Starting phenix.real_space_refine on Sat Jul 4 17:20:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u1s_26304/07_2026/7u1s_26304.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u1s_26304/07_2026/7u1s_26304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u1s_26304/07_2026/7u1s_26304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u1s_26304/07_2026/7u1s_26304.map" model { file = "/net/cci-nas-00/data/ceres_data/7u1s_26304/07_2026/7u1s_26304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u1s_26304/07_2026/7u1s_26304.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7u1s_26304/07_2026/7u1s_26304.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u1s_26304/07_2026/7u1s_26304.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 1 8.98 5 P 32 5.49 5 S 113 5.16 5 C 13738 2.51 5 N 3571 2.21 5 O 3770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.12s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21225 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2641 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 16, 'TRANS': 343} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 15, 'TYR:plan': 2, 'ASP:plan': 4, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 135 Chain: "B" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2508 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 317} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2497 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 13, 'TRANS': 318} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2485 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 13, 'TRANS': 316} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 81 Chain: "E" Number of atoms: 10181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1439, 10181 Classifications: {'peptide': 1439} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 343} Link IDs: {'PTRANS': 49, 'TRANS': 1389} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1198 Unresolved non-hydrogen angles: 1498 Unresolved non-hydrogen dihedrals: 959 Unresolved non-hydrogen chiralities: 119 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 6, 'ARG:plan': 28, 'TYR:plan': 3, 'GLU:plan': 34, 'ASN:plan1': 8, 'ASP:plan': 32, 'PHE:plan': 16, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 633 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 207 Unusual residues: {' K': 1, 'ATP': 2, 'POV': 1} Classifications: {'peptide': 2, 'undetermined': 4} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'POV': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 152 Unusual residues: {'ATP': 2, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'POV': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 346 Unusual residues: {'ATP': 1, 'BJX': 1, 'POV': 1, 'PTY': 6} Classifications: {'peptide': 1, 'undetermined': 9} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 124 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.83, per 1000 atoms: 0.18 Number of scatterers: 21225 At special positions: 0 Unit cell: (166.155, 104.5, 147.345, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 1 19.00 S 113 16.00 P 32 15.00 O 3770 8.00 N 3571 7.00 C 13738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 26 " distance=2.03 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG F 1 " - " ASN E 10 " Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 990.0 milliseconds 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5274 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 31 sheets defined 52.7% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 53 through 58 removed outlier: 3.923A pdb=" N ASP A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 67 through 98 Processing helix chain 'A' and resid 116 through 129 Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.943A pdb=" N ILE A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 345 through 357 Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 58 through 66 Processing helix chain 'B' and resid 67 through 98 Processing helix chain 'B' and resid 116 through 129 Processing helix chain 'B' and resid 142 through 172 removed outlier: 4.053A pdb=" N ILE B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 179 removed outlier: 3.503A pdb=" N ALA B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 179 " --> pdb=" O HIS B 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 174 through 179' Processing helix chain 'B' and resid 265 through 270 removed outlier: 4.226A pdb=" N ASP B 269 " --> pdb=" O PRO B 266 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 270 " --> pdb=" O LEU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.645A pdb=" N LEU B 275 " --> pdb=" O PRO B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 345 through 360 removed outlier: 3.855A pdb=" N ASP B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 66 removed outlier: 3.531A pdb=" N THR C 62 " --> pdb=" O ASP C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 98 Processing helix chain 'C' and resid 116 through 129 Processing helix chain 'C' and resid 142 through 172 removed outlier: 3.914A pdb=" N ILE C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.728A pdb=" N LEU C 275 " --> pdb=" O PRO C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 333 No H-bonds generated for 'chain 'C' and resid 331 through 333' Processing helix chain 'C' and resid 345 through 361 Processing helix chain 'D' and resid 53 through 58 Processing helix chain 'D' and resid 58 through 66 removed outlier: 3.685A pdb=" N THR D 62 " --> pdb=" O ASP D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 98 Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 142 through 172 removed outlier: 4.057A pdb=" N ILE D 146 " --> pdb=" O CYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 329 through 333 Processing helix chain 'D' and resid 345 through 359 Processing helix chain 'E' and resid 8 through 13 removed outlier: 4.417A pdb=" N ALA E 13 " --> pdb=" O GLU E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 32 removed outlier: 4.056A pdb=" N ASP E 29 " --> pdb=" O GLY E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 54 removed outlier: 3.556A pdb=" N PHE E 41 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Proline residue: E 45 - end of helix removed outlier: 3.503A pdb=" N ILE E 49 " --> pdb=" O PRO E 45 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'E' and resid 58 through 62 Processing helix chain 'E' and resid 71 through 99 removed outlier: 3.528A pdb=" N ILE E 76 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU E 88 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY E 97 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL E 98 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR E 99 " --> pdb=" O SER E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 106 Processing helix chain 'E' and resid 107 through 130 removed outlier: 3.597A pdb=" N MET E 115 " --> pdb=" O GLY E 111 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER E 130 " --> pdb=" O ASN E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 135 removed outlier: 3.681A pdb=" N LEU E 135 " --> pdb=" O PHE E 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 132 through 135' Processing helix chain 'E' and resid 136 through 159 removed outlier: 3.856A pdb=" N THR E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 194 removed outlier: 3.550A pdb=" N ILE E 177 " --> pdb=" O GLY E 173 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 182 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE E 190 " --> pdb=" O GLU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.657A pdb=" N ASP E 212 " --> pdb=" O ASP E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 230 Processing helix chain 'E' and resid 232 through 243 removed outlier: 4.200A pdb=" N PHE E 236 " --> pdb=" O TRP E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 277 Processing helix chain 'E' and resid 283 through 314 removed outlier: 6.005A pdb=" N ARG E 297 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU E 301 " --> pdb=" O ARG E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 327 Processing helix chain 'E' and resid 347 through 352 Processing helix chain 'E' and resid 354 through 401 removed outlier: 3.955A pdb=" N GLN E 374 " --> pdb=" O ARG E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 434 removed outlier: 3.881A pdb=" N THR E 425 " --> pdb=" O VAL E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 456 removed outlier: 3.802A pdb=" N LEU E 438 " --> pdb=" O LEU E 434 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TRP E 439 " --> pdb=" O CYS E 435 " (cutoff:3.500A) Proline residue: E 442 - end of helix Processing helix chain 'E' and resid 457 through 503 removed outlier: 3.923A pdb=" N LEU E 461 " --> pdb=" O GLY E 457 " (cutoff:3.500A) Proline residue: E 472 - end of helix Processing helix chain 'E' and resid 505 through 512 removed outlier: 3.571A pdb=" N TYR E 512 " --> pdb=" O LEU E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 565 removed outlier: 3.809A pdb=" N PHE E 518 " --> pdb=" O TRP E 514 " (cutoff:3.500A) Proline residue: E 551 - end of helix Processing helix chain 'E' and resid 572 through 591 removed outlier: 3.723A pdb=" N ALA E 578 " --> pdb=" O SER E 574 " (cutoff:3.500A) Proline residue: E 589 - end of helix Processing helix chain 'E' and resid 592 through 615 Processing helix chain 'E' and resid 718 through 726 removed outlier: 3.516A pdb=" N LEU E 722 " --> pdb=" O GLY E 718 " (cutoff:3.500A) Processing helix chain 'E' and resid 783 through 790 Processing helix chain 'E' and resid 795 through 807 Processing helix chain 'E' and resid 807 through 813 removed outlier: 4.392A pdb=" N ASP E 811 " --> pdb=" O SER E 807 " (cutoff:3.500A) Processing helix chain 'E' and resid 817 through 821 removed outlier: 3.551A pdb=" N THR E 821 " --> pdb=" O GLY E 818 " (cutoff:3.500A) Processing helix chain 'E' and resid 831 through 846 removed outlier: 3.732A pdb=" N GLN E 846 " --> pdb=" O ARG E 842 " (cutoff:3.500A) Processing helix chain 'E' and resid 862 through 881 Processing helix chain 'E' and resid 914 through 921 Processing helix chain 'E' and resid 988 through 993 removed outlier: 4.037A pdb=" N ARG E 993 " --> pdb=" O VAL E 989 " (cutoff:3.500A) Processing helix chain 'E' and resid 996 through 1009 removed outlier: 3.579A pdb=" N LYS E1003 " --> pdb=" O ARG E 999 