G 88 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7734 (tp30) REVERT: C 373 PHE cc_start: 0.9443 (OUTLIER) cc_final: 0.8804 (t80) REVERT: C 570 TYR cc_start: 0.9346 (OUTLIER) cc_final: 0.8239 (m-80) outliers start: 97 outliers final: 65 residues processed: 204 average time/residue: 0.3502 time to fit residues: 117.7575 Evaluate side-chains 175 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 104 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 606 HIS Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 866 ARG Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 981 ARG Chi-restraints excluded: chain D residue 995 VAL Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 783 ASP Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1041 ILE Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1127 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 66 optimal weight: 10.0000 chunk 284 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 299 optimal weight: 0.6980 chunk 257 optimal weight: 8.9990 chunk 267 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.064370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.041775 restraints weight = 93214.242| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 3.47 r_work: 0.2657 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25902 Z= 0.113 Angle : 0.493 8.502 35437 Z= 0.260 Chirality : 0.041 0.233 4044 Planarity : 0.004 0.065 4394 Dihedral : 15.362 177.559 4294 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.56 % Favored : 95.37 % Rotamer: Outliers : 3.13 % Allowed : 14.01 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.15), residues: 3045 helix: 0.83 (0.17), residues: 1052 sheet: 0.17 (0.26), residues: 432 loop : -1.46 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D1220 HIS 0.009 0.001 HIS C 323 PHE 0.016 0.001 PHE C 153 TYR 0.010 0.001 TYR C 731 ARG 0.008 0.000 ARG G 102 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 966) hydrogen bonds : angle 3.97947 ( 2647) metal coordination : bond 0.00529 ( 8) metal coordination : angle 2.18791 ( 12) covalent geometry : bond 0.00260 (25894) covalent geometry : angle 0.49147 (35425) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 110 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LYS cc_start: 0.9154 (ttpp) cc_final: 0.8792 (mtpp) REVERT: D 91 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8308 (mtt180) REVERT: D 126 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8942 (tp30) REVERT: D 243 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8762 (tp30) REVERT: D 507 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9188 (mm) REVERT: D 688 MET cc_start: 0.9025 (mmp) cc_final: 0.8801 (mmt) REVERT: D 925 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9014 (tt) REVERT: D 978 CYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8658 (m) REVERT: D 983 MET cc_start: 0.9099 (mmm) cc_final: 0.8765 (mmm) REVERT: D 1112 MET cc_start: 0.8631 (tpt) cc_final: 0.8386 (tpt) REVERT: G 83 GLU cc_start: 0.6174 (mp0) cc_final: 0.5863 (mp0) REVERT: G 102 ARG cc_start: 0.9136 (ttm110) cc_final: 0.8693 (ptp90) REVERT: C 103 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.8875 (pmm) REVERT: C 373 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.8778 (t80) REVERT: C 570 TYR cc_start: 0.9339 (OUTLIER) cc_final: 0.8291 (m-80) outliers start: 80 outliers final: 46 residues processed: 183 average time/residue: 0.3308 time to fit residues: 100.4056 Evaluate side-chains 162 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 107 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 606 HIS Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 978 CYS Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1127 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 294 optimal weight: 2.9990 chunk 260 optimal weight: 0.0970 chunk 25 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 97 optimal weight: 0.4980 chunk 215 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 143 optimal weight: 8.9990 chunk 254 optimal weight: 1.