Starting phenix.real_space_refine on Sat Jul 4 05:12:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u1e_26299/07_2026/7u1e_26299.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u1e_26299/07_2026/7u1e_26299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7u1e_26299/07_2026/7u1e_26299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u1e_26299/07_2026/7u1e_26299.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7u1e_26299/07_2026/7u1e_26299.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u1e_26299/07_2026/7u1e_26299.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u1e_26299/07_2026/7u1e_26299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u1e_26299/07_2026/7u1e_26299.map" } resolution = 4.52 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: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 68 5.16 5 C 11736 2.51 5 N 3273 2.21 5 O 3274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 18366 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2216 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 13, 'TRANS': 312} Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ASP:plan': 9, 'ASN:plan1': 4, 'HIS:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 8, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 165 Chain: "B" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2235 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 13, 'TRANS': 313} Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 427 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'ARG:plan': 7, 'PHE:plan': 1, 'ASN:plan1': 5, 'GLU:plan': 13, 'GLN:plan1': 4, 'ASP:plan': 9, 'HIS:plan': 5, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 183 Chain: "C" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2282 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 13, 'TRANS': 314} Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 377 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 12, 'GLN:plan1': 4, 'PHE:plan': 1, 'ASP:plan': 9, 'ASN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 161 Chain: "D" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2303 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 13, 'TRANS': 314} Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 213 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'ARG:plan': 9, 'ASN:plan1': 3, 'GLU:plan': 10, 'GLN:plan1': 3, 'ASP:plan': 6, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 141 Chain: "E" Number of atoms: 9161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1432, 9161 Classifications: {'peptide': 1432} Incomplete info: {'truncation_to_alanine': 671} Link IDs: {'PTRANS': 48, 'TRANS': 1383} Chain breaks: 5 Unresolved non-hydrogen bonds: 2211 Unresolved non-hydrogen angles: 2793 Unresolved non-hydrogen dihedrals: 1742 Unresolved non-hydrogen chiralities: 273 Planarities with less than four sites: {'GLU:plan': 52, 'ASP:plan': 48, 'ASN:plan1': 27, 'HIS:plan': 11, 'ARG:plan': 40, 'PHE:plan': 22, 'GLN:plan1': 39, 'TYR:plan': 4, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 1049 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.65, per 1000 atoms: 0.20 Number of scatterers: 18366 At special positions: 0 Unit cell: (167.58, 104.31, 145.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 15 15.00 O 3274 8.00 N 3273 7.00 C 11736 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 NAG-ASN " NAG E1602 " - " ASN E 10 " Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 910.2 milliseconds 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5166 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 28 sheets defined 54.5% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.992A pdb=" N VAL A 59 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 98 removed outlier: 3.538A pdb=" N HIS A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 129 Processing helix chain 'A' and resid 142 through 178 removed outlier: 3.661A pdb=" N ALA A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 4.109A pdb=" N ASP A 269 " --> pdb=" O PRO A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.830A pdb=" N HIS A 276 " --> pdb=" O SER A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.852A pdb=" N GLY A 334 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 Processing helix chain 'B' and resid 55 through 65 removed outlier: 4.150A pdb=" N LEU B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 64 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 97 Processing helix chain 'B' and resid 116 through 128 Processing helix chain 'B' and resid 142 through 174 removed outlier: 3.788A pdb=" N ALA B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 270 removed outlier: 4.383A pdb=" N ASP B 269 " --> pdb=" O PRO B 266 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 270 " --> pdb=" O LEU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 345 through 358 removed outlier: 4.000A pdb=" N ASP B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU B 351 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 64 removed outlier: 4.379A pdb=" N VAL C 59 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 96 Processing helix chain 'C' and resid 116 through 129 removed outlier: 3.972A pdb=" N VAL C 129 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 174 removed outlier: 3.687A pdb=" N VAL C 151 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE C 154 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 270 removed outlier: 3.817A pdb=" N ASP C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 345 through 358 Processing helix chain 'D' and resid 55 through 65 removed outlier: 3.620A pdb=" N ASP D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 97 Processing helix chain 'D' and resid 116 through 129 removed outlier: 3.662A pdb=" N VAL D 129 " --> pdb=" O ILE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 175 removed outlier: 4.144A pdb=" N ILE D 150 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 333 Processing helix chain 'D' and resid 345 through 358 removed outlier: 3.695A pdb=" N ASP D 350 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 13 Processing helix chain 'E' and resid 14 through 16 No H-bonds generated for 'chain 'E' and resid 14 through 16' Processing helix chain 'E' and resid 24 through 51 removed outlier: 3.802A pdb=" N VAL E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP E 29 " --> pdb=" O GLY E 25 " (cutoff:3.500A) Proline residue: E 35 - end of helix Proline residue: E 45 - end of helix removed outlier: 3.523A pdb=" N GLY E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 99 removed outlier: 3.643A pdb=" N ILE E 76 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL E 98 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 4.083A 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 129 Processing helix chain 'E' and resid 136 through 161 removed outlier: 3.608A pdb=" N LEU E 145 " --> pdb=" O ILE E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 194 removed outlier: 3.822A pdb=" N CYS E 170 " --> pdb=" O GLN E 166 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE E 177 " --> pdb=" O GLY E 173 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL E 189 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE E 190 " --> pdb=" O GLU E 186 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG E 191 " --> pdb=" O VAL E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 212 Processing helix chain 'E' and resid 223 through 230 Processing helix chain 'E' and resid 232 through 243 removed outlier: 4.369A pdb=" N PHE E 236 " --> pdb=" O TRP E 232 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N HIS E 241 " --> pdb=" O ILE E 237 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS E 242 " --> pdb=" O LYS E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 277 Processing helix chain 'E' and resid 283 through 329 removed outlier: 5.805A pdb=" N ARG E 297 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) Proline residue: E 317 - end of helix removed outlier: 4.141A pdb=" N GLY E 322 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE E 323 " --> pdb=" O CYS E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 352 Processing helix chain 'E' and resid 354 through 402 removed outlier: 4.086A pdb=" N GLN E 374 " --> pdb=" O ARG E 370 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR E 393 " --> pdb=" O GLY E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 456 removed outlier: 3.843A pdb=" N MET E 412 " --> pdb=" O SER E 408 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR E 413 " --> pdb=" O MET E 409 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY E 415 " --> pdb=" O GLU E 411 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR E 425 " --> pdb=" O VAL E 421 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Proline residue: E 436 - end of helix Proline residue: E 442 - end of helix Processing helix chain 'E' and resid 457 through 469 Processing helix chain 'E' and resid 469 through 505 removed outlier: 4.114A pdb=" N VAL E 473 " --> pdb=" O LEU E 469 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU E 494 " --> pdb=" O GLU E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 512 removed outlier: 3.598A pdb=" N LEU E 509 " --> pdb=" O GLY E 505 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR E 512 " --> pdb=" O LEU E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 566 removed outlier: 4.075A pdb=" N THR E 525 " --> pdb=" O ARG E 521 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER E 532 " --> pdb=" O LYS E 528 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA E 535 " --> pdb=" O THR E 531 " (cutoff:3.500A) Proline residue: E 551 - end of helix removed outlier: 4.140A pdb=" N VAL E 563 " --> pdb=" O PHE E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 615 removed outlier: 4.927A pdb=" N THR E 588 " --> pdb=" O HIS E 584 " (cutoff:3.500A) Proline residue: E 589 - end of helix removed outlier: 3.546A pdb=" N SER E 594 " --> pdb=" O LEU E 590 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER E 595 " --> pdb=" O PHE E 591 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS E 602 " --> pdb=" O ARG E 598 " (cutoff:3.500A) Processing helix chain 'E' and resid 718 through 728 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 815 removed outlier: 3.907A