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY E1009 " --> pdb=" O LEU E1005 " (cutoff:3.500A) Processing helix chain 'E' and resid 1010 through 1041 Processing helix chain 'E' and resid 1064 through 1107 Processing helix chain 'E' and resid 1109 through 1116 removed outlier: 3.548A pdb=" N PHE E1113 " --> pdb=" O PRO E1109 " (cutoff:3.500A) Processing helix chain 'E' and resid 1118 through 1135 removed outlier: 3.537A pdb=" N LEU E1122 " --> pdb=" O LEU E1118 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP E1128 " --> pdb=" O ARG E1124 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1135 through 1161 Processing helix chain 'E' and resid 1163 through 1210 removed outlier: 3.973A pdb=" N ALA E1167 " --> pdb=" O VAL E1163 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 3.543A pdb=" N ASP E1188 " --> pdb=" O VAL E1184 " (cutoff:3.500A) Proline residue: E1199 - end of helix Processing helix chain 'E' and resid 1210 through 1217 removed outlier: 3.541A pdb=" N PHE E1217 " --> pdb=" O THR E1213 " (cutoff:3.500A) Processing helix chain 'E' and resid 1219 through 1274 removed outlier: 3.668A pdb=" N PHE E1223 " --> pdb=" O TYR E1219 " (cutoff:3.500A) Processing helix chain 'E' and resid 1278 through 1320 removed outlier: 4.024A pdb=" N GLY E1282 " --> pdb=" O ALA E1278 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET E1290 " --> pdb=" O THR E1286 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER E1292 " --> pdb=" O ALA E1288 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASN E1293 " --> pdb=" O LEU E1289 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASN E1296 " --> pdb=" O SER E1292 " (cutoff:3.500A) Processing helix chain 'E' and resid 1383 through 1394 Processing helix chain 'E' and resid 1414 through 1421 removed outlier: 3.708A pdb=" N ARG E1421 " --> pdb=" O THR E1417 " (cutoff:3.500A) Processing helix chain 'E' and resid 1436 through 1441 removed outlier: 4.269A pdb=" N ASP E1441 " --> pdb=" O ARG E1437 " (cutoff:3.500A) Processing helix chain 'E' and resid 1450 through 1458 Processing helix chain 'E' and resid 1461 through 1467 removed outlier: 4.347A pdb=" N LYS E1465 " --> pdb=" O LYS E1461 " (cutoff:3.500A) Processing helix chain 'E' and resid 1469 through 1473 removed outlier: 4.256A pdb=" N ASP E1472 " --> pdb=" O GLY E1469 " (cutoff:3.500A) Processing helix chain 'E' and resid 1485 through 1498 Processing helix chain 'E' and resid 1512 through 1529 removed outlier: 3.857A pdb=" N THR E1516 " --> pdb=" O ILE E1512 " (cutoff:3.500A) Processing helix chain 'E' and resid 1539 through 1545 removed outlier: 3.792A pdb=" N ILE E1543 " --> pdb=" O ARG E1539 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER E1545 " --> pdb=" O HIS E1541 " (cutoff:3.500A) Processing helix chain 'E' and resid 1564 through 1570 removed outlier: 3.573A pdb=" N SER E1568 " --> pdb=" O GLU E1564 " (cutoff:3.500A) Processing helix chain 'E' and resid 1571 through 1578 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 259 through 260 Processing sheet with id=AA4, first strand: chain 'A' and resid 210 through 211 removed outlier: 3.525A pdb=" N GLU A 282 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 213 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 230 through 237 removed outlier: 4.871A pdb=" N LEU A 233 " --> pdb=" O ARG A 221 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ARG A 221 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN A 235 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL A 219 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASP A 237 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N MET A 217 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 282 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 315 Processing sheet with id=AA7, first strand: chain 'A' and resid 319 through 321 removed outlier: 6.311A pdb=" N TYR A 326 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LYS D 47 " --> pdb=" O TYR A 326 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL A 328 " --> pdb=" O LYS D 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 47 removed outlier: 7.104A pdb=" N ALA B 45 " --> pdb=" O VAL C 328 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.639A pdb=" N VAL B 202 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 255 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 259 through 260 removed outlier: 6.880A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 234 through 237 removed outlier: 4.039A pdb=" N ALA B 213 " --> pdb=" O ILE B 249 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 234 through 237 removed outlier: 5.153A pdb=" N SER B 212 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL B 290 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 36 through 37 Processing sheet with id=AB5, first strand: chain 'C' and resid 182 through 183 Processing sheet with id=AB6, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.587A pdb=" N ARG C 195 " --> pdb=" O ARG C 192 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 210 through 211 Processing sheet with id=AB8, first strand: chain 'C' and resid 230 through 238 removed outlier: 5.129A pdb=" N THR C 223 " --> pdb=" O PRO C 232 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 221 " --> pdb=" O HIS C 234 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 313 through 315 Processing sheet with id=AC1, first strand: chain 'D' and resid 36 through 37 Processing sheet with id=AC2, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.586A pdb=" N VAL D 202 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.768A pdb=" N VAL D 188 " --> pdb=" O MET D 199 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA D 187 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 230 through 237 removed outlier: 4.934A pdb=" N THR D 223 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SER D 212 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL D 290 " --> pdb=" O SER D 212 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR D 214 " --> pdb=" O GLU D 288 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 313 through 315 Processing sheet with id=AC6, first strand: chain 'E' and resid 338 through 340 removed outlier: 4.858A pdb=" N THR E 338 " --> pdb=" O PHE E 345 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE E 345 " --> pdb=" O THR E 338 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 679 through 681 Processing sheet with id=AC8, first strand: chain 'E' and resid 685 through 687 removed outlier: 6.904A pdb=" N PHE E 685 " --> pdb=" O VAL E 733 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 710 through 713 removed outlier: 5.840A pdb=" N MET E 710 " --> pdb=" O ILE E 901 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N MET E 903 " --> pdb=" O MET E 710 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL E 712 " --> pdb=" O MET E 903 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 771 through 772 Processing sheet with id=AD2, first strand: chain 'E' and resid 1348 through 1352 removed outlier: 4.824A pdb=" N ASN E1349 " --> pdb=" O ARG E1402 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ARG E1402 " --> pdb=" O ASN E1349 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 1373 through 1377 removed outlier: 7.200A pdb=" N GLN E1373 " --> pdb=" O VAL E1533 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N THR E1535 " --> pdb=" O GLN E1373 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE E1375 " --> pdb=" O THR E1535 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'E' and resid 1549 through 1553 removed outlier: 5.358A pdb=" N LYS E1553 " --> pdb=" O ILE E1557 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE E1557 " --> pdb=" O LYS E1553 " (cutoff:3.500A) 1177 hydrogen bonds defined for protein. 3420 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.29 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3506 1.32 - 1.45: 5504 1.45 - 1.57: 12416 1.57 - 1.69: 63 1.69 - 1.81: 174 Bond restraints: 21663 Sorted by residual: bond pdb=" C16 BJX E1602 " pdb=" N1 BJX E1602 " ideal model delta sigma weight residual 1.344 1.455 -0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" N BJX E1602 " pdb=" C6 BJX E1602 " ideal model delta sigma weight residual 1.412 1.513 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C5 BJX E1602 " pdb=" C7 BJX E1602 " ideal model delta sigma weight residual 1.518 1.615 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C21 BJX E1602 " pdb=" O1 BJX E1602 " ideal model delta sigma weight residual 1.347 1.423 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C5 BJX E1602 " pdb=" C8 BJX E1602 " ideal model delta sigma weight residual 1.536 1.610 -0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 21658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 29217 1.96 - 3.93: 233 3.93 - 5.89: 49 5.89 - 7.85: 12 7.85 - 9.81: 4 Bond angle restraints: 29515 Sorted by residual: angle pdb=" C HIS E1135 " pdb=" N ILE E1136 " pdb=" CA ILE E1136 " ideal model delta sigma weight residual 120.24 122.90 -2.66 6.30e-01 2.52e+00 1.78e+01 angle pdb=" C17 BJX E1602 " pdb=" C16 BJX E1602 " pdb=" N1 BJX E1602 " ideal model delta sigma weight residual 113.90 123.71 -9.81 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C ILE E1136 " pdb=" CA ILE E1136 " pdb=" CB ILE E1136 " ideal model delta sigma weight residual 114.35 111.03 3.32 1.06e+00 8.90e-01 9.83e+00 angle pdb=" O11 PTY E1606 " pdb=" P1 PTY E1606 " pdb=" O14 PTY E1606 " ideal model delta sigma weight residual 92.90 101.55 -8.65 3.00e+00 1.11e-01 8.32e+00 angle pdb=" CA LEU E 341 " pdb=" CB LEU E 341 " pdb=" CG LEU E 341 " ideal model delta sigma weight residual 116.30 125.61 -9.31 3.50e+00 8.16e-02 7.07e+00 ... (remaining 29510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.31: 12434 34.31 - 68.61: 191 68.61 - 102.92: 15 102.92 - 137.23: 9 137.23 - 171.53: 4 Dihedral angle restraints: 12653 sinusoidal: 4542 harmonic: 8111 Sorted by residual: dihedral pdb=" N1 PTY E1606 " pdb=" C2 PTY E1606 " pdb=" C3 PTY E1606 " pdb=" O11 PTY E1606 " ideal model delta sinusoidal sigma weight residual 65.33 -106.20 171.53 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C23 P5S A 406 " pdb=" C24 P5S A 406 " pdb=" C25 P5S A 406 " pdb=" C26 P5S A 406 " ideal model delta sinusoidal sigma weight residual 182.80 21.12 161.68 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CB