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.063621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.040952 restraints weight = 93525.700| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 3.49 r_work: 0.2632 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25902 Z= 0.141 Angle : 0.510 8.420 35437 Z= 0.269 Chirality : 0.042 0.202 4044 Planarity : 0.004 0.065 4394 Dihedral : 15.284 177.647 4278 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.39 % Favored : 94.55 % Rotamer: Outliers : 3.64 % Allowed : 14.28 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3045 helix: 0.93 (0.17), residues: 1056 sheet: 0.24 (0.26), residues: 420 loop : -1.42 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1220 HIS 0.002 0.001 HIS E 100 PHE 0.013 0.001 PHE C 153 TYR 0.011 0.001 TYR C 731 ARG 0.006 0.000 ARG G 102 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 966) hydrogen bonds : angle 3.96302 ( 2647) metal coordination : bond 0.00681 ( 8) metal coordination : angle 2.15418 ( 12) covalent geometry : bond 0.00336 (25894) covalent geometry : angle 0.50833 (35425) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 111 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LYS cc_start: 0.9171 (ttpp) cc_final: 0.8811 (mtpp) REVERT: D 11 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8800 (ttp80) REVERT: D 91 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8399 (mtt180) REVERT: D 243 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8769 (tp30) REVERT: D 507 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9197 (mm) REVERT: D 688 MET cc_start: 0.9078 (mmp) cc_final: 0.8873 (mmt) REVERT: D 978 CYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8650 (m) REVERT: D 983 MET cc_start: 0.9118 (mmm) cc_final: 0.8682 (mmm) REVERT: D 1112 MET cc_start: 0.8616 (tpt) cc_final: 0.8396 (tpt) REVERT: G 43 ARG cc_start: 0.9194 (ttp-110) cc_final: 0.8986 (ttp-110) REVERT: G 88 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7622 (tp30) REVERT: G 102 ARG cc_start: 0.9166 (ttm110) cc_final: 0.8600 (ptp90) REVERT: C 103 MET cc_start: 0.9330 (ptt) cc_final: 0.8888 (pmm) REVERT: C 373 PHE cc_start: 0.9430 (OUTLIER) cc_final: 0.8775 (t80) REVERT: C 396 MET cc_start: 0.8721 (tmm) cc_final: 0.8402 (tmm) REVERT: C 570 TYR cc_start: 0.9350 (OUTLIER) cc_final: 0.8280 (m-80) REVERT: C 762 THR cc_start: 0.6817 (OUTLIER) cc_final: 0.6589 (p) outliers start: 93 outliers final: 58 residues processed: 198 average time/residue: 0.3249 time to fit residues: 106.9902 Evaluate side-chains 171 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 105 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 606 HIS Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 978 CYS Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 762 THR Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 783 ASP Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 833 ARG Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1041 ILE Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1127 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 223 optimal weight: 9.9990 chunk 101 optimal weight: 0.0010 chunk 114 optimal weight: 4.9990 chunk 264 optimal weight: 0.0970 chunk 176 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 245 optimal weight: 0.0970 chunk 281 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 276 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 283 ASN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.063781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.041217 restraints weight = 93081.890| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.45 r_work: 0.2644 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25902 Z= 0.125 Angle : 0.497 8.075 35437 Z= 0.262 Chirality : 0.041 0.186 4044 Planarity : 0.004 0.065 4394 Dihedral : 15.208 177.171 4276 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.70 % Favored : 95.24 % Rotamer: Outliers : 3.21 % Allowed : 14.91 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3045 helix: 1.08 (0.17), residues: 1050 sheet: 0.29 (0.26), residues: 418 loop : -1.40 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D1220 HIS 0.002 0.000 HIS D 94 PHE 0.013 0.001 PHE C 153 TYR 0.011 0.001 TYR D 248 ARG 0.004 0.000 ARG G 102 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 966) hydrogen bonds : angle 3.89923 ( 2647) metal coordination : bond 0.00592 ( 8) metal coordination : angle 2.07149 ( 12) covalent geometry : bond 0.00297 (25894) covalent geometry : angle 0.49578 (35425) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 111 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LYS cc_start: 0.9172 (ttpp) cc_final: 0.8816 (mtpp) REVERT: D 11 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8833 (ttp80) REVERT: D 91 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8395 (mtt180) REVERT: D 126 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8921 (tp30) REVERT: D 243 GLU cc_start: 0.9178 (OUTLIER) cc_final: 0.8900 (tp30) REVERT: D 507 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9204 (mm) REVERT: D 978 CYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8630 (m) REVERT: D 983 MET cc_start: 0.9078 (mmm) cc_final: 0.8656 (mmm) REVERT: D 1112 MET cc_start: 0.8619 (tpt) cc_final: 0.8415 (tpt) REVERT: G 43 ARG cc_start: 0.9202 (ttp-110) cc_final: 0.8991 (ttp-110) REVERT: G 102 ARG cc_start: 0.9145 (ttm110) cc_final: 0.8481 (ptp90) REVERT: C 103 MET cc_start: 0.9290 (ptt) cc_final: 0.8855 (pmm) REVERT: C 373 PHE cc_start: 0.9417 (OUTLIER) cc_final: 0.8736 (t80) REVERT: C 396 MET cc_start: 0.8721 (tmm) cc_final: 0.8407 (tmm) REVERT: C 570 TYR cc_start: 0.9341 (OUTLIER) cc_final: 0.8260 (m-80) REVERT: C 762 THR cc_start: 0.6805 (OUTLIER) cc_final: 0.6582 (p) REVERT: C 830 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7312 (ptt180) REVERT: C 1127 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8052 (mp0) outliers start: 82 outliers final: 59 residues processed: 190 average time/residue: 0.3473 time to fit residues: 108.4766 Evaluate side-chains 176 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 106 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 606 HIS Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 978 CYS Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 762 THR Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 783 ASP Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 830 ARG Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1041 ILE Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1127 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 10.0000 chunk 198 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 294 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 165 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 284 optimal weight: 0.0980 chunk 186 optimal weight: 30.0000 chunk 34 optimal weight: 9.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.062983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.040343 restraints weight = 93912.494| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.47 r_work: 0.2610 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25902 Z= 0.185 Angle : 0.537 9.214 35437 Z= 0.282 Chirality : 0.043 0.243 4044 Planarity : 0.004 0.064 4394 Dihedral : 15.247 177.685 4275 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.52 % Favored : 94.42 % Rotamer: Outliers : 3.48 % Allowed : 14.75 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.15), residues: 3045 helix: 1.03 (0.17), residues: 1056 sheet: 0.18 (0.26), residues: 419 loop : -1.42 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1220 HIS 0.003 0.001 HIS D 689 PHE 0.012 0.001 PHE C 430 TYR 0.012 0.001 TYR D 248 ARG 0.009 0.000 ARG D 173 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 966) hydrogen bonds : angle 4.00432 ( 2647) metal coordination : bond 0.00894 ( 8) metal coordination : angle 2.25760 ( 12) covalent geometry : bond 0.00443 (25894) covalent geometry : angle 0.53583 (35425) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 106 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LYS cc_start: 0.9180 (ttpp) cc_final: 0.8825 (mtpp) REVERT: D 91 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8492 (mtt180) REVERT: D 126 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.8926 (tp30) REVERT: D 243 GLU cc_start: 0.9199 (OUTLIER) cc_final: 0.8922 (tp30) REVERT: D 507 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9202 (mm) REVERT: D 901 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8676 (tm) REVERT: D 978 CYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8636 (m) REVERT: D 983 MET cc_start: 0.9126 (mmm) cc_final: 0.8639 (mmm) REVERT: D 1112 MET cc_start: 0.8558 (tpt) cc_final: 0.8117 (tpp) REVERT: G 43 ARG cc_start: 0.9223 (ttp-110) cc_final: 0.9012 (ttp-110) REVERT: G 88 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7561 (tp30) REVERT: G 102 ARG cc_start: 0.9116 (ttm110) cc_final: 0.8466 (ptp90) REVERT: C 103 MET cc_start: 0.9341 (OUTLIER) cc_final: 0.8885 (pmm) REVERT: C 373 PHE cc_start: 0.9447 (OUTLIER) cc_final: 0.8764 (t80) REVERT: C 396 MET cc_start: 0.8726 (tmm) cc_final: 0.8410 (tmm) REVERT: C 570 TYR cc_start: 0.9360 (OUTLIER) cc_final: 0.8252 (m-80) REVERT: C 762 THR cc_start: 0.6880 (OUTLIER) cc_final: 0.6649 (p) REVERT: C 830 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7310 (ptt180) REVERT: C 1127 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7979 (mp0) outliers start: 89 outliers final: 64 residues processed: 189 average time/residue: 0.3492 time to fit residues: 108.2214 Evaluate side-chains 179 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 103 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 606 HIS Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 978 CYS Chi-restraints excluded: chain D residue 995 VAL Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 762 THR Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 783 ASP Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 830 ARG Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1041 ILE Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1127 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 211 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 156 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 105 optimal weight: 0.2980 chunk 294 optimal weight: 5.9990 chunk 218 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 283 ASN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.064194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.041413 restraints weight = 93609.589| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.48 r_work: 0.2617 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25902 Z= 0.155 Angle : 0.519 8.200 35437 Z= 0.273 Chirality : 0.042 0.238 4044 Planarity : 0.004 0.064 4394 Dihedral : 15.195 177.509 4272 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.02 % Favored : 94.91 % Rotamer: Outliers : 3.36 % Allowed : 14.98 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 3045 helix: 1.09 (0.17), residues: 1055 sheet: 0.18 (0.26), residues: 419 loop : -1.41 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1220 HIS 0.003 0.001 HIS E 100 PHE 0.011 0.001 PHE C 153 TYR 0.011 0.001 TYR C 731 ARG 0.007 0.000 ARG D 173 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 966) hydrogen bonds : angle 3.97107 ( 2647) metal coordination : bond 0.00751 ( 8) metal coordination : angle 2.19925 ( 12) covalent geometry : bond 0.00369 (25894) covalent geometry : angle 0.51752 (35425) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 106 time to evaluate : 2.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LYS cc_start: 0.9172 (ttpp) cc_final: 0.8803 (mtpp) REVERT: D 91 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8419 (mtt180) REVERT: D 126 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.8914 (tp30) REVERT: D 205 MET cc_start: 0.8788 (ppp) cc_final: 0.8379 (ppp) REVERT: D 243 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8962 (tp30) REVERT: D 507 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9205 (mm) REVERT: D 585 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9062 (mp) REVERT: D 978 CYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8616 (m) REVERT: D 983 MET cc_start: 0.9114 (mmm) cc_final: 0.8623 (mmm) REVERT: D 1112 MET cc_start: 0.8522 (tpt) cc_final: 0.8127 (tpp) REVERT: G 43 ARG cc_start: 0.9237 (ttp-110) cc_final: 0.9020 (ttp-110) REVERT: G 88 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7700 (tp30) REVERT: C 103 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.8777 (pmm) REVERT: C 373 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.8729 (t80) REVERT: C 396 MET cc_start: 0.8727 (tmm) cc_final: 0.8414 (tmm) REVERT: C 570 TYR cc_start: 0.9358 (OUTLIER) cc_final: 0.8331 (m-80) REVERT: C 762 THR cc_start: 0.6893 (OUTLIER) cc_final: 0.6677 (p) REVERT: C 830 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7336 (ptt180) REVERT: C 1127 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7977 (mp0) outliers start: 86 outliers final: 64 residues processed: 186 average time/residue: 0.3413 time to fit residues: 104.5252 Evaluate side-chains 180 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 104 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 606 HIS Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 978 CYS Chi-restraints excluded: chain D residue 995 VAL Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 762 THR Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 783 ASP Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 830 