pdb=" N ASP E 811 " --> pdb=" O SER E 807 " (cutoff:3.500A) Processing helix chain 'E' and resid 831 through 847 removed outlier: 4.334A pdb=" N GLN E 847 " --> pdb=" O ALA E 843 " (cutoff:3.500A) Processing helix chain 'E' and resid 855 through 861 Processing helix chain 'E' and resid 862 through 881 removed outlier: 3.844A pdb=" N ARG E 878 " --> pdb=" O LEU E 874 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP E 879 " --> pdb=" O GLU E 875 " (cutoff:3.500A) Processing helix chain 'E' and resid 893 through 898 removed outlier: 4.146A pdb=" N ALA E 897 " --> pdb=" O TYR E 893 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP E 898 " --> pdb=" O LEU E 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 893 through 898' Processing helix chain 'E' and resid 913 through 920 removed outlier: 3.797A pdb=" N GLN E 918 " --> pdb=" O LEU E 914 " (cutoff:3.500A) Processing helix chain 'E' and resid 922 through 928 Processing helix chain 'E' and resid 981 through 994 Processing helix chain 'E' and resid 996 through 1009 removed outlier: 3.543A pdb=" N GLY E1009 " --> pdb=" O LEU E1005 " (cutoff:3.500A) Processing helix chain 'E' and resid 1009 through 1044 Processing helix chain 'E' and resid 1061 through 1106 removed outlier: 3.695A pdb=" N MET E1066 " --> pdb=" O SER E1062 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL E1067 " --> pdb=" O VAL E1063 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE E1068 " --> pdb=" O TYR E1064 " (cutoff:3.500A) Processing helix chain 'E' and resid 1109 through 1116 removed outlier: 3.569A pdb=" N PHE E1113 " --> pdb=" O PRO E1109 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU E1114 " --> pdb=" O MET E1110 " (cutoff:3.500A) Processing helix chain 'E' and resid 1117 through 1135 removed outlier: 3.720A pdb=" N SER E1127 " --> pdb=" O ASN E1123 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASP E1128 " --> pdb=" O ARG E1124 " (cutoff:3.500A) Processing helix chain 'E' and resid 1135 through 1161 Processing helix chain 'E' and resid 1163 through 1210 removed outlier: 4.063A pdb=" N ALA E1167 " --> pdb=" O VAL E1163 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 3.529A pdb=" N VAL E1173 " --> pdb=" O LEU E1169 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL E1174 " --> pdb=" O PRO E1170 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA E1185 " --> pdb=" O TYR E1181 " (cutoff:3.500A) removed outlier: 4.411A 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 1218 Processing helix chain 'E' and resid 1219 through 1275 removed outlier: 3.736A pdb=" N THR E1242 " --> pdb=" O SER E1238 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR E1266 " --> pdb=" O ILE E1262 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS E1273 " --> pdb=" O SER E1269 " (cutoff:3.500A) Processing helix chain 'E' and resid 1277 through 1321 removed outlier: 3.656A pdb=" N VAL E1281 " --> pdb=" O SER E1277 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET E1290 " --> pdb=" O THR E1286 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER E1292 " --> pdb=" O ALA E1288 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ASN E1293 " --> pdb=" O LEU E1289 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E1295 " --> pdb=" O VAL E1291 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN E1296 " --> pdb=" O SER E1292 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA E1311 " --> pdb=" O ILE E1307 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG E1314 " --> pdb=" O GLY E1310 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA E1317 " --> pdb=" O LYS E1313 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR E1321 " --> pdb=" O ALA E1317 " (cutoff:3.500A) Processing helix chain 'E' and resid 1386 through 1391 removed outlier: 3.906A pdb=" N ALA E1391 " --> pdb=" O SER E1387 " (cutoff:3.500A) Processing helix chain 'E' and resid 1414 through 1421 Processing helix chain 'E' and resid 1436 through 1441 Processing helix chain 'E' and resid 1447 through 1459 removed outlier: 3.740A pdb=" N ILE E1457 " --> pdb=" O GLU E1453 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN E1459 " --> pdb=" O LEU E1455 " (cutoff:3.500A) Processing helix chain 'E' and resid 1460 through 1467 Processing helix chain 'E' and resid 1476 through 1479 removed outlier: 3.902A pdb=" N GLY E1479 " --> pdb=" O THR E1476 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1476 through 1479' Processing helix chain 'E' and resid 1483 through 1499 removed outlier: 3.750A pdb=" N GLN E1488 " --> pdb=" O GLN E1484 " (cutoff:3.500A) Processing helix chain 'E' and resid 1512 through 1531 Processing helix chain 'E' and resid 1539 through 1544 removed outlier: 3.637A pdb=" N ILE E1543 " --> pdb=" O ARG E1539 " (cutoff:3.500A) Processing helix chain 'E' and resid 1564 through 1570 removed outlier: 4.334A pdb=" N SER E1568 " --> pdb=" O GLU E1564 " (cutoff:3.500A) Processing helix chain 'E' and resid 1573 through 1578 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.542A pdb=" N GLY A 203 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.542A pdb=" N GLY A 203 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 189 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 237 removed outlier: 5.527A pdb=" N SER A 212 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL A 290 " --> pdb=" O SER A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 315 removed outlier: 3.506A pdb=" N ARG A 314 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 320 Processing sheet with id=AA6, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.157A pdb=" N VAL C 328 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AA8, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.718A pdb=" N VAL B 188 " --> pdb=" O MET B 199 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 234 through 236 removed outlier: 5.428A pdb=" N SER B 212 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL B 290 " --> pdb=" O SER B 212 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR B 302 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU B 287 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 300 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 314 through 315 Processing sheet with id=AB2, first strand: chain 'C' and resid 181 through 183 removed outlier: 3.875A pdb=" N GLY C 203 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET C 199 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL C 188 " --> pdb=" O MET C 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 181 through 183 removed outlier: 3.875A pdb=" N GLY C 203 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 210 through 211 removed outlier: 3.573A pdb=" N VAL C 290 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 231 through 238 removed outlier: 4.700A pdb=" N THR C 223 " --> pdb=" O PRO C 232 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG C 221 " --> pdb=" O HIS C 234 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 213 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 231 through 238 removed outlier: 4.700A pdb=" N THR C 223 " --> pdb=" O PRO C 232 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG C 221 " --> pdb=" O HIS C 234 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 314 through 315 removed outlier: 3.708A pdb=" N ARG C 314 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 182 through 183 removed outlier: 3.771A pdb=" N ILE D 182 " --> pdb=" O GLY D 203 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 190 through 191 Processing sheet with id=AC1, first strand: chain 'D' and resid 210 through 211 Processing sheet with id=AC2, first strand: chain 'D' and resid 229 through 238 removed outlier: 5.364A pdb=" N VAL D 230 " --> pdb=" O SER D 225 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N SER D 225 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N THR D 223 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS D 234 " --> pdb=" O ARG D 221 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG D 221 " --> pdb=" O HIS D 234 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 313 through 314 Processing sheet with id=AC4, first strand: chain 'D' and resid 319 through 321 Processing sheet with id=AC5, first strand: chain 'E' and resid 702 through 703 removed outlier: 3.811A pdb=" N GLN E 680 " --> pdb=" O PHE E 738 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 696 through 697 removed outlier: 6.874A pdb=" N PHE E 685 " --> pdb=" O VAL E 733 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 710 through 711 removed outlier: 3.797A pdb=" N VAL E 851 " --> pdb=" O THR E 883 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 1347 through 1348 removed outlier: 3.918A pdb=" N ARG E1402 " --> pdb=" O GLN E1348 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 1534 through 1536 removed outlier: 7.399A pdb=" N VAL E1549 " --> pdb=" O PHE E1560 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N PHE E1560 " --> pdb=" O VAL E1549 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL E1551 " --> pdb=" O LEU E1558 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 1434 through 1435 removed outlier: 3.839A pdb=" N GLY E1434 " --> pdb=" O ILE E1475 " (cutoff:3.500A) 1193 hydrogen bonds defined for protein. 