P5S D 402 " pdb=" OG P5S D 402 " pdb=" P12 P5S D 402 " pdb=" O16 P5S D 402 " ideal model delta sinusoidal sigma weight residual 150.82 -49.35 -159.83 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 12650 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3012 0.057 - 0.114: 479 0.114 - 0.170: 30 0.170 - 0.227: 1 0.227 - 0.284: 1 Chirality restraints: 3523 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN E 10 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C5 BJX E1602 " pdb=" C7 BJX E1602 " pdb=" C8 BJX E1602 " pdb=" N1 BJX E1602 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" C4 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" C5 NAG F 1 " pdb=" O4 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.40 -0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 3520 not shown) Planarity restraints: 3626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 588 " -0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO E 589 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO E 589 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 589 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 243 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.22e+00 pdb=" N PRO E 244 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 244 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 244 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 265 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO A 266 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 266 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 266 " 0.023 5.00e-02 4.00e+02 ... (remaining 3623 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 6413 2.83 - 3.41: 23534 3.41 - 3.99: 38261 3.99 - 4.56: 52782 4.56 - 5.14: 77492 Nonbonded interactions: 198482 Sorted by model distance: nonbonded pdb=" NH1 ARG A 177 " pdb=" OG SER A 208 " model vdw 2.253 3.120 nonbonded pdb=" OD1 ASP C 329 " pdb=" OG SER C 331 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASN E 234 " pdb=" NE1 TRP E1247 " model vdw 2.264 3.120 nonbonded pdb=" NH1 ARG E 216 " pdb=" O ALA E 249 " model vdw 2.276 3.120 nonbonded pdb=" O LEU E1192 " pdb=" OG1 THR E1196 " model vdw 2.277 3.040 ... (remaining 198477 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 30 through 50 or (resid 51 through 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 64 or (resid 65 and ( \ name N or name CA or name C or name O or name CB )) or resid 66 or (resid 67 and \ (name N or name CA or name C or name O or name CB )) or resid 68 through 72 or \ (resid 73 and (name N or name CA or name C or name O or name CB )) or resid 74 t \ hrough 76 or (resid 77 and (name N or name CA or name C or name O or name CB )) \ or resid 78 through 98 or (resid 99 and (name N or name CA or name C or name O o \ r name CB )) or resid 100 through 105 or (resid 106 through 107 and (name N or n \ ame CA or name C or name O or name CB )) or resid 108 through 112 or (resid 113 \ and (name N or name CA or name C or name O or name CB )) or resid 114 through 11 \ 7 or (resid 118 and (name N or name CA or name C or name O or name CB )) or resi \ d 119 through 139 or (resid 140 through 141 and (name N or name CA or name C or \ name O or name CB )) or resid 142 through 145 or (resid 146 and (name N or name \ CA or name C or name O or name CB )) or resid 147 through 157 or (resid 158 and \ (name N or name CA or name C or name O or name CB )) or resid 159 through 205 or \ (resid 206 through 207 and (name N or name CA or name C or name O or name CB )) \ or resid 208 through 261 or (resid 262 and (name N or name CA or name C or name \ O or name CB )) or resid 263 through 272 or (resid 273 and (name N or name CA o \ r name C or name O or name CB )) or resid 274 through 279 or (resid 280 and (nam \ e N or name CA or name C or name O or name CB )) or resid 281 through 313 or (re \ sid 314 and (name N or name CA or name C or name O or name CB )) or resid 315 th \ rough 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) \ or resid 326 through 328 or (resid 329 and (name N or name CA or name C or name \ O or name CB )) or resid 330 or (resid 331 through 332 and (name N or name CA o \ r name C or name O or name CB )) or resid 333 through 349 or (resid 350 through \ 359 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and ((resid 30 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 46 or (resid 47 and (name N or na \ me CA or name C or name O or name CB )) or resid 48 through 51 or (resid 52 and \ (name N or name CA or name C or name O or name CB )) or resid 53 or (resid 54 an \ d (name N or name CA or name C or name O or name CB )) or resid 55 through 64 or \ (resid 65 and (name N or name CA or name C or name O or name CB )) or resid 66 \ or (resid 67 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 8 through 72 or (resid 73 and (name N or name CA or name C or name O or name CB \ )) or resid 74 through 76 or (resid 77 and (name N or name CA or name C or name \ O or name CB )) or resid 78 through 98 or (resid 99 and (name N or name CA or na \ me C or name O or name CB )) or resid 100 through 105 or (resid 106 through 107 \ and (name N or name CA or name C or name O or name CB )) or resid 108 through 11 \ 2 or (resid 113 and (name N or name CA or name C or name O or name CB )) or resi \ d 114 through 117 or (resid 118 and (name N or name CA or name C or name O or na \ me CB )) or resid 119 through 125 or (resid 126 and (name N or name CA or name C \ or name O or name CB )) or resid 127 through 157 or (resid 158 and (name N or n \ ame CA or name C or name O or name CB )) or resid 159 through 174 or (resid 175 \ and (name N or name CA or name C or name O or name CB )) or resid 176 through 20 \ 5 or (resid 206 through 207 and (name N or name CA or name C or name O or name C \ B )) or resid 208 through 261 or (resid 262 and (name N or name CA or name C or \ name O or name CB )) or resid 263 through 272 or (resid 273 and (name N or name \ CA or name C or name O or name CB )) or resid 274 through 279 or (resid 280 and \ (name N or name CA or name C or name O or name CB )) or resid 281 through 287 or \ (resid 288 and (name N or name CA or name C or name O or name CB )) or resid 28 \ 9 through 313 or (resid 314 and (name N or name CA or name C or name O or name C \ B )) or resid 315 through 320 or (resid 321 through 323 and (name N or name CA o \ r name C or name O or name CB )) or resid 324 through 328 or (resid 329 and (nam \ e N or name CA or name C or name O or name CB )) or resid 330 or (resid 331 thro \ ugh 332 and (name N or name CA or name C or name O or name CB )) or resid 333 th \ rough 338 or (resid 339 and (name N or name CA or name C or name O or name CB )) \ or resid 340 through 347 or (resid 348 through 359 and (name N or name CA or na \ me C or name O or name CB )))) selection = (chain 'C' and ((resid 30 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 46 or (resid 47 and (name N or name CA or name \ C or name O or name CB )) or resid 48 through 50 or (resid 51 through 52 and (n \ ame N or name CA or name C or name O or name CB )) or resid 53 through 64 or (re \ sid 65 and (name N or name CA or name C or name O or name CB )) or resid 66 thro \ ugh 125 or (resid 126 and (name N or name CA or name C or name O or name CB )) o \ r resid 127 through 139 or (resid 140 through 141 and (name N or name CA or name \ C or name O or name CB )) or resid 142 through 145 or (resid 146 and (name N or \ name CA or name C or name O or name CB )) or resid 147 through 174 or (resid 17 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 176 through \ 205 or (resid 206 through 207 and (name N or name CA or name C or name O or name \ CB )) or resid 208 through 272 or (resid 273 and (name N or name CA or name C o \ r name O or name CB )) or resid 274 through 279 or (resid 280 and (name N or nam \ e CA or name C or name O or name CB )) or resid 281 through 287 or (resid 288 an \ d (name N or name CA or name C or name O or name CB )) or resid 289 through 313 \ or (resid 314 and (name N or name CA or name C or name O or name CB )) or resid \ 315 through 320 or (resid 321 through 323 and (name N or name CA or name C or na \ me O or name CB )) or resid 324 or (resid 325 and (name N or name CA or name C o \ r name O or name CB )) or resid 326 through 328 or (resid 329 and (name N or nam \ e CA or name C or name O or name CB )) or resid 330 or (resid 331 through 332 an \ d (name N or name CA or name C or name O or name CB )) or resid 333 through 338 \ or (resid 339 and (name N or name CA or name C or name O or name CB )) or resid \ 340 through 348 or (resid 349 through 359 and (name N or name CA or name C or na \ me O or name CB )))) selection = (chain 'D' and ((resid 30 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 46 or (resid 47 and (name N or name CA or name \ C or name O or name CB )) or resid 48 through 53 or (resid 54 and (name N or na \ me CA or name C or name O or name CB )) or resid 55 through 66 or (resid 67 and \ (name N or name CA or name C or name O or name CB )) or resid 68 through 72 or ( \ resid 73 and (name N or name CA or name C or name O or name CB )) or resid 74 th \ rough 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) o \ r resid 100 through 105 or (resid 106 through 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 through 112 or (resid 113 and (name N or \ name CA or name C or name O or name CB )) or resid 114 through 117 or (resid 11 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 119 through \ 125 or (resid 126 and (name N or name CA or name C or name O or name CB )) or re \ sid 127 through 139 or (resid 140 through 141 and (name N or name CA or name C o \ r name O or name CB )) or resid 142 through 145 or (resid 146 and (name N or nam \ e CA or name C or name O or name CB )) or resid 147 through 157 or (resid 158 an \ d (name N or name CA or name C or name O or name CB )) or resid 159 through 174 \ or (resid 175 and (name N or name CA or name C or name O or name CB )) or resid \ 176 through 206 or (resid 207 and (name N or name CA or name C or name O or name \ CB )) or resid 208 through 261 or (resid 262 and (name N or name CA or name C o \ r name O or name CB )) or resid 263 through 287 or (resid 288 and (name N or nam \ e CA or name C or name O or name CB )) or resid 289 through 320 or (resid 321 th \ rough 323 and (name N or name CA or name C or name O or name CB )) or resid 324 \ or (resid 325 and (name N or name CA or name C or name O or name CB )) or resid \ 326 through 338 or (resid 339 and (name N or name CA or name C or name O or name \ CB )) or resid 340 through 347 or (resid 348 through 359 and (name N or name CA \ or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.450 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 : 0.003 0.111 21670 Z= 0.129 Angle : 0.499 9.814 29531 Z= 0.240 Chirality : 0.040 0.284 3523 Planarity : 0.004 0.054 3625 Dihedral : 13.474 171.533 7364 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.10 % Allowed : 5.33 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.16), residues: 2774 helix: 1.43 (0.15), residues: 1315 sheet: -2.36 (0.29), residues: 287 loop : -1.95 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1145 TYR 0.009 0.001 TYR E1064 PHE 0.013 0.001 PHE C 168 TRP 0.008 0.001 TRP E 899 HIS 0.003 0.000 HIS E 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (21663) covalent geometry : angle 0.49767 / 0.24 (29515) SS BOND : bond 0.00171 / 0.08 ( 5) SS BOND : angle 0.61901 / 0.35 ( 10) hydrogen bonds : bond 0.18311 / 12.91 ( 1164) hydrogen bonds : angle 6.42653 / 4.56 ( 3420) link_BETA1-4 : bond 0.00927 / 0.49 ( 1) link_BETA1-4 : angle 3.08380 / 1.60 ( 3) link_NAG-ASN : bond 0.00414 / 0.22 ( 1) link_NAG-ASN : angle 2.46486 / 1.