ARG Chi-restraints excluded: chain C residue 833 ARG Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1041 ILE Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1127 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 42 optimal weight: 4.9990 chunk 288 optimal weight: 0.0870 chunk 44 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 143 optimal weight: 5.9990 chunk 90 optimal weight: 0.1980 chunk 2 optimal weight: 0.2980 chunk 135 optimal weight: 0.5980 chunk 257 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.064803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.042493 restraints weight = 93305.360| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.47 r_work: 0.2679 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25902 Z= 0.093 Angle : 0.501 14.071 35437 Z= 0.258 Chirality : 0.041 0.236 4044 Planarity : 0.004 0.065 4394 Dihedral : 15.064 176.599 4268 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.27 % Favored : 95.67 % Rotamer: Outliers : 2.35 % Allowed : 16.00 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 3045 helix: 1.29 (0.17), residues: 1046 sheet: 0.33 (0.26), residues: 417 loop : -1.26 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D1220 HIS 0.001 0.000 HIS D 94 PHE 0.011 0.001 PHE C 153 TYR 0.010 0.001 TYR E 78 ARG 0.014 0.000 ARG G 102 Details of bonding type rmsd hydrogen bonds : bond 0.02812 ( 966) hydrogen bonds : angle 3.80279 ( 2647) metal coordination : bond 0.00253 ( 8) metal coordination : angle 1.91181 ( 12) covalent geometry : bond 0.00206 (25894) covalent geometry : angle 0.49981 (35425) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 115 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LYS cc_start: 0.9141 (ttpp) cc_final: 0.8767 (mtpp) REVERT: B 109 ASP cc_start: 0.9088 (OUTLIER) cc_final: 0.8862 (p0) REVERT: D 11 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8845 (ttp80) REVERT: D 91 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8216 (mtt180) REVERT: D 126 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.8913 (tp30) REVERT: D 143 MET cc_start: 0.8529 (mpp) cc_final: 0.7794 (ptp) REVERT: D 205 MET cc_start: 0.8755 (ppp) cc_final: 0.8345 (ppp) REVERT: D 243 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.9010 (tp30) REVERT: D 978 CYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8631 (m) REVERT: D 983 MET cc_start: 0.9077 (mmm) cc_final: 0.8638 (mmm) REVERT: D 1196 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8696 (pm20) REVERT: G 43 ARG cc_start: 0.9247 (ttp-110) cc_final: 0.9047 (ttp-110) REVERT: G 60 ASN cc_start: 0.9464 (OUTLIER) cc_final: 0.9170 (p0) REVERT: G 88 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7791 (tp30) REVERT: G 102 ARG cc_start: 0.9046 (ttm110) cc_final: 0.8410 (ptp90) REVERT: C 103 MET cc_start: 0.9304 (ptt) cc_final: 0.8862 (pmm) REVERT: C 373 PHE cc_start: 0.9354 (OUTLIER) cc_final: 0.8671 (t80) REVERT: C 396 MET cc_start: 0.8691 (tmm) cc_final: 0.8392 (tmm) REVERT: C 570 TYR cc_start: 0.9316 (OUTLIER) cc_final: 0.8370 (m-80) REVERT: C 762 THR cc_start: 0.6820 (OUTLIER) cc_final: 0.6618 (p) REVERT: C 830 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7384 (ptt180) outliers start: 60 outliers final: 43 residues processed: 171 average time/residue: 0.3636 time to fit residues: 101.5089 Evaluate side-chains 163 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 108 time to evaluate : 2.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 606 HIS Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 978 CYS Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1196 GLU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 762 THR Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 830 ARG Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1041 ILE Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1063 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 204 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 250 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 216 optimal weight: 10.0000 chunk 212 optimal weight: 0.5980 chunk 265 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.062726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.040332 restraints weight = 93492.382| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 3.45 r_work: 0.2601 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25902 Z= 0.203 Angle : 0.569 13.613 35437 Z= 0.295 Chirality : 0.043 0.232 4044 Planarity : 0.004 0.065 4394 Dihedral : 15.161 177.572 4262 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.35 % Favored : 94.58 % Rotamer: Outliers : 2.43 % Allowed : 15.92 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 3045 helix: 1.15 (0.17), residues: 1055 sheet: 0.22 (0.26), residues: 417 loop : -1.33 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1220 HIS 0.004 0.001 HIS E 100 PHE 0.014 0.001 PHE C 430 TYR 0.012 0.001 TYR C 731 ARG 0.013 0.000 ARG G 102 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 966) hydrogen bonds : angle 4.01024 ( 2647) metal coordination : bond 0.00966 ( 8) metal coordination : angle 2.29296 ( 12) covalent geometry : bond 0.00489 (25894) covalent geometry : angle 0.56719 (35425) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 108 time to evaluate : 2.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LYS cc_start: 0.9181 (ttpp) cc_final: 0.8826 (mtpp) REVERT: D 91 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8548 (mtt180) REVERT: D 126 GLU cc_start: 0.9235 (OUTLIER) cc_final: 0.8901 (tp30) REVERT: D 205 MET cc_start: 0.8786 (ppp) cc_final: 0.8401 (ppp) REVERT: D 243 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.8990 (tp30) REVERT: D 507 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9199 (mm) REVERT: D 983 MET cc_start: 0.9119 (mmm) cc_final: 0.8620 (mmm) REVERT: D 1196 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8668 (pm20) REVERT: G 43 ARG cc_start: 0.9269 (ttp-110) cc_final: 0.9050 (ttp-110) REVERT: G 88 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7710 (tp30) REVERT: G 102 ARG cc_start: 0.9077 (ttm110) cc_final: 0.8216 (ptp90) REVERT: C 103 MET cc_start: 0.9321 (ptt) cc_final: 0.8833 (pmm) REVERT: C 373 PHE cc_start: 0.9447 (OUTLIER) cc_final: 0.8732 (t80) REVERT: C 396 MET cc_start: 0.8738 (tmm) cc_final: 0.8423 (tmm) REVERT: C 570 TYR cc_start: 0.9384 (OUTLIER) cc_final: 0.8341 (m-80) REVERT: C 762 THR cc_start: 0.7020 (OUTLIER) cc_final: 0.6790 (p) REVERT: C 830 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7402 (ptt180) outliers start: 62 outliers final: 49 residues processed: 166 average time/residue: 0.3420 time to fit residues: 94.1739 Evaluate side-chains 163 residues out of total 2579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 105 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 606 HIS Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1196 GLU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 762 THR Chi-restraints excluded: chain C residue 783 ASP Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 830 ARG Chi-restraints excluded: chain C residue 915 ILE Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1041 ILE Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1063 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 10.0000 chunk 276 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 265 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 301 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 229 optimal weight: 4.9990 chunk 109 optimal weight: 0.0870 chunk 138 optimal weight: 20.0000 chunk 240 optimal weight: 3.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.062870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.040482 restraints weight = 93357.765| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.43 r_work: 0.2610 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.181 25902 Z= 0.202 Angle : 0.714 59.182 35437 Z= 0.397 Chirality : 0.044 0.869 4044 Planarity : 0.004 0.065 4394 Dihedral : 15.152 177.542 4260 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.62 % Favored : 94.32 % Rotamer: Outliers : 2.58 % Allowed : 15.73 % Favored : 81.69 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 3045 helix: 1.16 (0.17), residues: 1054 sheet: 0.22 (0.26), residues: 417 loop : -1.33 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1220 HIS 0.003 0.001 HIS D 748 PHE 0.014 0.001 PHE C 430 TYR 0.012 0.001 TYR C 731 ARG 0.011 0.000 ARG G 102 Details of bonding type rmsd hydrogen bonds : bond 0.04159 ( 966) hydrogen bonds : angle 4.01749 ( 2647) metal coordination : bond 0.00851 ( 8) metal coordination : angle 2.28569 ( 12) covalent geometry : bond 0.00464 (25894) covalent geometry : angle 0.71289 (35425) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12265.23 seconds wall clock time: 212 minutes 44.25 seconds (12764.25 seconds total)