3453 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: 3.23 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6152 1.34 - 1.46: 4492 1.46 - 1.58: 8016 1.58 - 1.70: 20 1.70 - 1.82: 99 Bond restraints: 18779 Sorted by residual: bond pdb=" C1 NAG E1602 " pdb=" O5 NAG E1602 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C5 NAG E1602 " pdb=" O5 NAG E1602 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.31e+00 bond pdb=" C3 NAG E1602 " pdb=" O3 NAG E1602 " ideal model delta sigma weight residual 1.403 1.422 -0.019 2.00e-02 2.50e+03 9.34e-01 bond pdb=" C GLY A 103 " pdb=" O GLY A 103 " ideal model delta sigma weight residual 1.243 1.235 0.008 9.30e-03 1.16e+04 7.66e-01 bond pdb=" C VAL C 231 " pdb=" O VAL C 231 " ideal model delta sigma weight residual 1.232 1.240 -0.007 8.90e-03 1.26e+04 6.97e-01 ... (remaining 18774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 25444 1.21 - 2.41: 289 2.41 - 3.62: 98 3.62 - 4.83: 25 4.83 - 6.03: 19 Bond angle restraints: 25875 Sorted by residual: angle pdb=" C VAL E 33 " pdb=" N VAL E 34 " pdb=" CA VAL E 34 " ideal model delta sigma weight residual 120.43 123.40 -2.97 9.60e-01 1.09e+00 9.55e+00 angle pdb=" C VAL E 34 " pdb=" CA VAL E 34 " pdb=" CB VAL E 34 " ideal model delta sigma weight residual 113.70 110.87 2.83 9.50e-01 1.11e+00 8.89e+00 angle pdb=" N GLY E 818 " pdb=" CA GLY E 818 " pdb=" C GLY E 818 " ideal model delta sigma weight residual 111.34 115.88 -4.54 1.82e+00 3.02e-01 6.22e+00 angle pdb=" C VAL C 231 " pdb=" CA VAL C 231 " pdb=" CB VAL C 231 " ideal model delta sigma weight residual 110.13 112.32 -2.19 9.70e-01 1.06e+00 5.12e+00 angle pdb=" C HIS E 817 " pdb=" N GLY E 818 " pdb=" CA GLY E 818 " ideal model delta sigma weight residual 120.07 123.59 -3.52 1.61e+00 3.86e-01 4.79e+00 ... (remaining 25870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 10146 17.68 - 35.35: 495 35.35 - 53.03: 93 53.03 - 70.71: 10 70.71 - 88.38: 5 Dihedral angle restraints: 10749 sinusoidal: 2803 harmonic: 7946 Sorted by residual: dihedral pdb=" N PHE B 315 " pdb=" CA PHE B 315 " pdb=" CB PHE B 315 " pdb=" CG PHE B 315 " ideal model delta sinusoidal sigma weight residual -60.00 -118.98 58.98 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA GLN A 57 " pdb=" CB GLN A 57 " pdb=" CG GLN A 57 " pdb=" CD GLN A 57 " ideal model delta sinusoidal sigma weight residual -60.00 -118.87 58.87 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LEU A 349 " pdb=" CA LEU A 349 " pdb=" CB LEU A 349 " pdb=" CG LEU A 349 " ideal model delta sinusoidal sigma weight residual -60.00 -117.45 57.45 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 10746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1943 0.029 - 0.057: 747 0.057 - 0.086: 252 0.086 - 0.114: 194 0.114 - 0.143: 24 Chirality restraints: 3160 Sorted by residual: chirality pdb=" CB THR C 214 " pdb=" CA THR C 214 " pdb=" OG1 THR C 214 " pdb=" CG2 THR C 214 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA ILE A 189 " pdb=" N ILE A 189 " pdb=" C ILE A 189 " pdb=" CB ILE A 189 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA ILE B 283 " pdb=" N ILE B 283 " pdb=" C ILE B 283 " pdb=" CB ILE B 283 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 3157 not shown) Planarity restraints: 3340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 101 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO A 102 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 339 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO A 340 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 340 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 340 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E1198 " -0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO E1199 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO E1199 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO E1199 " -0.016 5.00e-02 4.00e+02 ... (remaining 3337 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3561 2.77 - 3.30: 18673 3.30 - 3.84: 29978 3.84 - 4.37: 30364 4.37 - 4.90: 53445 Nonbonded interactions: 136021 Sorted by model distance: nonbonded pdb=" O SER B 116 " pdb=" OG SER B 119 " model vdw 2.240 3.040 nonbonded pdb=" OG1 THR A 139 " pdb=" OE1 GLU A 140 " model vdw 2.242 3.040 nonbonded pdb=" O GLY B 156 " pdb=" ND2 ASN B 160 " model vdw 2.253 3.120 nonbonded pdb=" O GLY D 156 " pdb=" ND2 ASN D 160 " model vdw 2.299 3.120 nonbonded pdb=" O ASN D 48 " pdb=" N6 ATP D 401 " model vdw 2.307 3.120 ... (remaining 136016 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 33 through 35 or (resid 36 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 or (resid 41 and (name N or nam \ e CA or name C or name O or name CB )) or resid 42 or (resid 43 through 45 and ( \ name N or name CA or name C or name O or name CB )) or resid 46 through 48 or (r \ esid 49 and (name N or name CA or name C or name O or name CB )) or resid 50 thr \ ough 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 through 59 and (name N or name CA or name C or name O or \ name CB )) or resid 60 through 61 or (resid 62 through 63 and (name N or name CA \ or name C or name O or name CB )) or resid 64 through 70 or (resid 71 and (name \ N or name CA or name C or name O or name CB )) or resid 72 through 73 or (resid \ 74 and (name N or name CA or name C or name O or name CB )) or resid 75 through \ 76 or (resid 77 and (name N or name CA or name C or name O or name CB )) or res \ id 78 through 80 or (resid 81 through 82 and (name N or name CA or name C or nam \ e O or name CB )) or resid 83 through 87 or (resid 88 and (name N or name CA or \ name C or name O or name CB )) or resid 89 through 91 or (resid 92 and (name N o \ r name CA or name C or name O or name CB )) or resid 93 through 107 or (resid 10 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 109 through \ 121 or (resid 122 and (name N or name CA or name C or name O or name CB )) or re \ sid 123 through 124 or (resid 125 through 127 and (name N or name CA or name C o \ r name O or name CB )) or resid 128 through 138 or (resid 139 through 141 and (n \ ame N or name CA or name C or name O or name CB )) or resid 142 through 147 or ( \ resid 148 and (name N or name CA or name C or name O or name CB )) or resid 149 \ through 150 or (resid 151 through 154 and (name N or name CA or name C or name O \ or name CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 through 161 or (resid 162 through 16 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 165 or (resi \ d 166 and (name N or name CA or name C or name O or name CB )) or resid 167 thro \ ugh 168 or (resid 169 through 182 and (name N or name CA or name C or name O or \ name CB )) or resid 183 or (resid 184 and (name N or name CA or name C or name O \ or name CB )) or resid 185 through 187 or (resid 188 and (name N or name CA or \ name C or name O or name CB )) or resid 189 through 192 or (resid 193 and (name \ N or name CA or name C or name O or name CB )) or resid 194 through 195 or (resi \ d 196 and (name N or name CA or name C or name O or name CB )) or resid 197 thro \ ugh 201 or (resid 202 and (name N or name CA or name C or name O or name CB )) o \ r resid 203 through 209 or (resid 210 through 211 and (name N or name CA or name \ C or name O or name CB )) or resid 212 through 217 or (resid 218 and (name N or \ name CA or name C or name O or name CB )) or resid 219 through 237 or (resid 23 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 239 through \ 241 or (resid 242 and (name N or name CA or name C or name O or name CB )) or re \ sid 243 through 274 or (resid 275 through 277 and (name N or name CA or name C o \ r name O or name CB )) or resid 278 or (resid 279 through 282 and (name N or nam \ e CA or name C or name O or name CB )) or resid 283 through 291 or (resid 292 an \ d (name N or name CA or name C or name O or name CB )) or resid 293 through 302 \ or (resid 303 through 310 and (name N or name CA or name C or name O or name CB \ )) or resid 311 through 317 or (resid 318 through 323 and (name N or name CA or \ name C or name O or name CB )) or resid 324 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 throug \ h 333 and (name N or name CA or name C or name O or name CB )) or resid 334 thro \ ugh 358)) selection = (chain 'B' and (resid 33 through 35 or (resid 36 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 through 54 or (resid 55 through \ 59 and (name N or name CA or name C or name O or name CB )) or resid 60 through \ 61 or (resid 62 through 63 and (name N or name CA or name C or name O or name C \ B )) or resid 64 through 70 or (resid 71 and (name N or name CA or name C or nam \ e O or name CB )) or resid 72 through 76 or (resid 77 and (name N or name CA or \ name C or name O or name CB )) or resid 78 through 80 or (resid 81 through 82 an \ d (name N or name CA or name C or name O or name CB )) or resid 83 through 87 or \ (resid 88 and (name N or name CA or name C or name O or name CB )) or resid 89 \ through 121 or (resid 122 and (name N or name CA or name C or name O or name CB \ )) or resid 123 through 124 or (resid 125 through 127 and (name N or name CA or \ name C or name O or name CB )) or resid 128 through 130 or (resid 131 and (name \ N or name CA or name C or name O or name CB )) or resid 132 through 136 or (resi \ d 137 and (name N or name CA or name C or name O or name CB )) or resid 138 thro \ ugh 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 147 or (resid 148 and (name N or name CA or name \ C or name O or name CB )) or resid 149 through 150 or (resid 151 through 154 an \ d (name N or name CA or name C or name O or name CB )) or resid 155 through 157 \ or (resid 158 and (name N or name CA or name C or name O or name CB )) or resid \ 159 through 161 or (resid 162 through 164 and (name N or name CA or name C or na \ me O or name CB )) or resid 165 or (resid 166 and (name N or name CA or name C o \ r name O or name CB )) or resid 167 through 169 or (resid 170 through 182 and (n \ ame N or name CA or name C or name O or name CB )) or resid 183 or (resid 184 an \ d (name N or name CA or name C or name O or name CB )) or resid 185 through 187 \ or (resid 188 and (name N or name CA or name C or name O or name CB )) or resid \ 189 through 191 or (resid 192 through 193 and (name N or name CA or name C or na \ me O or name CB )) or resid 194 through 195 or (resid 196 and (name N or name CA \ or name C or name O or name CB )) or resid 197 through 200 or (resid 201 throug \ h 202 and (name N or name CA or name C or name O or name CB )) or resid 203 thro \ ugh 206 or (resid 207 and (name N or name CA or name C or name O or name CB )) o \ r resid 208 or (resid 209 through 211 and (name N or name CA or name C or name O \ or name CB )) or resid 212 through 214 or (resid 215 and (name N or name CA or \ name C or name O or name CB )) or resid 216 through 217 or (resid 218 and (name \ N or name CA or name C or name O or name CB )) or resid 219 through 230 or (resi \ d 231 and (name N or name CA or name C or name O or name CB )) or resid 232 or ( \ resid 233 and (name N or name CA or name C or name O or name CB )) or resid 234 \ through 237 or (resid 238 and (name N or name CA or name C or name O or name CB \ )) or resid 239 through 241 or (resid 242 and (name N or name CA or name C or na \ me O or name CB )) or resid 243 through 248 or (resid 249 and (name N or