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 722 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8313 (mm-30) REVERT: A 304 TYR cc_start: 0.8536 (m-80) cc_final: 0.8299 (m-80) REVERT: A 343 LEU cc_start: 0.7061 (mt) cc_final: 0.6618 (tp) REVERT: B 47 LYS cc_start: 0.7983 (mttt) cc_final: 0.7722 (mtpp) REVERT: B 67 LYS cc_start: 0.8514 (mppt) cc_final: 0.8232 (mptt) REVERT: B 224 THR cc_start: 0.8407 (p) cc_final: 0.8200 (p) REVERT: B 264 ASN cc_start: 0.8070 (m-40) cc_final: 0.7782 (m-40) REVERT: B 286 ILE cc_start: 0.9419 (mm) cc_final: 0.9167 (mm) REVERT: C 64 VAL cc_start: 0.8729 (t) cc_final: 0.8498 (t) REVERT: C 114 ILE cc_start: 0.8421 (mm) cc_final: 0.8027 (tp) REVERT: C 119 SER cc_start: 0.8339 (p) cc_final: 0.8108 (m) REVERT: C 199 MET cc_start: 0.8627 (mtt) cc_final: 0.8305 (mtp) REVERT: D 114 ILE cc_start: 0.9258 (mm) cc_final: 0.8958 (mm) REVERT: D 212 SER cc_start: 0.9133 (m) cc_final: 0.8771 (p) REVERT: D 255 LEU cc_start: 0.8093 (mt) cc_final: 0.7888 (mt) REVERT: D 274 ASP cc_start: 0.6851 (t70) cc_final: 0.6456 (t0) REVERT: D 317 PRO cc_start: 0.8716 (Cg_exo) cc_final: 0.8461 (Cg_endo) REVERT: E 292 CYS cc_start: 0.7900 (m) cc_final: 0.7621 (t) REVERT: E 298 ARG cc_start: 0.8014 (mmm160) cc_final: 0.7642 (mmm160) REVERT: E 323 ILE cc_start: 0.8459 (mt) cc_final: 0.8135 (mt) REVERT: E 369 GLN cc_start: 0.8296 (tt0) cc_final: 0.8088 (tm-30) REVERT: E 370 ARG cc_start: 0.7984 (mtt180) cc_final: 0.7697 (mtt180) REVERT: E 381 ILE cc_start: 0.9446 (mm) cc_final: 0.9182 (mt) REVERT: E 400 MET cc_start: 0.8378 (mmp) cc_final: 0.8089 (mmt) REVERT: E 486 ARG cc_start: 0.6806 (tpp-160) cc_final: 0.6596 (mmm160) REVERT: E 493 ASN cc_start: 0.8223 (m-40) cc_final: 0.7568 (m110) REVERT: E 506 MET cc_start: 0.6847 (mmm) cc_final: 0.6610 (mmm) REVERT: E 585 ILE cc_start: 0.8234 (mt) cc_final: 0.8031 (mt) REVERT: E 787 ASN cc_start: 0.8165 (t0) cc_final: 0.7860 (t0) REVERT: E 815 LEU cc_start: 0.6476 (mt) cc_final: 0.6205 (mt) REVERT: E 995 LYS cc_start: 0.7076 (mtmm) cc_final: 0.6839 (mtmm) REVERT: E 1068 PHE cc_start: 0.8526 (t80) cc_final: 0.8311 (t80) REVERT: E 1143 LEU cc_start: 0.8646 (tp) cc_final: 0.8155 (tp) REVERT: E 1290 MET cc_start: 0.6745 (mmm) cc_final: 0.6538 (mmt) REVERT: E 1294 TYR cc_start: 0.8443 (m-10) cc_final: 0.7548 (m-10) outliers start: 2 outliers final: 0 residues processed: 723 average time/residue: 0.1387 time to fit residues: 155.4589 Evaluate side-chains 597 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 597 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 50.0000 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 overall best weight: 9.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN B 216 HIS C 313 GLN C 335 ASN D 279 GLN E 71 HIS E 293 HIS E 326 HIS ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1103 ASN E1521 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.173525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.149203 restraints weight = 27174.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.150689 restraints weight = 17290.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.153023 restraints weight = 13161.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.153558 restraints weight = 9240.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.154028 restraints weight = 7527.986| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 21670 Z= 0.351 Angle : 0.835 13.645 29531 Z= 0.425 Chirality : 0.052 0.353 3523 Planarity : 0.006 0.069 3625 Dihedral : 13.918 169.282 3400 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 6.35 % Allowed : 13.22 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.16), residues: 2774 helix: 0.97 (0.14), residues: 1309 sheet: -2.27 (0.29), residues: 269 loop : -2.14 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 168 TYR 0.030 0.003 TYR E1032 PHE 0.034 0.003 PHE D 75 TRP 0.018 0.002 TRP E 232 HIS 0.011 0.002 HIS E 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00801 / 0.35 (21663) covalent geometry : angle 0.83298 / 0.42 (29515) SS BOND : bond 0.01630 / 0.82 ( 5) SS BOND : angle 2.08127 / 1.10 ( 10) hydrogen bonds : bond 0.05680 / 4.02 ( 1164) hydrogen bonds : angle 5.23053 / 3.71 ( 3420) link_BETA1-4 : bond 0.00520 / 0.27 ( 1) link_BETA1-4 : angle 1.71284 / 0.87 ( 3) link_NAG-ASN : bond 0.00278 / 0.15 ( 1) link_NAG-ASN : angle 3.68252 / 1.93 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 622 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.7391 (t0) cc_final: 0.7090 (t0) REVERT: A 93 ILE cc_start: 0.9085 (tt) cc_final: 0.8763 (mt) REVERT: A 158 MET cc_start: 0.7691 (mmm) cc_final: 0.7101 (mtm) REVERT: A 177 ARG cc_start: 0.8982 (tpt-90) cc_final: 0.8536 (tpt170) REVERT: A 258 TYR cc_start: 0.8463 (p90) cc_final: 0.8169 (p90) REVERT: A 304 TYR cc_start: 0.8943 (m-80) cc_final: 0.8533 (m-80) REVERT: A 338 LYS cc_start: 0.7729 (mtpp) cc_final: 0.7498 (tppt) REVERT: B 42 CYS cc_start: 0.8325 (p) cc_final: 0.8020 (p) REVERT: B 47 LYS cc_start: 0.8153 (mttt) cc_final: 0.7905 (mttm) REVERT: B 56 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6651 (mt) REVERT: B 72 LEU cc_start: 0.8252 (mm) cc_final: 0.6844 (mm) REVERT: B 75 PHE cc_start: 0.8376 (t80) cc_final: 0.8154 (t80) REVERT: B 264 ASN cc_start: 0.8142 (m-40) cc_final: 0.7875 (m-40) REVERT: B 313 GLN cc_start: 0.7580 (mt0) cc_final: 0.7000 (mm-40) REVERT: C 114 ILE cc_start: 0.8914 (mm) cc_final: 0.8676 (tp) REVERT: C 199 MET cc_start: 0.8692 (mtt) cc_final: 0.8454 (mtp) REVERT: C 200 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8339 (tt) REVERT: C 247 ASN cc_start: 0.7692 (m-40) cc_final: 0.7368 (p0) REVERT: D 113 SER cc_start: 0.8794 (m) cc_final: 0.8432 (p) REVERT: D 114 ILE cc_start: 0.9391 (mm) cc_final: 0.9143 (mm) REVERT: D 212 SER cc_start: 0.9321 (m) cc_final: 0.9059 (p) REVERT: D 274 ASP cc_start: 0.7264 (t70) cc_final: 0.6759 (t0) REVERT: E 104 LEU cc_start: 0.9450 (mp) cc_final: 0.9220 (mt) REVERT: E 234 ASN cc_start: 0.8465 (m-40) cc_final: 0.8018 (m-40) REVERT: E 282 GLN cc_start: 0.5291 (mt0) cc_final: 0.4340 (pp30) REVERT: E 347 SER cc_start: 0.8068 (p) cc_final: 0.7831 (t) REVERT: E 369 GLN cc_start: 0.8374 (tt0) cc_final: 0.8169 (tt0) REVERT: E 381 ILE cc_start: 0.9587 (mm) cc_final: 0.9341 (mt) REVERT: E 409 MET cc_start: 0.8605 (tpt) cc_final: 0.8084 (tpt) REVERT: E 486 ARG cc_start: 0.6974 (tpp-160) cc_final: 0.6753 (mmm160) REVERT: E 547 ASN cc_start: 0.8163 (t0) cc_final: 0.7775 (m-40) REVERT: E 785 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6635 (mt-10) REVERT: E 1099 ARG cc_start: 0.7698 (ttp80) cc_final: 0.7404 (tpt170) REVERT: E 1224 GLN cc_start: 0.7820 (mt0) cc_final: 0.7560 (tt0) REVERT: E 1248 LEU cc_start: 0.9258 (tp) cc_final: 0.9043 (tp) REVERT: E 1290 MET cc_start: 0.7082 (mmm) cc_final: 0.6654 (mmt) REVERT: E 1308 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7912 (mp10) REVERT: E 1320 LYS cc_start: 0.8341 (mttt) cc_final: 0.8049 (mttt) outliers start: 124 outliers final: 82 residues processed: 675 average time/residue: 0.1316 time to fit residues: 139.9350 Evaluate side-chains 664 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 578 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 257 MET Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 701 ILE Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 865 SER Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1074 LEU Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1276 LEU Chi-restraints excluded: chain E residue 1308 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 13 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 257 optimal weight: 0.0070 chunk 255 optimal weight: 0.0370 chunk 81 optimal weight: 2.9990 chunk 191 optimal weight: 20.0000 chunk 269 optimal weight: 30.0000 chunk 127 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 overall best weight: 1.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN B 173 GLN B 175 HIS C 335 ASN D 235 GLN D 277 HIS E 264 GLN E 293 HIS E 326 HIS E 787 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.180454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.157397 restraints weight = 26996.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.158888 restraints weight = 15219.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.160249 restraints weight = 11778.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.161587 restraints weight = 8533.