name CA \ or name C or name O or name CB )) or resid 250 or (resid 251 through 253 and (n \ ame N or name CA or name C or name O or name CB )) or resid 254 through 255 or ( \ resid 256 through 257 and (name N or name CA or name C or name O or name CB )) o \ r resid 258 or (resid 259 through 265 and (name N or name CA or name C or name O \ or name CB )) or resid 266 or (resid 267 and (name N or name CA or name C or na \ me O or name CB )) or resid 268 through 269 or (resid 270 through 271 and (name \ N or name CA or name C or name O or name CB )) or resid 272 or (resid 273 throug \ h 277 and (name N or name CA or name C or name O or name CB )) or resid 278 thro \ ugh 280 or (resid 281 through 282 and (name N or name CA or name C or name O or \ name CB )) or resid 283 through 284 or (resid 285 through 288 and (name N or nam \ e CA or name C or name O or name CB )) or resid 289 through 298 or (resid 299 th \ rough 301 and (name N or name CA or name C or name O or name CB )) or resid 302 \ through 303 or (resid 304 through 310 and (name N or name CA or name C or name O \ or name CB )) or resid 311 through 318 or (resid 319 through 323 and (name N or \ name CA or name C or name O or name CB )) or resid 324 through 328 or (resid 32 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 330 or (resi \ d 331 through 333 and (name N or name CA or name C or name O or name CB )) or re \ sid 334 through 337 or (resid 338 and (name N or name CA or name C or name O or \ name CB )) or resid 339 through 342 or (resid 343 through 344 and (name N or nam \ e CA or name C or name O or name CB )) or resid 345 through 358)) selection = (chain 'C' and (resid 33 through 34 or (resid 35 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 or (resid 41 and (name N or nam \ e CA or name C or name O or name CB )) or resid 42 or (resid 43 through 45 and ( \ name N or name CA or name C or name O or name CB )) or resid 46 through 48 or (r \ esid 49 and (name N or name CA or name C or name O or name CB )) or resid 50 thr \ ough 58 or (resid 59 and (name N or name CA or name C or name O or name CB )) or \ resid 60 through 62 or (resid 63 and (name N or name CA or name C or name O or \ name CB )) or resid 64 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 70 or (resid 71 and (name N or name \ CA or name C or name O or name CB )) or resid 72 through 73 or (resid 74 and (na \ me N or name CA or name C or name O or name CB )) or resid 75 through 81 or (res \ id 82 and (name N or name CA or name C or name O or name CB )) or resid 83 throu \ gh 107 or (resid 108 and (name N or name CA or name C or name O or name CB )) or \ resid 109 through 130 or (resid 131 and (name N or name CA or name C or name O \ or name CB )) or resid 132 through 136 or (resid 137 and (name N or name CA or n \ ame C or name O or name CB )) or resid 138 or (resid 139 through 141 and (name N \ or name CA or name C or name O or name CB )) or resid 142 through 150 or (resid \ 151 through 154 and (name N or name CA or name C or name O or name CB )) or res \ id 155 through 161 or (resid 162 through 164 and (name N or name CA or name C or \ name O or name CB )) or resid 165 through 169 or (resid 170 through 182 and (na \ me N or name CA or name C or name O or name CB )) or resid 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 191 o \ r (resid 192 through 193 and (name N or name CA or name C or name O or name CB ) \ ) or resid 194 through 200 or (resid 201 through 202 and (name N or name CA or n \ ame C or name O or name CB )) or resid 203 through 206 or (resid 207 and (name N \ or name CA or name C or name O or name CB )) or resid 208 or (resid 209 through \ 211 and (name N or name CA or name C or name O or name CB )) or resid 212 throu \ gh 214 or (resid 215 and (name N or name CA or name C or name O or name CB )) or \ resid 216 through 217 or (resid 218 and (name N or name CA or name C or name O \ or name CB )) or resid 219 through 220 or (resid 221 through 222 and (name N or \ name CA or name C or name O or name CB )) or resid 223 through 230 or (resid 231 \ and (name N or name CA or name C or name O or name CB )) or resid 232 or (resid \ 233 and (name N or name CA or name C or name O or name CB )) or resid 234 throu \ gh 248 or (resid 249 and (name N or name CA or name C or name O or name CB )) or \ resid 250 or (resid 251 through 253 and (name N or name CA or name C or name O \ or name CB )) or resid 254 or (resid 255 through 257 and (name N or name CA or n \ ame C or name O or name CB )) or resid 258 or (resid 259 through 265 and (name N \ or name CA or name C or name O or name CB )) or resid 266 through 272 or (resid \ 273 through 277 and (name N or name CA or name C or name O or name CB )) or res \ id 278 or (resid 279 through 282 and (name N or name CA or name C or name O or n \ ame CB )) or resid 283 through 284 or (resid 285 through 288 and (name N or name \ CA or name C or name O or name CB )) or resid 289 through 291 or (resid 292 and \ (name N or name CA or name C or name O or name CB )) or resid 293 through 298 o \ r (resid 299 through 301 and (name N or name CA or name C or name O or name CB ) \ ) or resid 302 through 303 or (resid 304 through 310 and (name N or name CA or n \ ame C or name O or name CB )) or resid 311 through 317 or (resid 318 through 323 \ and (name N or name CA or name C or name O or name CB )) or resid 324 through 3 \ 27 or (resid 328 through 329 and (name N or name CA or name C or name O or name \ CB )) or resid 330 through 331 or (resid 332 through 333 and (name N or name CA \ or name C or name O or name CB )) or resid 334 through 337 or (resid 338 and (na \ me N or name CA or name C or name O or name CB )) or resid 339 through 342 or (r \ esid 343 through 344 and (name N or name CA or name C or name O or name CB )) or \ resid 345 through 358)) selection = (chain 'D' and (resid 33 through 34 or (resid 35 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 through 42 or (resid 43 through \ 45 and (name N or name CA or name C or name O or name CB )) or resid 46 through \ 48 or (resid 49 and (name N or name CA or name C or name O or name CB )) or res \ id 50 through 54 or (resid 55 through 59 and (name N or name CA or name C or nam \ e O or name CB )) or resid 60 through 61 or (resid 62 through 63 and (name N or \ name CA or name C or name O or name CB )) or resid 64 through 76 or (resid 77 an \ d (name N or name CA or name C or name O or name CB )) or resid 78 through 81 or \ (resid 82 and (name N or name CA or name C or name O or name CB )) or resid 83 \ through 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) \ or resid 89 through 91 or (resid 92 and (name N or name CA or name C or name O \ or name CB )) or resid 93 through 107 or (resid 108 and (name N or name CA or na \ me C or name O or name CB )) or resid 109 through 121 or (resid 122 and (name N \ or name CA or name C or name O or name CB )) or resid 123 through 126 or (resid \ 127 and (name N or name CA or name C or name O or name CB )) or resid 128 throug \ h 136 or (resid 137 and (name N or name CA or name C or name O or name CB )) or \ resid 138 or (resid 139 through 141 and (name N or name CA or name C or name O o \ r name CB )) or resid 142 through 147 or (resid 148 and (name N or name CA or na \ me C or name O or name CB )) or resid 149 through 151 or (resid 152 through 154 \ and (name N or name CA or name C or name O or name CB )) or resid 155 through 15 \ 7 or (resid 158 and (name N or name CA or name C or name O or name CB )) or resi \ d 159 through 163 or (resid 164 and (name N or name CA or name C or name O or na \ me CB )) or resid 165 through 179 or (resid 180 through 182 and (name N or name \ CA or name C or name O or name CB )) or resid 183 through 192 or (resid 193 and \ (name N or name CA or name C or name O or name CB )) or resid 194 through 195 or \ (resid 196 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 7 through 198 or (resid 199 through 202 and (name N or name CA or name C or name \ O or name CB )) or resid 203 or (resid 204 and (name N or name CA or name C or \ name O or name CB )) or resid 205 through 208 or (resid 209 through 211 and (nam \ e N or name CA or name C or name O or name CB )) or resid 212 through 214 or (re \ sid 215 and (name N or name CA or name C or name O or name CB )) or resid 216 th \ rough 221 or (resid 222 and (name N or name CA or name C or name O or name CB )) \ or resid 223 through 224 or (resid 225 and (name N or name CA or name C or name \ O or name CB )) or resid 226 through 228 or (resid 229 and (name N or name CA o \ r name C or name O or name CB )) or resid 230 or (resid 231 and (name N or name \ CA or name C or name O or name CB )) or resid 232 or (resid 233 and (name N or n \ ame CA or name C or name O or name CB )) or resid 234 through 237 or (resid 238 \ and (name N or name CA or name C or name O or name CB )) or resid 239 through 24 \ 1 or (resid 242 and (name N or name CA or name C or name O or name CB )) or resi \ d 243 through 248 or (resid 249 and (name N or name CA or name C or name O or na \ me CB )) or resid 250 or (resid 251 through 253 and (name N or name CA or name C \ or name O or name CB )) or resid 254 or (resid 255 through 257 and (name N or n \ ame CA or name C or name O or name CB )) or resid 258 or (resid 259 through 265 \ and (name N or name CA or name C or name O or name CB )) or resid 266 or (resid \ 267 and (name N or name CA or name C or name O or name CB )) or resid 268 throug \ h 269 or (resid 270 through 271 and (name N or name CA or name C or name O or na \ me CB )) or resid 272 or (resid 273 through 277 and (name N or name CA or name C \ or name O or name CB )) or resid 278 or (resid 279 through 282 and (name N or n \ ame CA or name C or name O or name CB )) or resid 283 through 286 or (resid 287 \ through 288 and (name N or name CA or name C or name O or name CB )) or resid 28 \ 9 through 291 or (resid 292 and (name N or name CA or name C or name O or name C \ B )) or resid 293 through 298 or (resid 299 through 301 and (name N or name CA o \ r name C or name O or name CB )) or resid 302 through 306 or (resid 307 through \ 310 and (name N or name CA or name C or name O or name CB )) or resid 311 throug \ h 320 or (resid 321 through 323 and (name N or name CA or name C or name O or na \ me CB )) or resid 324 through 325 or (resid 326 through 329 and (name N or name \ CA or name C or name O or name CB )) or resid 330 or (resid 331 through 333 and \ (name N or name CA or name C or name O or name CB )) or resid 334 through 337 or \ (resid 338 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 9 through 342 or (resid 343 through 344 and (name N or name CA or name C or name \ O or name CB )) or resid 345 through 358)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.020 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: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.800 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 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 : 0.001 0.038 18785 Z= 0.075 Angle : 0.424 6.033 25888 Z= 0.215 Chirality : 0.041 0.143 3160 Planarity : 0.003 0.038 3339 Dihedral : 11.182 88.382 5568 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.68 % Allowed : 7.15 % Favored : 90.16 % 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: -1.42 (0.15), residues: 2721 helix: 0.47 (0.14), residues: 1354 sheet: -2.05 (0.29), residues: 268 loop : -2.48 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 50 TYR 0.006 0.001 TYR D 268 PHE 0.011 0.001 PHE E 221 TRP 0.009 0.001 TRP A 90 HIS 0.006 0.000 HIS C 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00150 / 0.08 (18779) covalent geometry : angle 0.42333 / 0.22 (25875) SS BOND : bond 0.00140 / 0.07 ( 5) SS BOND : angle 0.57365 / 0.29 ( 10) hydrogen bonds : bond 0.21084 / 14.46 ( 1185) hydrogen bonds : angle 6.07857 / 4.46 ( 3453) link_NAG-ASN : bond 0.00343 / 0.18 ( 1) link_NAG-ASN : angle 1.15528 / 0.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 758 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.6083 (m-10) cc_final: 0.5453 (m-10) REVERT: A 234 HIS cc_start: 0.7073 (t-170) cc_final: 0.6794 (t-170) REVERT: A 329 ASP cc_start: 0.7386 (t0) cc_final: 0.6878 (t0) REVERT: A 350 ASP cc_start: 0.8979 (t0) cc_final: 0.8776 (t0) REVERT: B 75 PHE cc_start: 0.8200 (m-10) cc_final: 0.7667 (m-80) REVERT: B 137 MET cc_start: 0.3390 (OUTLIER) cc_final: 0.2896 (tmm) REVERT: B 168 PHE cc_start: 0.7925 (m-80) cc_final: 0.7558 (m-80) REVERT: B 282 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7478 (tm-30) REVERT: B 315 PHE cc_start: 0.6938 (OUTLIER) cc_final: 0.6250 (t80) REVERT: B 330 TYR cc_start: 0.7042 (m-80) cc_final: 0.6705 (m-80) REVERT: B 335 ASN cc_start: 0.9007 (t0) cc_final: 0.8736 (t0) REVERT: C 91 TRP cc_start: 0.6581 (t60) cc_final: 0.6143 (t60) REVERT: C 114 ILE cc_start: 0.8410 (mm) cc_final: 0.7378 (tp) REVERT: C 276 HIS cc_start: 0.8718 (p-80) cc_final: 0.8517 (p-80) REVERT: C 352 ASP cc_start: 0.7021 (t70) cc_final: 0.6506 (t70) REVERT: D 44 VAL cc_start: 0.8485 (m) cc_final: 0.7340 (p) REVERT: D 76 THR cc_start: 0.9066 (m) cc_final: 0.8843 (m) REVERT: D 112 THR cc_start: 0.8658 (m) cc_final: 0.8441 (m) REVERT: D 123 PHE cc_start: 0.9052 (t80) cc_final: 0.8785 (t80) REVERT: D 136 ARG cc_start: 0.8799 (mpp80) cc_final: 0.7876 (mpp80) REVERT: D 158 MET cc_start: 0.8301 (mmp) cc_final: 0.7950 (mmp) REVERT: D 160 ASN cc_start: 0.8801 (m-40) cc_final: 0.8531 (m-40) REVERT: D 215 ILE cc_start: 0.8470 (mt) cc_final: 0.8212 (mt) REVERT: D 255 LEU cc_start: 0.8672 (mt) cc_final: 0.8216 (mt) REVERT: D 287 LEU cc_start: 0.8546 (tp) cc_final: 0.8098 (tp) REVERT: D 301 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7404 (pmt-80) REVERT: D 313 GLN cc_start: 0.5941 (pp30) cc_final: 0.5576 (pp30) REVERT: D 325 ARG cc_start: 0.6265 (pmm-80) cc_final: 0.6038 (pmm-80) REVERT: D 348 GLN cc_start: 0.7313 (mt0) cc_final: 0.6558 (mt0) REVERT: D 351 GLU cc_start: 0.8012 (pp20) cc_final: 0.7716 (pp20) REVERT: D 352 ASP cc_start: 0.7793 (p0) cc_final: 0.7397 (p0) REVERT: E 35 PRO cc_start: 0.9102 (Cg_exo) cc_final: 0.8528 (Cg_endo) REVERT: E 112 MET cc_start: 0.8149 (mmp) cc_final: 0.7686 (mmp) REVERT: E 135 LEU cc_start: 0.9316 (mm) cc_final: 0.8938 (mm) REVERT: E 179 TYR cc_start: 0.8905 (m-80) cc_final: 0.8618 (m-80) REVERT: E 181 MET cc_start: 0.8656 (mmp) cc_final: 0.8237 (mmm) REVERT: E 218 LEU cc_start: 0.7702 (pt) cc_final: 0.7498 (pt) REVERT: E 219 GLN cc_start: 0.7300 (tm-30) cc_final: 0.6667 (tm-30) REVERT: E 265 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8513 (tpp-160) REVERT: E 306 ARG cc_start: 0.8400 (tpt-90) cc_final: 0.7304 (tpt-90) REVERT: E 358 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8322 (tt) REVERT: E 374 GLN cc_start: 0.8568 (mm110) cc_final: 0.8055 (mm110) REVERT: E 377 TYR cc_start: 0.7946 (m-10) cc_final: 0.7543 (m-10) REVERT: E 437 ASN cc_start: 0.9213 (t0) cc_final: 0.8238 (m-40) REVERT: E 609 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8408 (pttm) REVERT: E 817 HIS cc_start: 0.8110 (t-90) cc_final: 0.7212 (t-90) REVERT: E 995 LYS cc_start: 0.6940 (pttm) cc_final: 0.5814 (pttm) REVERT: E 1202 SER cc_start: 0.8253 (m) cc_final: 0.7681 (p) REVERT: E 1231 THR cc_start: 0.8805 (p) cc_final: 0.8351 (t) REVERT: E 1235 ASN cc_start: 0.9496 (m-40) cc_final: 0.8433 (m110) REVERT: E 1292 SER cc_start: 0.8966 (p) cc_final: 0.8600 (p) REVERT: E 1296 ASN cc_start: 0.8687 (m-40) cc_final: 0.8449 (m-40) REVERT: E 1306 GLU cc_start: 0.7981 (tp30) cc_final: 0.7130 (tp30) REVERT: E 1314 ARG cc_start: 0.8689 (ptp-170) cc_final: 0.8324 (ptp-170) outliers start: 36 outliers final: 9 residues processed: 771 average time/residue: 0.1081 time to fit residues: 130.5508 Evaluate side-chains 656 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 641 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 50.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 30.0000 chunk 111 optimal weight: 20.0000 overall best weight: 12.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 HIS ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN C 193 HIS ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN C 299 GLN C 348 GLN D 216 HIS ** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS E 437 ASN E 775 GLN ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.150686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.125937 restraints weight = 41981.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.128808 restraints weight = 25774.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.131642 restraints weight = 16152.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131745 restraints weight = 10959.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.131922 restraints weight = 10986.618| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 18785 Z= 0.348 Angle : 0.789 10.234 25888 Z= 0.431 Chirality : 0.050 0.215 3160 Planarity : 0.006 0.070 3339 Dihedral : 5.312 67.550 2865 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.67 % Allowed : 6.41 % Favored : 92.92 % 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: -0.90 (0.16), residues: 2721 helix: 0.84 (0.14), residues: 1370 sheet: -1.70 (0.30), residues: 277 loop : -2.22 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 325 TYR 0.028 0.003 TYR E 475 PHE 0.036 0.003 PHE B 95 TRP 0.048 0.003 TRP C 83 HIS 0.016 0.003 HIS E1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00719 / 0.35 (18779) covalent geometry : angle 0.78651 / 0.43 (25875) SS BOND : bond 0.00534 / 0.30 ( 5) SS BOND : angle 3.34759 / 1.97 ( 10) hydrogen bonds : bond 0.05370 / 3.66 ( 1185) hydrogen bonds : angle 5.13738 / 3.74 ( 3453) link_NAG-ASN : bond 0.00070 / 0.04 ( 1) link_NAG-ASN : angle 1.24564 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 687 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.6533 (m-10) cc_final: 0.6284 (m-10) REVERT: A 75 PHE cc_start: 0.8364 (m-80) cc_final: 0.8121 (m-80) REVERT: A 117 PHE cc_start: 0.9020 (t80) cc_final: 0.8805 (t80) REVERT: A 122 LEU cc_start: 0.9195 (mt) cc_final: 0.8984 (mt) REVERT: A 160 ASN cc_start: 0.8175 (t0) cc_final: 0.7929 (t0) REVERT: A 162 ILE cc_start: 0.9539 (mm) cc_final: 0.9192 (mm) REVERT: A 168 PHE cc_start: 0.8241 (t80) cc_final: 0.8005 (t80) REVERT: A 218 GLN cc_start: 0.7456 (mt0) cc_final: 0.6953 (mm-40) REVERT: A 258 TYR cc_start: 0.8373 (p90) cc_final: 0.7696 (p90) REVERT: A 329 ASP cc_start: 0.7584 (t0) cc_final: 0.7239 (t0) REVERT: A 348 GLN cc_start: 0.8963 (mt0) cc_final: 0.8686 (mt0) REVERT: B 88 MET cc_start: 0.8528 (tpp) cc_final: 0.7778 (tpp) REVERT: B 164 LEU cc_start: 0.9040 (tt) cc_final: 0.8800 (tt) REVERT: B 168 PHE cc_start: 0.7851 (m-80) cc_final: 0.7344 (m-80) REVERT: B 205 LEU cc_start: 0.8419 (mt) cc_final: 0.8147 (mt) REVERT: B 258 TYR cc_start: 0.8655 (p90) cc_final: 0.8162 (p90) REVERT: B 330 TYR cc_start: 0.7355 (m-80) cc_final: 0.6014 (m-80) REVERT: B 351 GLU cc_start: 0.7264 (mp0) cc_final: 0.6982 (mp0) REVERT: C 78 SER cc_start: 0.8099 (p) cc_final: 0.7696 (p) REVERT: C 325 ARG cc_start: 0.8022 (tpp80) cc_final: 0.7571 (tpp80) REVERT: C 335 ASN cc_start: 0.7854 (p0) cc_final: 0.7640 (p0) REVERT: C 352 ASP cc_start: 0.7036 (t70) cc_final: 0.6501 (t70) REVERT: D 43 ASN cc_start: 0.6053 (m-40) cc_final: 0.5730 (m-40) REVERT: D 91 TRP cc_start: 0.8565 (t60) cc_final: 0.8224 (t60) REVERT: D 95 PHE cc_start: 0.7434 (t80) cc_final: 0.7228 (t80) REVERT: D 147 LEU cc_start: 0.9548 (tp) cc_final: 0.9333 (tp) REVERT: D 149 LEU cc_start: 0.9589 (tt) cc_final: 0.9127 (tt) REVERT: D 153 ASN cc_start: 0.9483 (m-40) cc_final: 0.8726 (m110) REVERT: D 255 LEU cc_start: 0.8697 (mt) cc_final: 0.8308 (mt) REVERT: D 287 LEU cc_start: 0.8945 (tp) cc_final: 0.8712 (tp) REVERT: D 292 GLU cc_start: 0.9516 (pm20) cc_final: 0.9229 (pm20) REVERT: D 350 ASP cc_start: 0.7932 (m-30) cc_final: 0.7732 (m-30) REVERT: D 351 GLU cc_start: 0.8153 (pp20) cc_final: 0.7681 (pp20) REVERT: D 352 ASP cc_start: 0.8318 (p0) cc_final: 0.7672 (p0) REVERT: E 51 TRP cc_start: 0.5187 (t60) cc_final: 0.4698 (t60) REVERT: E 81 LEU cc_start: 0.9200 (tp) cc_final: 0.8993 (tt) REVERT: E 112 MET cc_start: 0.8284 (mmp) cc_final: 0.8039 (mmp) REVERT: E 142 TYR cc_start: 0.9063 (t80) cc_final: 0.8247 (t80) REVERT: E 181 MET cc_start: 0.8639 (mmp) cc_final: 0.8418 (mmm) REVERT: E 183 LEU cc_start: 0.9038 (mm) cc_final: 0.8820 (mm) REVERT: E 186 GLU cc_start: 0.7883 (tp30) cc_final: 0.7635 (tp30) REVERT: E 266 LEU cc_start: 0.9362 (tp) cc_final: 0.8810 (tp) REVERT: E 270 PHE cc_start: 0.8836 (m-80) cc_final: 0.7916 (m-80) REVERT: E 373 LEU cc_start: 0.9627 (tt) cc_final: 0.9395 (tt) REVERT: E 374 GLN cc_start: 0.8959 (mm110) cc_final: 0.8327 (mm-40) REVERT: E 377 TYR cc_start: 0.8401 (m-10) cc_final: 0.8054 (m-10) REVERT: E 432 PHE cc_start: 0.8612 (t80) cc_final: 0.7620 (t80) REVERT: E 451 LEU cc_start: 0.9149 (tt) cc_final: 0.8911 (tt) REVERT: E 609 LYS cc_start: 0.9137 (ptmt) cc_final: 0.8495 (pttm) REVERT: E 817 HIS cc_start: 0.7903 (t-90) cc_final: 0.7360 (t-90) REVERT: E 995 LYS cc_start: 0.7103 (pttm) cc_final: 0.6485 (pttm) REVERT: E 1024 HIS cc_start: 0.7719 (m90) cc_final: 0.6166 (m90) REVERT: E 1033 TRP cc_start: 0.8743 (t-100) cc_final: 0.8542 (t-100) REVERT: E 1126 SER cc_start: 0.8946 (t) cc_final: 0.8717 (p) REVERT: E 1145 ARG cc_start: 0.8690 (tpp-160) cc_final: 0.8466 (tpp-160) REVERT: E 1150 CYS cc_start: 0.8625 (t) cc_final: 0.8311 (t) REVERT: E 1164 PHE cc_start: 0.9289 (t80) cc_final: 0.9068 (t80) REVERT: E 1189 LEU cc_start: 0.9152 (mt) cc_final: 0.8865 (mt) REVERT: E 1224 GLN cc_start: 0.8768 (mm110) cc_final: 0.8499 (mm110) REVERT: E 1231 THR cc_start: 0.9212 (p) cc_final: 0.8828 (t) REVERT: E 1235 ASN cc_start: 0.9486 (m-40) cc_final: 0.8446 (m-40) REVERT: E 1296 ASN cc_start: 0.9100 (m-40) cc_final: 0.8829 (m-40) REVERT: E 1314 ARG cc_start: 0.9026 (ptp-170) cc_final: 0.8593 (ptp-170) outliers start: 9 outliers final: 3 residues processed: 690 average time/residue: 0.1046 time to fit residues: 114.4037 Evaluate side-chains 604 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 601 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 49 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 208 optimal weight: 40.0000 chunk 109 optimal weight: 20.0000 chunk 97 optimal weight: 40.0000 chunk 236 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 117 optimal weight: 30.0000 chunk 92 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 195 optimal weight: 50.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 HIS A 218 GLN ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 259 HIS C 335 ASN C 348 GLN D 277 HIS ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1308 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.153157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.128277 restraints weight = 41235.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.131291 restraints weight = 25345.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133389 restraints weight = 17386.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.134834 restraints weight = 13014.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.135805 restraints weight = 10441.577| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18785 Z= 0.186 Angle : 0.593 8.213 25888 Z= 0.318 Chirality : 0.045 0.178 3160 Planarity : 0.004 0.047 3339 Dihedral : 4.911 64.031 2865 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.22 % Allowed : 5.37 % Favored : 94.41 % 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: -0.33 (0.16), residues: 2721 helix: 1.33 (0.14), residues: 1372 sheet: -1.58 (0.31), residues: 291 loop : -1.94 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E1187 TYR 0.027 0.002 TYR E 539 PHE 0.039 0.002 PHE E 433 TRP 0.051 0.002 TRP C 83 HIS 0.011 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 (18779) covalent geometry : angle 0.59177 / 0.32 (25875) SS BOND : bond 0.00446 / 0.24 ( 5) SS BOND : angle 2.19880 / 1.36 ( 10) hydrogen bonds : bond 0.04426 / 3.02 ( 1185) hydrogen bonds : angle 4.55212 / 3.31 ( 3453) link_NAG-ASN : bond 0.00088 / 0.05 ( 1) link_NAG-ASN : angle 0.79756 / 0.51 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 686 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 PHE cc_start: 0.9038 (t80) cc_final: 0.8520 (t80) REVERT: A 122 LEU cc_start: 0.9257 (mt) cc_final: 0.9032 (mt) REVERT: A 160 ASN cc_start: 0.8099 (t0) cc_final: 0.7820 (t0) REVERT: A 168 PHE cc_start: 0.8054 (t80) cc_final: 0.7512 (t80) REVERT: A 191 LEU cc_start: 0.8058 (tp) cc_final: 0.7741 (tp) REVERT: A 218 GLN cc_start: 0.7553 (mt0) cc_final: 0.7198 (tp40) REVERT: A 258 TYR cc_start: 0.8386 (p90) cc_final: 0.7753 (p90) REVERT: A 269 ASP cc_start: 0.6443 (m-30) cc_final: 0.6196 (m-30) REVERT: A 329 ASP cc_start: 0.7349 (t0) cc_final: 0.7011 (t0) REVERT: A 347 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7022 (ttm110) REVERT: A 348 GLN cc_start: 0.8980 (mt0) cc_final: 0.8417 (mt0) REVERT: A 351 GLU cc_start: 0.8831 (mp0) cc_final: 0.8302 (mp0) REVERT: B 75 PHE cc_start: 0.8265 (m-10) cc_final: 0.8057 (m-80) REVERT: B 88 MET cc_start: 0.8581 (tpp) cc_final: 0.7822 (tpp) REVERT: B 158 MET cc_start: 0.8047 (mmp) cc_final: 0.7843 (mmp) REVERT: B 168 PHE cc_start: 0.8013 (m-80) cc_final: 0.7623 (m-80) REVERT: B 192 ARG cc_start: 0.9238 (tpp-160) cc_final: 0.8567 (mmm160) REVERT: B 205 LEU cc_start: 0.8449 (mt) cc_final: 0.8184 (mt) REVERT: B 215 ILE cc_start: 0.9053 (mm) cc_final: 0.8659 (pt) REVERT: B 330 TYR cc_start: 0.7222 (m-80) cc_final: 0.6236 (m-80) REVERT: B 351 GLU cc_start: 0.7167 (mp0) cc_final: 0.6738 (mp0) REVERT: C 192 ARG cc_start: 0.9171 (tpt-90) cc_final: 0.8581 (mmm-85) REVERT: C 201 ARG cc_start: 0.5968 (mmt180) cc_final: 0.5220 (mmt180) REVERT: C 235 GLN cc_start: 0.8591 (mt0) cc_final: 0.8391 (mt0) REVERT: C 315 PHE cc_start: 0.8692 (m-80) cc_final: 0.8446 (m-80) REVERT: C 333 PHE cc_start: 0.8364 (t80) cc_final: 0.7997 (t80) REVERT: C 335 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7936 (p0) REVERT: C 352 ASP cc_start: 0.6949 (t70) cc_final: 0.6420 (t70) REVERT: D 43 ASN cc_start: 0.5987 (m-40) cc_final: 0.5774 (m-40) REVERT: D 95 PHE cc_start: 0.7387 (t80) cc_final: 0.7136 (t80) REVERT: D 136 ARG cc_start: 0.9018 (mpp80) cc_final: 0.8566 (mpp80) REVERT: D 147 LEU cc_start: 0.9486 (tp) cc_final: 0.9275 (tp) REVERT: D 149 LEU cc_start: 0.9590 (tt) cc_final: 0.9169 (tt) REVERT: D 153 ASN cc_start: 0.9526 (m-40) cc_final: 0.8964 (m-40) REVERT: D 160 ASN cc_start: 0.9179 (m-40) cc_final: 0.8581 (m-40) REVERT: D 255 LEU cc_start: 0.8740 (mt) cc_final: 0.8385 (mt) REVERT: D 351 GLU cc_start: 0.7937 (pp20) cc_final: 0.7695 (pp20) REVERT: D 352 ASP cc_start: 0.8025 (p0) cc_final: 0.7217 (p0) REVERT: E 51 TRP cc_start: 0.4975 (t60) cc_final: 0.4712 (t60) REVERT: E 79 PHE cc_start: 0.9063 (m-10) cc_final: 0.8761 (m-80) REVERT: E 142 TYR cc_start: 0.8899 (t80) cc_final: 0.8497 (t80) REVERT: E 160 HIS cc_start: 0.7959 (m-70) cc_final: 0.7757 (m90) REVERT: E 181 MET cc_start: 0.8553 (mmp) cc_final: 0.8350 (mmm) REVERT: E 363 PHE cc_start: 0.9563 (t80) cc_final: 0.9056 (t80) REVERT: E 374 GLN cc_start: 0.8871 (mm110) cc_final: 0.8195 (mm-40) REVERT: E 383 THR cc_start: 0.9325 (p) cc_final: 0.9065 (p) REVERT: E 427 GLN cc_start: 0.8419 (mt0) cc_final: 0.7890 (tt0) REVERT: E 432 PHE cc_start: 0.8778 (t80) cc_final: 0.7440 (t80) REVERT: E 437 ASN cc_start: 0.9184 (t0) cc_final: 0.8653 (m110) REVERT: E 582 LEU cc_start: 0.9553 (mt) cc_final: 0.9302 (mt) REVERT: E 995 LYS cc_start: 0.7105 (pttm) cc_final: 0.6547 (pttm) REVERT: E 1024 HIS cc_start: 0.7283 (m90) cc_final: 0.6884 (m90) REVERT: E 1231 THR cc_start: 0.9210 (p) cc_final: 0.8851 (t) REVERT: E 1235 ASN cc_start: 0.9461 (m-40) cc_final: 0.8722 (m-40) REVERT: E 1249 GLU cc_start: 0.8170 (tt0) cc_final: 0.7857 (tt0) REVERT: E 1296 ASN cc_start: 0.9173 (m-40) cc_final: 0.8914 (m-40) REVERT: E 1314 ARG cc_start: 0.8986 (ptp-170) cc_final: 0.8400 (ptp-170) outliers start: 3 outliers final: 0 residues processed: 686 average time/residue: 0.1074 time to fit residues: 116.2593 Evaluate side-chains 611 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 610 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 246 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 chunk 140 optimal weight: 0.0870 chunk 52 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 222 optimal weight: 30.0000 chunk 50 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 98 optimal weight: 50.0000 overall best weight: 3.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 HIS A 218 GLN A 335 ASN B 218 GLN B 335 ASN C 160 ASN C 348 GLN D 216 HIS D 279 GLN ** E1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.157832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.133063 restraints weight = 41634.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.136175 restraints weight = 26455.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.139252 restraints weight = 16457.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.139979 restraints weight = 10969.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.140039 restraints weight = 9897.043| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18785 Z= 0.131 Angle : 0.558 8.624 25888 Z= 0.292 Chirality : 0.044 0.178 3160 Planarity : 0.004 0.047 3339 Dihedral : 4.712 61.511 2865 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.22 % Allowed : 3.95 % Favored : 95.83 % 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: 0.03 (0.16), residues: 2721 helix: 1.58 (0.14), residues: 1383 sheet: -1.19 (0.33), residues: 267 loop : -1.80 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1187 TYR 0.025 0.002 TYR E 230 PHE 0.026 0.002 PHE B 95 TRP 0.033 0.001 TRP C 83 HIS 0.008 0.001 HIS E1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (18779) covalent geometry : angle 0.55633 / 0.29 (25875) SS BOND : bond 0.00657 / 0.44 ( 5) SS BOND : angle 1.91745 / 1.18 ( 10) hydrogen bonds : bond 0.03931 / 2.66 ( 1185) hydrogen bonds : angle 4.25761 / 3.08 ( 3453) link_NAG-ASN : bond 0.00097 / 0.05 ( 1) link_NAG-ASN : angle 1.02746 / 0.