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.161677 restraints weight = 7155.274| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21670 Z= 0.134 Angle : 0.590 9.635 29531 Z= 0.298 Chirality : 0.044 0.345 3523 Planarity : 0.004 0.067 3625 Dihedral : 13.150 170.669 3400 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.76 % Allowed : 17.67 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.16), residues: 2774 helix: 1.55 (0.14), residues: 1324 sheet: -2.02 (0.29), residues: 264 loop : -1.84 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 325 TYR 0.018 0.002 TYR E1064 PHE 0.021 0.002 PHE C 75 TRP 0.009 0.001 TRP C 68 HIS 0.005 0.001 HIS E1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (21663) covalent geometry : angle 0.58840 / 0.30 (29515) SS BOND : bond 0.00120 / 0.07 ( 5) SS BOND : angle 1.61562 / 0.84 ( 10) hydrogen bonds : bond 0.04872 / 3.43 ( 1164) hydrogen bonds : angle 4.63376 / 3.29 ( 3420) link_BETA1-4 : bond 0.01167 / 0.61 ( 1) link_BETA1-4 : angle 1.89917 / 0.95 ( 3) link_NAG-ASN : bond 0.00162 / 0.09 ( 1) link_NAG-ASN : angle 3.15647 / 1.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 607 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.7117 (t0) cc_final: 0.6714 (t0) REVERT: A 93 ILE cc_start: 0.8963 (tt) cc_final: 0.8663 (mt) REVERT: A 158 MET cc_start: 0.7322 (mmm) cc_final: 0.7065 (mtm) REVERT: A 177 ARG cc_start: 0.8849 (tpt-90) cc_final: 0.8544 (tpt170) REVERT: A 304 TYR cc_start: 0.8883 (m-80) cc_final: 0.8457 (m-80) REVERT: B 47 LYS cc_start: 0.8118 (mttt) cc_final: 0.7887 (mttm) REVERT: B 72 LEU cc_start: 0.8052 (mm) cc_final: 0.6704 (mm) REVERT: B 77 MET cc_start: 0.6911 (mmm) cc_final: 0.6534 (mmt) REVERT: B 264 ASN cc_start: 0.8071 (m-40) cc_final: 0.7807 (m-40) REVERT: B 313 GLN cc_start: 0.7230 (mt0) cc_final: 0.6726 (mm-40) REVERT: C 114 ILE cc_start: 0.8849 (mm) cc_final: 0.8585 (tp) REVERT: C 200 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8328 (tt) REVERT: D 113 SER cc_start: 0.8541 (m) cc_final: 0.8270 (p) REVERT: D 114 ILE cc_start: 0.9310 (mm) cc_final: 0.9109 (mm) REVERT: D 158 MET cc_start: 0.7794 (mmm) cc_final: 0.7394 (tmm) REVERT: D 212 SER cc_start: 0.9178 (m) cc_final: 0.8915 (p) REVERT: D 269 ASP cc_start: 0.8131 (m-30) cc_final: 0.7829 (m-30) REVERT: D 274 ASP cc_start: 0.6971 (t70) cc_final: 0.6527 (t0) REVERT: E 369 GLN cc_start: 0.8268 (tt0) cc_final: 0.8055 (tt0) REVERT: E 409 MET cc_start: 0.8643 (tpt) cc_final: 0.8214 (tpt) REVERT: E 486 ARG cc_start: 0.6943 (tpp-160) cc_final: 0.6668 (mmm160) REVERT: E 559 PHE cc_start: 0.7798 (m-80) cc_final: 0.6990 (m-80) REVERT: E 591 PHE cc_start: 0.6058 (t80) cc_final: 0.5815 (t80) REVERT: E 778 TRP cc_start: 0.8016 (t60) cc_final: 0.7509 (t60) REVERT: E 785 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6618 (mt-10) REVERT: E 893 TYR cc_start: 0.4600 (OUTLIER) cc_final: 0.4309 (t80) REVERT: E 1290 MET cc_start: 0.6584 (mmm) cc_final: 0.6123 (mmt) REVERT: E 1294 TYR cc_start: 0.8345 (m-10) cc_final: 0.7430 (m-10) REVERT: E 1308 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7745 (mp10) outliers start: 93 outliers final: 55 residues processed: 642 average time/residue: 0.1302 time to fit residues: 132.0996 Evaluate side-chains 627 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 568 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 257 MET Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 701 ILE Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 893 TYR Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1165 LEU Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1308 GLN Chi-restraints excluded: chain E residue 1309 LEU Chi-restraints excluded: chain E residue 1312 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 50.0000 chunk 114 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 211 optimal weight: 30.0000 chunk 264 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 198 optimal weight: 6.9990 chunk 187 optimal weight: 20.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 216 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN B 173 GLN B 175 HIS ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN D 278 HIS E 293 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.177691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.151605 restraints weight = 27413.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.154270 restraints weight = 15328.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.155996 restraints weight = 10478.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.157326 restraints weight = 7635.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.157630 restraints weight = 6505.157| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 21670 Z= 0.279 Angle : 0.728 11.382 29531 Z= 0.368 Chirality : 0.048 0.346 3523 Planarity : 0.005 0.061 3625 Dihedral : 13.122 172.302 3400 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 7.33 % Allowed : 17.21 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.16), residues: 2774 helix: 1.37 (0.14), residues: 1322 sheet: -2.03 (0.29), residues: 263 loop : -2.04 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 202 TYR 0.026 0.002 TYR E1032 PHE 0.028 0.002 PHE D 75 TRP 0.012 0.002 TRP E 65 HIS 0.005 0.001 HIS E 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.28 (21663) covalent geometry : angle 0.72658 / 0.37 (29515) SS BOND : bond 0.00341 / 0.18 ( 5) SS BOND : angle 1.83972 / 0.95 ( 10) hydrogen bonds : bond 0.05158 / 3.63 ( 1164) hydrogen bonds : angle 4.81346 / 3.42 ( 3420) link_BETA1-4 : bond 0.00845 / 0.44 ( 1) link_BETA1-4 : angle 1.66640 / 0.84 ( 3) link_NAG-ASN : bond 0.00172 / 0.09 ( 1) link_NAG-ASN : angle 3.73600 / 1.95 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 588 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.7320 (t0) cc_final: 0.6851 (t0) REVERT: A 59 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8543 (t) REVERT: A 83 TRP cc_start: 0.9021 (m-10) cc_final: 0.8632 (m-10) REVERT: A 93 ILE cc_start: 0.9078 (tt) cc_final: 0.8748 (mt) REVERT: A 100 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8193 (tp) REVERT: A 177 ARG cc_start: 0.9060 (tpt-90) cc_final: 0.8518 (tpt170) REVERT: A 304 TYR cc_start: 0.8850 (m-80) cc_final: 0.8481 (m-80) REVERT: B 47 LYS cc_start: 0.8325 (mttt) cc_final: 0.8054 (mttm) REVERT: B 75 PHE cc_start: 0.8334 (t80) cc_final: 0.7915 (t80) REVERT: B 77 MET cc_start: 0.7075 (OUTLIER) cc_final: 0.6662 (mmt) REVERT: B 264 ASN cc_start: 0.8121 (m-40) cc_final: 0.7895 (m-40) REVERT: B 313 GLN cc_start: 0.7656 (mt0) cc_final: 0.7010 (mm-40) REVERT: C 200 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8354 (tt) REVERT: C 247 ASN cc_start: 0.7919 (m-40) cc_final: 0.7409 (p0) REVERT: D 38 LYS cc_start: 0.8588 (mmmt) cc_final: 0.8374 (mmmt) REVERT: D 113 SER cc_start: 0.8802 (m) cc_final: 0.8413 (p) REVERT: D 158 MET cc_start: 0.8032 (mmm) cc_final: 0.7640 (tmm) REVERT: D 212 SER cc_start: 0.9321 (m) cc_final: 0.9048 (p) REVERT: D 274 ASP cc_start: 0.7307 (t70) cc_final: 0.6777 (t0) REVERT: E 39 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8144 (tt) REVERT: E 282 GLN cc_start: 0.5071 (mt0) cc_final: 0.4543 (pp30) REVERT: E 400 MET cc_start: 0.8327 (mmp) cc_final: 0.7517 (mtp) REVERT: E 409 MET cc_start: 0.8697 (tpt) cc_final: 0.8158 (tpt) REVERT: E 486 ARG cc_start: 0.6920 (tpp-160) cc_final: 0.6684 (mmm160) REVERT: E 502 MET cc_start: 0.8151 (ttt) cc_final: 0.7858 (ttt) REVERT: E 547 ASN cc_start: 0.8065 (t0) cc_final: 0.7803 (t0) REVERT: E 559 PHE cc_start: 0.8060 (m-80) cc_final: 0.7310 (m-80) REVERT: E 598 ARG cc_start: 0.8805 (ttm-80) cc_final: 0.8416 (ttm110) REVERT: E 785 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6543 (mt-10) REVERT: E 1294 TYR cc_start: 0.8454 (m-10) cc_final: 0.7772 (m-10) REVERT: E 1305 MET cc_start: 0.8190 (tpp) cc_final: 0.7901 (tpp) REVERT: E 1308 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7733 (mp10) REVERT: E 1320 LYS cc_start: 0.8465 (mttt) cc_final: 0.8093 (mttt) outliers start: 143 outliers final: 106 residues processed: 645 average time/residue: 0.1211 time to fit residues: 124.4221 Evaluate side-chains 676 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 563 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 170 CYS Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 257 MET Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 701 ILE Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 865 SER Chi-restraints excluded: chain E residue 893 TYR Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1074 LEU Chi-restraints excluded: chain E residue 1089 THR Chi-restraints excluded: chain E residue 1165 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1276 LEU Chi-restraints excluded: chain E residue 1308 GLN Chi-restraints excluded: chain E residue 1312 VAL Chi-restraints excluded: chain E residue 1557 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 220 optimal weight: 0.1980 chunk 190 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 263 optimal weight: 40.0000 chunk 134 optimal weight: 20.0000 chunk 235 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 211 optimal weight: 30.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN B 175 HIS ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN D 128 GLN D 235 GLN D 277 HIS E 293 HIS E 326 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.176860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.153894 restraints weight = 27028.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.154983 restraints weight = 15988.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.156894 restraints weight = 12403.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.157677 restraints weight = 8813.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.157880 restraints weight = 7144.007| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21670 Z= 0.177 Angle : 0.631 9.934 29531 Z= 0.318 Chirality : 0.045 0.314 3523 Planarity : 0.004 0.056 3625 Dihedral : 12.783 174.367 3400 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 6.25 % Allowed : 20.29 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.16), residues: 2774 helix: 1.57 (0.14), residues: 1320 sheet: -2.00 (0.29), residues: 273 loop : -1.87 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 195 TYR 0.020 0.002 TYR E1032 PHE 0.027 0.002 PHE B 198 TRP 0.013 0.001 TRP E 65 HIS 0.004 0.001 HIS E 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (21663) covalent geometry : angle 0.62864 / 0.32 (29515) SS BOND : bond 0.00184 / 0.11 ( 5) SS BOND : angle 1.74956 / 0.91 ( 10) hydrogen bonds : bond 0.04737 / 3.33 ( 1164) hydrogen bonds : angle 4.56961 / 3.26 ( 3420) link_BETA1-4 : bond 0.00718 / 0.38 ( 1) link_BETA1-4 : angle 1.83815 / 0.93 ( 3) link_NAG-ASN : bond 0.00111 / 0.06 ( 1) link_NAG-ASN : angle 3.70646 / 1.89 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 566 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.7255 (t0) cc_final: 0.6778 (t0) REVERT: A 59 VAL cc_start: 0.8772 (OUTLIER) cc_final: 0.8538 (t) REVERT: A 93 ILE cc_start: 0.9042 (tt) cc_final: 0.8655 (mt) REVERT: A 177 ARG cc_start: 0.9022 (tpt-90) cc_final: 0.8572 (tpt170) REVERT: A 304 TYR cc_start: 0.8787 (m-80) cc_final: 0.8402 (m-80) REVERT: A 343 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7068 (tp) REVERT: B 313 GLN cc_start: 0.7449 (mt0) cc_final: 0.6821 (mm-40) REVERT: C 200 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8337 (tt) REVERT: D 38 LYS cc_start: 0.8580 (mmmt) cc_final: 0.8331 (mmmt) REVERT: D 113 SER cc_start: 0.8645 (m) cc_final: 0.8362 (p) REVERT: D 158 MET cc_start: 0.7914 (mmm) cc_final: 0.7561 (tmm) REVERT: D 212 SER cc_start: 0.9409 (m) cc_final: 0.8964 (p) REVERT: D 274 ASP cc_start: 0.7241 (t70) cc_final: 0.6679 (t0) REVERT: D 338 LYS cc_start: 0.7244 (mmtm) cc_final: 0.6823 (mppt) REVERT: E 221 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8629 (p90) REVERT: E 234 ASN cc_start: 0.8377 (m-40) cc_final: 0.7935 (m110) REVERT: E 282 GLN cc_start: 0.4914 (mt0) cc_final: 0.4640 (pp30) REVERT: E 400 MET cc_start: 0.8275 (mmp) cc_final: 0.7460 (mtp) REVERT: E 409 MET cc_start: 0.8657 (tpt) cc_final: 0.8391 (tpt) REVERT: E 486 ARG cc_start: 0.6916 (tpp-160) cc_final: 0.6682 (mmm160) REVERT: E 502 MET cc_start: 0.8115 (ttt) cc_final: 0.7777 (ttt) REVERT: E 559 PHE cc_start: 0.7865 (m-80) cc_final: 0.7066 (m-80) REVERT: E 591 PHE cc_start: 0.6442 (t80) cc_final: 0.6208 (t80) REVERT: E 598 ARG cc_start: 0.8752 (ttm-80) cc_final: 0.8320 (ttm110) REVERT: E 785 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6626 (mt-10) REVERT: E 1034 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8632 (tp) REVERT: E 1294 TYR cc_start: 0.8370 (m-10) cc_final: 0.7820 (m-10) REVERT: E 1308 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7773 (mp10) REVERT: E 1320 LYS cc_start: 0.8495 (mttt) cc_final: 0.8104 (mttt) outliers start: 122 outliers final: 87 residues processed: 617 average time/residue: 0.1185 time to fit residues: 116.8955 Evaluate side-chains 643 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 549 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 257 MET Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 462 ILE Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 893 TYR Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1074 LEU Chi-restraints excluded: chain E residue 1165 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1308 GLN Chi-restraints excluded: chain E residue 1309 LEU Chi-restraints excluded: chain E residue 1312 VAL Chi-restraints excluded: chain E residue 1557 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 120 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 47 optimal weight: 30.0000 chunk 187 optimal weight: 20.0000 chunk 186 optimal weight: 30.0000 chunk 150 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 221 optimal weight: 30.0000 chunk 10 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN B 48 ASN B 173 GLN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN D 278 HIS E 293 HIS E 584 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.175229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.152216 restraints weight = 27090.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.153362 restraints weight = 16090.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.154352 restraints weight = 12428.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.155160 restraints weight = 9688.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.155335 restraints weight = 8177.910| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21670 Z= 0.207 Angle : 0.648 11.199 29531 Z= 0.327 Chirality : 0.046 0.313 3523 Planarity : 0.004 0.059 3625 Dihedral : 12.640 174.863 3400 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 6.86 % Allowed : 20.59 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.16), residues: 2774 helix: 1.59 (0.14), residues: 1325 sheet: -1.97 (0.29), residues: 273 loop : -1.87 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 195 TYR 0.021 0.002 TYR E1032 PHE 0.026 0.002 PHE B 198 TRP 0.013 0.001 TRP E 65 HIS 0.004 0.001 HIS E 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 (21663) covalent geometry : angle 0.64590 / 0.33 (29515) SS BOND : bond 0.00285 / 0.16 ( 5) SS BOND : angle 1.82080 / 0.94 ( 10) hydrogen bonds : bond 0.04739 / 3.32 ( 1164) hydrogen bonds : angle 4.58491 / 3.27 ( 3420) link_BETA1-4 : bond 0.01005 / 0.53 ( 1) link_BETA1-4 : angle 1.70817 / 0.84 ( 3) link_NAG-ASN : bond 0.00043 / 0.02 ( 1) link_NAG-ASN : angle 3.83307 / 1.98 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 572 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.7320 (t0) cc_final: 0.6870 (t0) REVERT: A 59 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8570 (t) REVERT: A 83 TRP cc_start: 0.8939 (m-10) cc_final: 0.8586 (m-10) REVERT: A 93 ILE cc_start: 0.9077 (tt) cc_final: 0.8781 (mt) REVERT: A 158 MET cc_start: 0.7490 (mmm) cc_final: 0.7058 (mtm) REVERT: A 177 ARG cc_start: 0.9052 (tpt-90) cc_final: 0.8632 (tpt170) REVERT: A 304 TYR cc_start: 0.8786 (m-80) cc_final: 0.8372 (m-80) REVERT: A 343 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7119 (tp) REVERT: B 313 GLN cc_start: 0.7432 (mt0) cc_final: 0.6900 (mm-40) REVERT: C 200 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8263 (tt) REVERT: C 284 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.9023 (mt) REVERT: D 38 LYS cc_start: 0.8600 (mmmt) cc_final: 0.8394 (mmmt) REVERT: D 113 SER cc_start: 0.8608 (m) cc_final: 0.8308 (p) REVERT: D 158 MET cc_start: 0.8002 (mmm) cc_final: 0.7560 (tmm) REVERT: D 212 SER cc_start: 0.9410 (m) cc_final: 0.8954 (p) REVERT: D 274 ASP cc_start: 0.7237 (t70) cc_final: 0.6700 (t0) REVERT: E 181 MET cc_start: 0.7897 (ttp) cc_final: 0.7611 (ttm) REVERT: E 221 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8626 (p90) REVERT: E 348 SER cc_start: 0.7978 (p) cc_final: 0.7615 (m) REVERT: E 400 MET cc_start: 0.8258 (mmp) cc_final: 0.7836 (mtp) REVERT: E 409 MET cc_start: 0.8701 (tpt) cc_final: 0.8400 (tpt) REVERT: E 486 ARG cc_start: 0.6944 (tpp-160) cc_final: 0.6681 (mmm160) REVERT: E 502 MET cc_start: 0.8132 (ttt) cc_final: 0.7778 (ttt) REVERT: E 559 PHE cc_start: 0.7862 (m-80) cc_final: 0.7152 (m-80) REVERT: E 591 PHE cc_start: 0.6552 (t80) cc_final: 0.6008 (t80) REVERT: E 598 ARG cc_start: 0.8797 (ttm-80) cc_final: 0.8347 (ttm110) REVERT: E 785 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6578 (mt-10) REVERT: E 1034 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8652 (tp) REVERT: E 1294 TYR cc_start: 0.8398 (m-10) cc_final: 0.7606 (m-10) REVERT: E 1305 MET cc_start: 0.8247 (tpp) cc_final: 0.7695 (tpp) REVERT: E 1308 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7800 (mp10) REVERT: E 1320 LYS cc_start: 0.8508 (mttt) cc_final: 0.8135 (mttt) outliers start: 134 outliers final: 105 residues processed: 630 average time/residue: 0.1148 time to fit residues: 115.3749 Evaluate side-chains 678 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 565 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 170 CYS Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 257 MET Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 462 ILE Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 722 LEU Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 865 SER Chi-restraints excluded: chain E residue 893 TYR Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1074 LEU Chi-restraints excluded: chain E residue 1165 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1308 GLN Chi-restraints excluded: chain E residue 1312 VAL Chi-restraints excluded: chain E residue 1557 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 67 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 218 optimal weight: 30.0000 chunk 265 optimal weight: 0.0270 chunk 99 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 overall best weight: 5.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 ASN A 52 GLN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 HIS E 293 HIS E 787 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.174238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.150887 restraints weight = 27315.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.152652 restraints weight = 15293.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.153675 restraints weight = 12008.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.154976 restraints weight = 8992.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.155269 restraints weight = 7479.009| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21670 Z= 0.219 Angle : 0.665 10.881 29531 Z= 0.335 Chirality : 0.046 0.311 3523 Planarity : 0.004 0.060 3625 Dihedral : 12.599 175.176 3400 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 6.97 % Allowed : 21.57 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.16), residues: 2774 helix: 1.56 (0.14), residues: 1325 sheet: -1.96 (0.29), residues: 273 loop : -1.85 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 194 TYR 0.022 0.002 TYR E1032 PHE 0.031 0.002 PHE B 198 TRP 0.014 0.002 TRP A 68 HIS 0.005 0.001 HIS E 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (21663) covalent geometry : angle 0.66288 / 0.33 (29515) SS BOND : bond 0.00235 / 0.14 ( 5) SS BOND : angle 1.88783 / 0.97 ( 10) hydrogen bonds : bond 0.04742 / 3.33 ( 1164) hydrogen bonds : angle 4.61494 / 3.29 ( 3420) link_BETA1-4 : bond 0.00830 / 0.44 ( 1) link_BETA1-4 : angle 1.73742 / 0.86 ( 3) link_NAG-ASN : bond 0.00028 / 0.01 ( 1) link_NAG-ASN : angle 3.86716 / 1.99 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 574 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.7476 (t0) cc_final: 0.6940 (t0) REVERT: A 59 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8578 (t) REVERT: A 83 TRP cc_start: 0.8950 (m-10) cc_final: 0.8608 (m-10) REVERT: A 93 ILE cc_start: 0.9060 (tt) cc_final: 0.8821 (mt) REVERT: A 177 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8570 (tpt170) REVERT: A 304 TYR cc_start: 0.8792 (m-80) cc_final: 0.8375 (m-80) REVERT: A 343 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7165 (tp) REVERT: B 192 ARG cc_start: 0.7398 (mtp85) cc_final: 0.7074 (mtt-85) REVERT: B 313 GLN cc_start: 0.7557 (mm-40) cc_final: 0.6920 (mm-40) REVERT: C 200 