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 713 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.6924 (t0) cc_final: 0.6216 (t0) REVERT: A 97 HIS cc_start: 0.9063 (t70) cc_final: 0.8767 (t-170) REVERT: A 117 PHE cc_start: 0.8809 (t80) cc_final: 0.8341 (t80) REVERT: A 122 LEU cc_start: 0.9250 (mt) cc_final: 0.8995 (mt) REVERT: A 168 PHE cc_start: 0.7929 (t80) cc_final: 0.7342 (t80) REVERT: A 218 GLN cc_start: 0.7844 (tt0) cc_final: 0.7598 (mm-40) REVERT: A 329 ASP cc_start: 0.7311 (t0) cc_final: 0.6953 (t0) REVERT: A 348 GLN cc_start: 0.8886 (mt0) cc_final: 0.8372 (mt0) REVERT: A 351 GLU cc_start: 0.8842 (mp0) cc_final: 0.8383 (mp0) REVERT: B 88 MET cc_start: 0.8398 (tpp) cc_final: 0.7683 (tpp) REVERT: B 168 PHE cc_start: 0.8177 (m-80) cc_final: 0.7793 (m-80) REVERT: B 192 ARG cc_start: 0.9220 (tpp-160) cc_final: 0.8535 (mmm160) REVERT: B 205 LEU cc_start: 0.8468 (mt) cc_final: 0.8213 (mt) REVERT: B 258 TYR cc_start: 0.8857 (p90) cc_final: 0.8307 (p90) REVERT: B 330 TYR cc_start: 0.7013 (m-80) cc_final: 0.5789 (m-80) REVERT: B 351 GLU cc_start: 0.7265 (mp0) cc_final: 0.6745 (mp0) REVERT: C 78 SER cc_start: 0.7762 (p) cc_final: 0.7486 (p) REVERT: C 192 ARG cc_start: 0.9132 (tpt-90) cc_final: 0.8590 (mmm-85) REVERT: C 201 ARG cc_start: 0.6008 (mmt180) cc_final: 0.5463 (mmt180) REVERT: C 315 PHE cc_start: 0.8404 (m-80) cc_final: 0.8161 (m-80) REVERT: C 333 PHE cc_start: 0.8371 (t80) cc_final: 0.8069 (t80) REVERT: C 347 ARG cc_start: 0.7869 (ttp-170) cc_final: 0.7565 (ttp-170) REVERT: C 352 ASP cc_start: 0.6963 (t70) cc_final: 0.6481 (t70) REVERT: D 43 ASN cc_start: 0.6090 (m-40) cc_final: 0.5864 (m-40) REVERT: D 147 LEU cc_start: 0.9533 (tp) cc_final: 0.9330 (tp) REVERT: D 149 LEU cc_start: 0.9503 (tt) cc_final: 0.9114 (tt) REVERT: D 153 ASN cc_start: 0.9467 (m-40) cc_final: 0.8946 (m-40) REVERT: D 255 LEU cc_start: 0.8606 (mt) cc_final: 0.8178 (mt) REVERT: D 351 GLU cc_start: 0.8021 (pp20) cc_final: 0.7803 (pp20) REVERT: D 352 ASP cc_start: 0.8019 (p0) cc_final: 0.7107 (p0) REVERT: E 42 ILE cc_start: 0.9104 (tt) cc_final: 0.8789 (tp) REVERT: E 51 TRP cc_start: 0.5182 (t60) cc_final: 0.4653 (t60) REVERT: E 74 ARG cc_start: 0.9205 (ttp-110) cc_final: 0.8912 (ttp-110) REVERT: E 219 GLN cc_start: 0.7270 (tm-30) cc_final: 0.6473 (tm-30) REVERT: E 306 ARG cc_start: 0.8074 (tpt-90) cc_final: 0.7754 (tpt-90) REVERT: E 366 LEU cc_start: 0.9468 (mt) cc_final: 0.9220 (mt) REVERT: E 368 LEU cc_start: 0.9208 (tp) cc_final: 0.9001 (tp) REVERT: E 374 GLN cc_start: 0.8477 (mm110) cc_final: 0.7887 (mm-40) REVERT: E 377 TYR cc_start: 0.8605 (m-10) cc_final: 0.8173 (m-10) REVERT: E 383 THR cc_start: 0.9338 (p) cc_final: 0.9037 (p) REVERT: E 432 PHE cc_start: 0.8706 (t80) cc_final: 0.7778 (t80) REVERT: E 437 ASN cc_start: 0.9095 (t0) cc_final: 0.8541 (m110) REVERT: E 995 LYS cc_start: 0.7001 (pttm) cc_final: 0.6429 (pttm) REVERT: E 1024 HIS cc_start: 0.7301 (m90) cc_final: 0.6788 (m90) REVERT: E 1147 THR cc_start: 0.9559 (m) cc_final: 0.9238 (m) REVERT: E 1164 PHE cc_start: 0.9171 (t80) cc_final: 0.8796 (t80) REVERT: E 1231 THR cc_start: 0.9260 (p) cc_final: 0.8837 (t) REVERT: E 1235 ASN cc_start: 0.9527 (m-40) cc_final: 0.8803 (m-40) REVERT: E 1314 ARG cc_start: 0.8972 (ptp-170) cc_final: 0.8357 (ptp-170) outliers start: 3 outliers final: 1 residues processed: 713 average time/residue: 0.1053 time to fit residues: 119.5464 Evaluate side-chains 620 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 619 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 73 optimal weight: 10.0000 chunk 115 optimal weight: 30.0000 chunk 250 optimal weight: 8.9990 chunk 120 optimal weight: 30.0000 chunk 243 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN B 70 HIS B 97 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN D 216 HIS D 277 HIS ** D 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS E 437 ASN ** E1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.153639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.127806 restraints weight = 41511.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.130952 restraints weight = 25854.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.133095 restraints weight = 17741.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.134594 restraints weight = 13274.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.135647 restraints weight = 10676.687| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 18785 Z= 0.213 Angle : 0.610 8.495 25888 Z= 0.330 Chirality : 0.045 0.223 3160 Planarity : 0.004 0.045 3339 Dihedral : 4.920 60.228 2865 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.07 % Allowed : 4.02 % Favored : 95.90 % 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: -0.01 (0.16), residues: 2721 helix: 1.50 (0.14), residues: 1382 sheet: -1.24 (0.31), residues: 285 loop : -1.73 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E1187 TYR 0.027 0.002 TYR E 230 PHE 0.033 0.002 PHE C 168 TRP 0.033 0.002 TRP E 514 HIS 0.011 0.001 HIS D 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.21 (18779) covalent geometry : angle 0.60905 / 0.33 (25875) SS BOND : bond 0.00743 / 0.38 ( 5) SS BOND : angle 2.05181 / 1.25 ( 10) hydrogen bonds : bond 0.04174 / 2.85 ( 1185) hydrogen bonds : angle 4.46854 / 3.24 ( 3453) link_NAG-ASN : bond 0.00099 / 0.05 ( 1) link_NAG-ASN : angle 0.54486 / 0.34 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 676 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 PHE cc_start: 0.9038 (t80) cc_final: 0.8507 (t80) REVERT: A 122 LEU cc_start: 0.9317 (mt) cc_final: 0.9103 (mt) REVERT: A 168 PHE cc_start: 0.7924 (t80) cc_final: 0.7476 (t80) REVERT: A 218 GLN cc_start: 0.7818 (tt0) cc_final: 0.7578 (mm-40) REVERT: A 258 TYR cc_start: 0.8419 (p90) cc_final: 0.7773 (p90) REVERT: A 329 ASP cc_start: 0.7263 (t0) cc_final: 0.6915 (t0) REVERT: A 347 ARG cc_start: 0.7586 (ttp80) cc_final: 0.6972 (ttm110) REVERT: A 348 GLN cc_start: 0.9014 (mt0) cc_final: 0.8412 (mt0) REVERT: A 351 GLU cc_start: 0.9091 (mp0) cc_final: 0.8804 (mp0) REVERT: B 75 PHE cc_start: 0.7648 (m-80) cc_final: 0.7427 (m-80) REVERT: B 88 MET cc_start: 0.8573 (tpp) cc_final: 0.7859 (tpp) REVERT: B 128 GLN cc_start: 0.8225 (tt0) cc_final: 0.7242 (tm-30) REVERT: B 168 PHE cc_start: 0.8115 (m-80) cc_final: 0.7880 (m-80) REVERT: B 205 LEU cc_start: 0.8442 (mt) cc_final: 0.8145 (mt) REVERT: B 330 TYR cc_start: 0.7207 (m-80) cc_final: 0.6269 (m-80) REVERT: B 351 GLU cc_start: 0.7167 (mp0) cc_final: 0.6599 (mp0) REVERT: C 74 ILE cc_start: 0.8246 (tt) cc_final: 0.8042 (tt) REVERT: C 78 SER cc_start: 0.8097 (p) cc_final: 0.7893 (p) REVERT: C 154 ILE cc_start: 0.8975 (mt) cc_final: 0.8738 (mt) REVERT: C 192 ARG cc_start: 0.9185 (tpt-90) cc_final: 0.8652 (mmm-85) REVERT: C 201 ARG cc_start: 0.6125 (mmt180) cc_final: 0.5487 (mmt180) REVERT: C 315 PHE cc_start: 0.8748 (m-80) cc_final: 0.8459 (m-80) REVERT: C 333 PHE cc_start: 0.8678 (t80) cc_final: 0.8266 (t80) REVERT: C 335 ASN cc_start: 0.7952 (p0) cc_final: 0.7648 (p0) REVERT: C 352 ASP cc_start: 0.6927 (t70) cc_final: 0.6456 (t70) REVERT: D 43 ASN cc_start: 0.6221 (m-40) cc_final: 0.5995 (m-40) REVERT: D 147 LEU cc_start: 0.9494 (tp) cc_final: 0.9273 (tp) REVERT: D 149 LEU cc_start: 0.9572 (tt) cc_final: 0.9160 (tt) REVERT: D 153 ASN cc_start: 0.9491 (m-40) cc_final: 0.8876 (m-40) REVERT: D 209 MET cc_start: 0.7628 (tpp) cc_final: 0.7353 (tpp) REVERT: D 255 LEU cc_start: 0.8677 (mt) cc_final: 0.8250 (mt) REVERT: D 351 GLU cc_start: 0.7662 (pp20) cc_final: 0.7308 (pp20) REVERT: D 352 ASP cc_start: 0.8024 (p0) cc_final: 0.7338 (p0) REVERT: E 39 LEU cc_start: 0.9189 (tp) cc_final: 0.8789 (tp) REVERT: E 42 ILE cc_start: 0.9109 (tt) cc_final: 0.8792 (tp) REVERT: E 51 TRP cc_start: 0.5128 (t60) cc_final: 0.4613 (t60) REVERT: E 142 TYR cc_start: 0.8887 (t80) cc_final: 0.7807 (t80) REVERT: E 181 MET cc_start: 0.8922 (mmp) cc_final: 0.8621 (mmm) REVERT: E 306 ARG cc_start: 0.8413 (tpt-90) cc_final: 0.8202 (tpt-90) REVERT: E 366 LEU cc_start: 0.9527 (mt) cc_final: 0.9206 (mt) REVERT: E 377 TYR cc_start: 0.8726 (m-10) cc_final: 0.8366 (m-10) REVERT: E 383 THR cc_start: 0.9313 (p) cc_final: 0.8985 (p) REVERT: E 432 PHE cc_start: 0.8935 (t80) cc_final: 0.7848 (t80) REVERT: E 437 ASN cc_start: 0.8864 (t0) cc_final: 0.8451 (m-40) REVERT: E 546 MET cc_start: 0.8236 (mmt) cc_final: 0.7944 (mmp) REVERT: E 995 LYS cc_start: 0.6997 (pttm) cc_final: 0.6426 (pttm) REVERT: E 1024 HIS cc_start: 0.7345 (m90) cc_final: 0.6853 (m90) REVERT: E 1164 PHE cc_start: 0.9251 (t80) cc_final: 0.8886 (t80) REVERT: E 1231 THR cc_start: 0.9251 (p) cc_final: 0.9032 (p) REVERT: E 1235 ASN cc_start: 0.9560 (m-40) cc_final: 0.9131 (m-40) REVERT: E 1354 TYR cc_start: 0.7142 (t80) cc_final: 0.6865 (t80) outliers start: 1 outliers final: 0 residues processed: 676 average time/residue: 0.1007 time to fit residues: 108.5488 Evaluate side-chains 598 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 598 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 58 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 190 optimal weight: 0.0070 chunk 96 optimal weight: 20.0000 chunk 146 optimal weight: 1.9990 chunk 27 optimal weight: 50.0000 chunk 144 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 225 optimal weight: 0.0170 overall best weight: 2.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 HIS ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS B 218 GLN C 160 ASN C 235 GLN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN D 299 GLN ** E1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.158704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133279 restraints weight = 41208.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.136572 restraints weight = 25403.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.138820 restraints weight = 17347.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.140348 restraints weight = 12889.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.141456 restraints weight = 10278.779| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18785 Z= 0.120 Angle : 0.561 7.022 25888 Z= 0.292 Chirality : 0.044 0.175 3160 Planarity : 0.004 0.091 3339 Dihedral : 4.735 59.101 2865 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.07 % Allowed : 1.86 % Favored : 98.06 % 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: 0.26 (0.17), residues: 2721 helix: 1.69 (0.14), residues: 1376 sheet: -1.04 (0.33), residues: 267 loop : -1.56 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 325 TYR 0.025 0.001 TYR E 230 PHE 0.039 0.002 PHE C 75 TRP 0.034 0.001 TRP B 83 HIS 0.006 0.001 HIS E1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (18779) covalent geometry : angle 0.55918 / 0.29 (25875) SS BOND : bond 0.00748 / 0.39 ( 5) SS BOND : angle 2.14734 / 1.37 ( 10) hydrogen bonds : bond 0.03695 / 2.51 ( 1185) hydrogen bonds : angle 4.17656 / 3.01 ( 3453) link_NAG-ASN : bond 0.00147 / 0.08 ( 1) link_NAG-ASN : angle 1.26632 / 0.