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8267 (tt) REVERT: D 38 LYS cc_start: 0.8644 (mmmt) cc_final: 0.8431 (mmmt) REVERT: D 73 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8216 (tt) REVERT: D 113 SER cc_start: 0.8635 (m) cc_final: 0.8307 (p) REVERT: D 158 MET cc_start: 0.8054 (mmm) cc_final: 0.7613 (tmm) REVERT: D 212 SER cc_start: 0.9436 (m) cc_final: 0.8981 (p) REVERT: D 274 ASP cc_start: 0.7238 (t70) cc_final: 0.6706 (t0) REVERT: E 181 MET cc_start: 0.7934 (ttp) cc_final: 0.7564 (ttm) REVERT: E 221 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8676 (p90) REVERT: E 348 SER cc_start: 0.7989 (p) cc_final: 0.7600 (m) REVERT: E 400 MET cc_start: 0.8258 (mmp) cc_final: 0.7791 (mtp) REVERT: E 486 ARG cc_start: 0.6950 (tpp-160) cc_final: 0.6666 (mmm160) REVERT: E 529 GLU cc_start: 0.6230 (tm-30) cc_final: 0.5625 (tm-30) REVERT: E 559 PHE cc_start: 0.7906 (m-80) cc_final: 0.7178 (m-80) REVERT: E 598 ARG cc_start: 0.8816 (ttm-80) cc_final: 0.8323 (ttm110) REVERT: E 785 GLU cc_start: 0.7326 (pt0) cc_final: 0.6844 (mt-10) REVERT: E 1034 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8703 (tp) REVERT: E 1294 TYR cc_start: 0.8370 (m-10) cc_final: 0.7576 (m-10) REVERT: E 1305 MET cc_start: 0.8132 (tpp) cc_final: 0.7685 (tpp) REVERT: E 1308 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7824 (mp10) REVERT: E 1320 LYS cc_start: 0.8510 (mttt) cc_final: 0.8143 (mttt) outliers start: 136 outliers final: 117 residues processed: 633 average time/residue: 0.1218 time to fit residues: 122.6601 Evaluate side-chains 682 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 557 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 170 CYS Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 257 MET Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 462 ILE Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 514 TRP Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 709 THR Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 722 LEU Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 865 SER Chi-restraints excluded: chain E residue 893 TYR Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1074 LEU Chi-restraints excluded: chain E residue 1165 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1308 GLN Chi-restraints excluded: chain E residue 1312 VAL Chi-restraints excluded: chain E residue 1557 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 34 optimal weight: 7.9990 chunk 208 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 152 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 219 optimal weight: 0.0970 chunk 268 optimal weight: 50.0000 chunk 225 optimal weight: 9.9990 chunk 203 optimal weight: 40.0000 chunk 76 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 overall best weight: 6.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 ASN A 216 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN B 173 GLN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 HIS E 293 HIS E 326 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.174850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.150889 restraints weight = 27171.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.152473 restraints weight = 15332.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.153676 restraints weight = 11544.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.155193 restraints weight = 8985.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.155574 restraints weight = 6927.514| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 21670 Z= 0.232 Angle : 0.682 10.715 29531 Z= 0.345 Chirality : 0.047 0.305 3523 Planarity : 0.004 0.060 3625 Dihedral : 12.610 175.046 3400 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 7.07 % Allowed : 21.82 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.16), residues: 2774 helix: 1.52 (0.14), residues: 1326 sheet: -2.01 (0.29), residues: 278 loop : -1.89 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 195 TYR 0.021 0.002 TYR E1032 PHE 0.031 0.002 PHE B 198 TRP 0.015 0.002 TRP A 68 HIS 0.005 0.001 HIS E 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.23 (21663) covalent geometry : angle 0.68005 / 0.34 (29515) SS BOND : bond 0.00342 / 0.19 ( 5) SS BOND : angle 2.01815 / 1.03 ( 10) hydrogen bonds : bond 0.04782 / 3.35 ( 1164) hydrogen bonds : angle 4.66989 / 3.33 ( 3420) link_BETA1-4 : bond 0.00674 / 0.35 ( 1) link_BETA1-4 : angle 1.78782 / 0.90 ( 3) link_NAG-ASN : bond 0.00065 / 0.03 ( 1) link_NAG-ASN : angle 3.96685 / 2.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 560 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.7446 (t0) cc_final: 0.6964 (t0) REVERT: A 59 VAL cc_start: 0.8809 (OUTLIER) cc_final: 0.8587 (t) REVERT: A 83 TRP cc_start: 0.8948 (m-10) cc_final: 0.8565 (m-10) REVERT: A 85 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7953 (tp) REVERT: A 93 ILE cc_start: 0.9059 (tt) cc_final: 0.8816 (mt) REVERT: A 177 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8620 (tpt170) REVERT: A 304 TYR cc_start: 0.8796 (m-80) cc_final: 0.8378 (m-80) REVERT: A 343 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7236 (tp) REVERT: B 192 ARG cc_start: 0.7477 (mtp85) cc_final: 0.7158 (mtt-85) REVERT: B 313 GLN cc_start: 0.7471 (mm-40) cc_final: 0.6874 (mm-40) REVERT: C 200 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8262 (tt) REVERT: C 274 ASP cc_start: 0.5926 (t70) cc_final: 0.5434 (t0) REVERT: D 38 LYS cc_start: 0.8662 (mmmt) cc_final: 0.8449 (mmmt) REVERT: D 73 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8229 (tt) REVERT: D 113 SER cc_start: 0.8608 (m) cc_final: 0.8269 (p) REVERT: D 158 MET cc_start: 0.8085 (mmm) cc_final: 0.7644 (tmm) REVERT: D 212 SER cc_start: 0.9447 (m) cc_final: 0.9007 (p) REVERT: D 254 PRO cc_start: 0.9159 (Cg_exo) cc_final: 0.8928 (Cg_endo) REVERT: D 274 ASP cc_start: 0.7279 (t70) cc_final: 0.6760 (t0) REVERT: E 181 MET cc_start: 0.7942 (ttp) cc_final: 0.7541 (ttm) REVERT: E 221 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8722 (p90) REVERT: E 348 SER cc_start: 0.8026 (p) cc_final: 0.7603 (m) REVERT: E 400 MET cc_start: 0.8249 (mmp) cc_final: 0.7826 (mtp) REVERT: E 486 ARG cc_start: 0.6931 (tpp-160) cc_final: 0.6639 (mmm160) REVERT: E 502 MET cc_start: 0.8073 (ttt) cc_final: 0.7858 (ttt) REVERT: E 529 GLU cc_start: 0.6203 (tm-30) cc_final: 0.5980 (tm-30) REVERT: E 559 PHE cc_start: 0.7932 (m-80) cc_final: 0.7194 (m-80) REVERT: E 598 ARG cc_start: 0.8815 (ttm-80) cc_final: 0.8317 (ttm110) REVERT: E 785 GLU cc_start: 0.7259 (pt0) cc_final: 0.6761 (mt-10) REVERT: E 1034 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8701 (tp) REVERT: E 1252 MET cc_start: 0.8414 (mmm) cc_final: 0.8175 (mmm) REVERT: E 1294 TYR cc_start: 0.8360 (m-10) cc_final: 0.7539 (m-10) REVERT: E 1305 MET cc_start: 0.8121 (tpp) cc_final: 0.7749 (tpp) REVERT: E 1308 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7813 (mp10) REVERT: E 1320 LYS cc_start: 0.8539 (mttt) cc_final: 0.8154 (mttt) outliers start: 138 outliers final: 115 residues processed: 629 average time/residue: 0.1197 time to fit residues: 120.5646 Evaluate side-chains 681 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 557 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 170 CYS Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 257 MET Chi-restraints excluded: chain E residue 305 PHE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 462 ILE Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 514 TRP Chi-restraints excluded: chain E residue 531 THR Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 709 THR Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 722 LEU Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 865 SER Chi-restraints excluded: chain E residue 893 TYR Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1074 LEU Chi-restraints excluded: chain E residue 1089 THR Chi-restraints excluded: chain E residue 1165 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1308 GLN Chi-restraints excluded: chain E residue 1312 VAL Chi-restraints excluded: chain E residue 1557 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 265 optimal weight: 0.0050 chunk 259 optimal weight: 50.0000 chunk 206 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 chunk 252 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 214 optimal weight: 4.9990 overall best weight: 4.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN A 335 ASN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 HIS E 293 HIS E 326 HIS E 444 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.179213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.153683 restraints weight = 27168.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.156012 restraints weight = 15154.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.157632 restraints weight = 10774.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.159136 restraints weight = 7634.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.159212 restraints weight = 6395.879| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21670 Z= 0.178 Angle : 0.645 10.226 29531 Z= 0.324 Chirality : 0.046 0.306 3523 Planarity : 0.004 0.061 3625 Dihedral : 12.460 174.814 3400 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 6.25 % Allowed : 22.95 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.16), residues: 2774 helix: 1.64 (0.14), residues: 1324 sheet: -1.90 (0.29), residues: 272 loop : -1.83 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 195 TYR 0.019 0.002 TYR E1032 PHE 0.035 0.002 PHE E1164 TRP 0.014 0.001 TRP E 65 HIS 0.004 0.001 HIS E 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (21663) covalent geometry : angle 0.64195 / 0.32 (29515) SS BOND : bond 0.00465 / 0.24 ( 5) SS BOND : angle 2.40008 / 1.29 ( 10) hydrogen bonds : bond 0.04580 / 3.20 ( 1164) hydrogen bonds : angle 4.55411 / 3.25 ( 3420) link_BETA1-4 : bond 0.00776 / 0.41 ( 1) link_BETA1-4 : angle 1.83649 / 0.92 ( 3) link_NAG-ASN : bond 0.00049 / 0.03 ( 1) link_NAG-ASN : angle 3.80170 / 1.94 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 550 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.7360 (t0) cc_final: 0.6912 (t0) REVERT: A 59 VAL cc_start: 0.8774 (OUTLIER) cc_final: 0.8540 (t) REVERT: A 83 TRP cc_start: 0.8935 (m-10) cc_final: 0.8564 (m-10) REVERT: A 177 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8671 (tpt170) REVERT: A 304 TYR cc_start: 0.8803 (m-80) cc_final: 0.8343 (m-80) REVERT: A 343 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7071 (tp) REVERT: B 313 GLN cc_start: 0.7387 (mm-40) cc_final: 0.6807 (mm-40) REVERT: C 200 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8251 (tt) REVERT: C 274 ASP cc_start: 0.5874 (t70) cc_final: 0.5412 (t0) REVERT: D 38 LYS cc_start: 0.8655 (mmmt) cc_final: 0.7893 (tptm) REVERT: D 73 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8211 (tt) REVERT: D 113 SER cc_start: 0.8569 (m) cc_final: 0.8235 (p) REVERT: D 158 MET cc_start: 0.7981 (mmm) cc_final: 0.7596 (tmm) REVERT: D 212 SER cc_start: 0.9455 (m) cc_final: 0.8968 (p) REVERT: D 254 PRO cc_start: 0.9163 (Cg_exo) cc_final: 0.8920 (Cg_endo) REVERT: D 274 ASP cc_start: 0.7242 (t70) cc_final: 0.6776 (t0) REVERT: D 278 HIS cc_start: 0.7219 (m-70) cc_final: 0.7008 (m90) REVERT: E 181 MET cc_start: 0.7891 (ttp) cc_final: 0.7491 (ttm) REVERT: E 221 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8697 (p90) REVERT: E 348 SER cc_start: 0.8059 (p) cc_final: 0.7644 (m) REVERT: E 400 MET cc_start: 0.8183 (mmp) cc_final: 0.7754 (mtp) REVERT: E 444 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: E 486 ARG cc_start: 0.6919 (tpp-160) cc_final: 0.6645 (mmm160) REVERT: E 529 GLU cc_start: 0.6189 (tm-30) cc_final: 0.5770 (tm-30) REVERT: E 559 PHE cc_start: 0.7897 (m-80) cc_final: 0.7170 (m-80) REVERT: E 598 ARG cc_start: 0.8810 (ttm-80) cc_final: 0.8350 (ttm110) REVERT: E 785 GLU cc_start: 0.7314 (pt0) cc_final: 0.6811 (mt-10) REVERT: E 1034 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8659 (tp) REVERT: E 1252 MET cc_start: 0.8426 (mmm) cc_final: 0.8215 (mmm) REVERT: E 1294 TYR cc_start: 0.8310 (m-10) cc_final: 0.7550 (m-10) REVERT: E 1305 MET cc_start: 0.8050 (tpp) cc_final: 0.7666 (tpp) REVERT: E 1308 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7784 (mp10) REVERT: E 1320 LYS cc_start: 0.8572 (mttt) cc_final: 0.8155 (mttt) outliers start: 122 outliers final: 107 residues processed: 607 average time/residue: 0.1188 time to fit residues: 114.4957 Evaluate side-chains 654 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 538 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 170 CYS Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 257 MET Chi-restraints excluded: chain E residue 305 PHE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 444 GLN Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 462 ILE Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 709 THR Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 722 LEU Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 865 SER Chi-restraints excluded: chain E residue 893 TYR Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1074 LEU Chi-restraints excluded: chain E residue 1165 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1308 GLN Chi-restraints excluded: chain E residue 1312 VAL Chi-restraints excluded: chain E residue 1557 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 84 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 240 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 chunk 195 optimal weight: 5.9990 chunk 250 optimal weight: 8.9990 chunk 186 optimal weight: 40.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN A 335 ASN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 HIS ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 HIS E 326 HIS E 444 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.176445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.150917 restraints weight = 27336.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.152865 restraints weight = 15765.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.154726 restraints weight = 11116.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.157024 restraints weight = 7825.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.157051 restraints weight = 6150.880| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 21670 Z= 0.230 Angle : 0.693 10.446 29531 Z= 0.349 Chirality : 0.047 0.306 3523 Planarity : 0.004 0.061 3625 Dihedral : 12.521 174.180 3400 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 6.35 % Allowed : 23.31 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.16), residues: 2774 helix: 1.53 (0.14), residues: 1326 sheet: -1.94 (0.29), residues: 277 loop : -1.85 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 195 TYR 0.021 0.002 TYR E1032 PHE 0.040 0.002 PHE E1164 TRP 0.014 0.002 TRP E 65 HIS 0.005 0.001 HIS E 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.23 (21663) covalent geometry : angle 0.69154 / 0.35 (29515) SS BOND : bond 0.00613 / 0.32 ( 5) SS BOND : angle 1.78888 / 0.95 ( 10) hydrogen bonds : bond 0.04724 / 3.30 ( 1164) hydrogen bonds : angle 4.64533 / 3.31 ( 3420) link_BETA1-4 : bond 0.00769 / 0.40 ( 1) link_BETA1-4 : angle 1.76384 / 0.88 ( 3) link_NAG-ASN : bond 0.00085 / 0.04 ( 1) link_NAG-ASN : angle 3.92702 / 2.03 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 553 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.7385 (t0) cc_final: 0.6948 (t0) REVERT: A 59 VAL cc_start: 0.8785 (OUTLIER) cc_final: 0.8570 (t) REVERT: A 83 TRP cc_start: 0.8949 (m-10) cc_final: 0.8570 (m-10) REVERT: A 93 ILE cc_start: 0.9043 (tt) cc_final: 0.8787 (mt) REVERT: A 177 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8624 (tpt170) REVERT: A 304 TYR cc_start: 0.8835 (m-80) cc_final: 0.8425 (m-80) REVERT: A 343 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.6918 (tp) REVERT: B 313 GLN cc_start: 0.7503 (mm-40) cc_final: 0.6850 (mm-40) REVERT: C 200 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8300 (tt) REVERT: D 38 LYS cc_start: 0.8695 (mmmt) cc_final: 0.7948 (tptm) REVERT: D 73 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8234 (tt) REVERT: D 113 SER cc_start: 0.8587 (m) cc_final: 0.8173 (p) REVERT: D 158 MET cc_start: 0.8052 (mmm) cc_final: 0.7599 (tmm) REVERT: D 212 SER cc_start: 0.9457 (m) cc_final: 0.8974 (p) REVERT: D 254 PRO cc_start: 0.9223 (Cg_exo) cc_final: 0.9002 (Cg_endo) REVERT: D 274 ASP cc_start: 0.7185 (t70) cc_final: 0.6694 (t0) REVERT: E 151 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8472 (t) REVERT: E 181 MET cc_start: 0.7964 (ttp) cc_final: 0.7570 (ttm) REVERT: E 221 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8709 (p90) REVERT: E 348 SER cc_start: 0.8264 (p) cc_final: 0.7871 (m) REVERT: E 400 MET cc_start: 0.8174 (mmp) cc_final: 0.7771 (mtp) REVERT: E 486 ARG cc_start: 0.6954 (tpp-160) cc_final: 0.6651 (mmm160) REVERT: E 529 GLU cc_start: 0.6123 (tm-30) cc_final: 0.5883 (tm-30) REVERT: E 559 PHE cc_start: 0.7911 (m-80) cc_final: 0.7209 (m-80) REVERT: E 598 ARG cc_start: 0.8830 (ttm-80) cc_final: 0.8329 (ttm110) REVERT: E 1034 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8712 (tp) REVERT: E 1290 MET cc_start: 0.7131 (mtm) cc_final: 0.6719 (mpp) REVERT: E 1294 TYR cc_start: 0.8366 (m-10) cc_final: 0.7614 (m-10) REVERT: E 1305 MET cc_start: 0.8092 (tpp) cc_final: 0.7751 (tpp) REVERT: E 1308 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7774 (mp10) REVERT: E 1320 LYS cc_start: 0.8580 (mttt) cc_final: 0.8170 (mttt) REVERT: E 1525 MET cc_start: 0.2656 (mtm) cc_final: 0.2396 (ptp) outliers start: 124 outliers final: 111 residues processed: 610 average time/residue: 0.1242 time to fit residues: 121.1550 Evaluate side-chains 669 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 549 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 142 CYS Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 170 CYS Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 257 MET Chi-restraints excluded: chain E residue 305 PHE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 462 ILE Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 514 TRP Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 709 THR Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 722 LEU Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 865 SER Chi-restraints excluded: chain E residue 893 TYR Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1074 LEU Chi-restraints excluded: chain E residue 1165 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1308 GLN Chi-restraints excluded: chain E residue 1312 VAL Chi-restraints excluded: chain E residue 1424 ILE Chi-restraints excluded: chain E residue 1557 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 213 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 211 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 223 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 265 optimal weight: 0.1980 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN E 72 ASN E 293 HIS E 326 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.176116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.150367 restraints weight = 27458.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.152384 restraints weight = 15678.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.153696 restraints weight = 11185.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.155605 restraints weight = 8706.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.155967 restraints weight = 6638.338| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.177 21670 Z= 0.242 Angle : 0.821 59.200 29531 Z= 0.453 Chirality : 0.050 1.129 3523 Planarity : 0.004 0.062 3625 Dihedral : 12.522 174.167 3400 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 6.45 % Allowed : 23.46 % Favored : 70.08 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.16), residues: 2774 helix: 1.53 (0.14), residues: 1323 sheet: -1.93 (0.29), residues: 277 loop : -1.86 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 74 TYR 0.021 0.002 TYR E1032 PHE 0.035 0.002 PHE E1164 TRP 0.014 0.001 TRP E 65 HIS 0.005 0.001 HIS E 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.24 (21663) covalent geometry : angle 0.81953 / 0.45 (29515) SS BOND : bond 0.00543 / 0.28 ( 5) SS BOND : angle 1.80357 / 0.95 ( 10) hydrogen bonds : bond 0.04703 / 3.29 ( 1164) hydrogen bonds : angle 4.64227 / 3.31 ( 3420) link_BETA1-4 : bond 0.00735 / 0.39 ( 1) link_BETA1-4 : angle 1.77078 / 0.89 ( 3) link_NAG-ASN : bond 0.00055 / 0.03 ( 1) link_NAG-ASN : angle 3.91451 / 2.02 ( 3) =============================================================================== Job complete usr+sys time: 3196.03 seconds wall clock time: 56 minutes 0.09 seconds (3360.09 seconds total)