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 695 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.6994 (t0) cc_final: 0.6050 (t0) REVERT: A 117 PHE cc_start: 0.8779 (t80) cc_final: 0.8288 (t80) REVERT: A 152 GLN cc_start: 0.9112 (tt0) cc_final: 0.8521 (tt0) REVERT: A 168 PHE cc_start: 0.7829 (t80) cc_final: 0.7339 (t80) REVERT: A 218 GLN cc_start: 0.7833 (tt0) cc_final: 0.7580 (mm-40) REVERT: A 329 ASP cc_start: 0.7297 (t0) cc_final: 0.6967 (t0) REVERT: A 348 GLN cc_start: 0.8959 (mt0) cc_final: 0.8408 (mt0) REVERT: A 351 GLU cc_start: 0.8871 (mp0) cc_final: 0.8512 (mp0) REVERT: B 75 PHE cc_start: 0.7663 (m-80) cc_final: 0.7377 (m-80) REVERT: B 88 MET cc_start: 0.8432 (tpp) cc_final: 0.7761 (tpp) REVERT: B 122 LEU cc_start: 0.9613 (mm) cc_final: 0.9406 (mm) REVERT: B 137 MET cc_start: 0.3659 (tmm) cc_final: 0.3142 (tmm) REVERT: B 168 PHE cc_start: 0.7968 (m-80) cc_final: 0.7738 (m-80) REVERT: B 192 ARG cc_start: 0.9127 (tpp-160) cc_final: 0.8775 (mmm160) REVERT: B 282 GLU cc_start: 0.7335 (tm-30) cc_final: 0.7059 (tm-30) REVERT: B 330 TYR cc_start: 0.7420 (m-80) cc_final: 0.6588 (m-10) REVERT: B 351 GLU cc_start: 0.7454 (mp0) cc_final: 0.6880 (mp0) REVERT: C 78 SER cc_start: 0.7860 (p) cc_final: 0.7580 (p) REVERT: C 192 ARG cc_start: 0.9357 (tpt-90) cc_final: 0.8883 (mmm-85) REVERT: C 201 ARG cc_start: 0.6282 (mmt180) cc_final: 0.6012 (mmt180) REVERT: C 235 GLN cc_start: 0.8624 (mt0) cc_final: 0.8351 (mt0) REVERT: C 315 PHE cc_start: 0.8523 (m-80) cc_final: 0.8306 (m-80) REVERT: C 333 PHE cc_start: 0.8602 (t80) cc_final: 0.8142 (t80) REVERT: C 352 ASP cc_start: 0.6830 (t70) cc_final: 0.6383 (t70) REVERT: D 43 ASN cc_start: 0.6173 (m-40) cc_final: 0.5937 (m-40) REVERT: D 136 ARG cc_start: 0.8944 (mpp80) cc_final: 0.8498 (mpp80) REVERT: D 209 MET cc_start: 0.7498 (tpp) cc_final: 0.7113 (tpp) REVERT: D 222 LYS cc_start: 0.8758 (tptp) cc_final: 0.8495 (tptp) REVERT: D 352 ASP cc_start: 0.7850 (p0) cc_final: 0.7223 (p0) REVERT: E 39 LEU cc_start: 0.8979 (tp) cc_final: 0.8602 (tp) REVERT: E 42 ILE cc_start: 0.8942 (tt) cc_final: 0.8649 (tp) REVERT: E 51 TRP cc_start: 0.4733 (t60) cc_final: 0.4481 (t60) REVERT: E 74 ARG cc_start: 0.9250 (ttp-110) cc_final: 0.8652 (ttp-110) REVERT: E 142 TYR cc_start: 0.8709 (t80) cc_final: 0.7941 (t80) REVERT: E 181 MET cc_start: 0.8766 (mmp) cc_final: 0.8441 (mmm) REVERT: E 219 GLN cc_start: 0.7654 (tm-30) cc_final: 0.7231 (tm-30) REVERT: E 306 ARG cc_start: 0.8188 (tpt-90) cc_final: 0.7841 (tpt-90) REVERT: E 366 LEU cc_start: 0.9456 (mt) cc_final: 0.9174 (mt) REVERT: E 374 GLN cc_start: 0.8972 (mm110) cc_final: 0.7913 (mm110) REVERT: E 377 TYR cc_start: 0.8687 (m-10) cc_final: 0.8232 (m-10) REVERT: E 383 THR cc_start: 0.9277 (p) cc_final: 0.8976 (p) REVERT: E 432 PHE cc_start: 0.8761 (t80) cc_final: 0.7774 (t80) REVERT: E 437 ASN cc_start: 0.8779 (t0) cc_final: 0.8298 (m-40) REVERT: E 546 MET cc_start: 0.8155 (mmt) cc_final: 0.7890 (mmp) REVERT: E 995 LYS cc_start: 0.6984 (pttm) cc_final: 0.6486 (pttm) REVERT: E 1024 HIS cc_start: 0.7200 (m90) cc_final: 0.6715 (m90) REVERT: E 1164 PHE cc_start: 0.9154 (t80) cc_final: 0.8952 (t80) REVERT: E 1189 LEU cc_start: 0.8896 (mp) cc_final: 0.8619 (mp) REVERT: E 1231 THR cc_start: 0.9269 (p) cc_final: 0.9016 (p) REVERT: E 1235 ASN cc_start: 0.9544 (m-40) cc_final: 0.9160 (m-40) REVERT: E 1249 GLU cc_start: 0.8095 (tt0) cc_final: 0.7385 (tt0) REVERT: E 1354 TYR cc_start: 0.7259 (t80) cc_final: 0.7052 (t80) outliers start: 1 outliers final: 1 residues processed: 695 average time/residue: 0.0999 time to fit residues: 110.6202 Evaluate side-chains 614 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 613 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 159 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 185 optimal weight: 6.9990 chunk 153 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 213 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 51 optimal weight: 30.0000 overall best weight: 4.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 HIS A 335 ASN B 97 HIS C 128 GLN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN D 216 HIS D 277 HIS D 299 GLN E 160 HIS ** E1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.156577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.131062 restraints weight = 41430.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.134220 restraints weight = 25681.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.136418 restraints weight = 17579.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.137954 restraints weight = 13092.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.139013 restraints weight = 10457.907| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18785 Z= 0.151 Angle : 0.567 6.941 25888 Z= 0.300 Chirality : 0.045 0.172 3160 Planarity : 0.004 0.070 3339 Dihedral : 4.749 59.855 2865 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: 0.32 (0.17), residues: 2721 helix: 1.74 (0.14), residues: 1377 sheet: -0.99 (0.33), residues: 259 loop : -1.54 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 221 TYR 0.026 0.002 TYR E1219 PHE 0.031 0.002 PHE C 168 TRP 0.029 0.002 TRP E 514 HIS 0.011 0.001 HIS D 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (18779) covalent geometry : angle 0.56620 / 0.30 (25875) SS BOND : bond 0.00306 / 0.12 ( 5) SS BOND : angle 1.86583 / 1.13 ( 10) hydrogen bonds : bond 0.03722 / 2.52 ( 1185) hydrogen bonds : angle 4.22870 / 3.06 ( 3453) link_NAG-ASN : bond 0.00108 / 0.06 ( 1) link_NAG-ASN : angle 0.90602 / 0.54 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 677 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7112 (t0) cc_final: 0.6122 (t0) REVERT: A 117 PHE cc_start: 0.8819 (t80) cc_final: 0.8382 (t80) REVERT: A 122 LEU cc_start: 0.9364 (mt) cc_final: 0.9158 (mt) REVERT: A 168 PHE cc_start: 0.7586 (t80) cc_final: 0.7167 (t80) REVERT: A 218 GLN cc_start: 0.7822 (tt0) cc_final: 0.7591 (mm-40) REVERT: A 329 ASP cc_start: 0.7392 (t0) cc_final: 0.7046 (t0) REVERT: A 347 ARG cc_start: 0.7397 (ttp80) cc_final: 0.6791 (ttm110) REVERT: A 348 GLN cc_start: 0.8966 (mt0) cc_final: 0.8354 (mt0) REVERT: A 351 GLU cc_start: 0.8872 (mp0) cc_final: 0.8425 (mp0) REVERT: B 88 MET cc_start: 0.8409 (tpp) cc_final: 0.7727 (tpp) REVERT: B 137 MET cc_start: 0.3784 (tmm) cc_final: 0.3461 (tmm) REVERT: B 168 PHE cc_start: 0.7967 (m-80) cc_final: 0.7747 (m-80) REVERT: B 215 ILE cc_start: 0.8984 (mm) cc_final: 0.8598 (pt) REVERT: B 249 ILE cc_start: 0.9052 (tp) cc_final: 0.8840 (tp) REVERT: B 330 TYR cc_start: 0.7093 (m-80) cc_final: 0.6171 (m-80) REVERT: B 351 GLU cc_start: 0.7459 (mp0) cc_final: 0.6865 (mp0) REVERT: C 78 SER cc_start: 0.7910 (p) cc_final: 0.7594 (p) REVERT: C 352 ASP cc_start: 0.6905 (t70) cc_final: 0.6450 (t70) REVERT: D 136 ARG cc_start: 0.8864 (mpp80) cc_final: 0.8581 (mpp80) REVERT: D 158 MET cc_start: 0.8782 (mmp) cc_final: 0.8450 (mmp) REVERT: D 222 LYS cc_start: 0.8813 (tptp) cc_final: 0.8547 (tptp) REVERT: D 255 LEU cc_start: 0.8158 (mt) cc_final: 0.7692 (mt) REVERT: D 351 GLU cc_start: 0.7494 (pp20) cc_final: 0.7208 (pp20) REVERT: D 352 ASP cc_start: 0.7853 (p0) cc_final: 0.7180 (p0) REVERT: E 39 LEU cc_start: 0.9002 (tp) cc_final: 0.8726 (tp) REVERT: E 42 ILE cc_start: 0.8948 (tt) cc_final: 0.8738 (tp) REVERT: E 51 TRP cc_start: 0.4881 (t60) cc_final: 0.4476 (t60) REVERT: E 74 ARG cc_start: 0.9245 (ttp-110) cc_final: 0.9021 (ttp-110) REVERT: E 142 TYR cc_start: 0.8719 (t80) cc_final: 0.7954 (t80) REVERT: E 148 ILE cc_start: 0.9309 (mm) cc_final: 0.9097 (mm) REVERT: E 160 HIS cc_start: 0.7736 (m90) cc_final: 0.7110 (m90) REVERT: E 176 VAL cc_start: 0.9454 (t) cc_final: 0.9219 (p) REVERT: E 181 MET cc_start: 0.8779 (mmp) cc_final: 0.8461 (mmm) REVERT: E 219 GLN cc_start: 0.7762 (tm-30) cc_final: 0.7493 (tm-30) REVERT: E 374 GLN cc_start: 0.8700 (mm110) cc_final: 0.7988 (mm-40) REVERT: E 377 TYR cc_start: 0.8664 (m-10) cc_final: 0.8253 (m-10) REVERT: E 546 MET cc_start: 0.8253 (mmt) cc_final: 0.7958 (mmp) REVERT: E 995 LYS cc_start: 0.7015 (pttm) cc_final: 0.6578 (pttm) REVERT: E 1024 HIS cc_start: 0.7249 (m90) cc_final: 0.6814 (m90) REVERT: E 1189 LEU cc_start: 0.8962 (mp) cc_final: 0.8671 (mp) REVERT: E 1231 THR cc_start: 0.9292 (p) cc_final: 0.9056 (p) REVERT: E 1235 ASN cc_start: 0.9501 (m-40) cc_final: 0.9130 (m-40) outliers start: 0 outliers final: 0 residues processed: 677 average time/residue: 0.1009 time to fit residues: 108.5490 Evaluate side-chains 624 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 624 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 57 optimal weight: 30.0000 chunk 244 optimal weight: 0.9990 chunk 93 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 221 optimal weight: 50.0000 chunk 35 optimal weight: 2.9990 chunk 248 optimal weight: 50.0000 chunk 50 optimal weight: 6.9990 chunk 252 optimal weight: 20.0000 chunk 260 optimal weight: 40.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 ASN C 128 GLN C 160 ASN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN D 153 ASN D 216 HIS D 299 GLN ** D 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.155855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.131097 restraints weight = 40576.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.134309 restraints weight = 24643.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.136530 restraints weight = 16717.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.137924 restraints weight = 12324.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.139083 restraints weight = 9882.202| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18785 Z= 0.143 Angle : 0.579 6.792 25888 Z= 0.305 Chirality : 0.045 0.189 3160 Planarity : 0.004 0.054 3339 Dihedral : 4.752 59.208 2865 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.07 % Allowed : 1.71 % Favored : 98.21 % 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: 0.32 (0.17), residues: 2721 helix: 1.73 (0.14), residues: 1383 sheet: -0.91 (0.34), residues: 261 loop : -1.57 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 221 TYR 0.023 0.002 TYR E1219 PHE 0.041 0.002 PHE B 75 TRP 0.081 0.002 TRP C 83 HIS 0.006 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (18779) covalent geometry : angle 0.57780 / 0.30 (25875) SS BOND : bond 0.00284 / 0.12 ( 5) SS BOND : angle 1.89278 / 1.15 ( 10) hydrogen bonds : bond 0.03735 / 2.53 ( 1185) hydrogen bonds : angle 4.20479 / 3.04 ( 3453) link_NAG-ASN : bond 0.00128 / 0.07 ( 1) link_NAG-ASN : angle 0.96569 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 679 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7022 (t0) cc_final: 0.6085 (t0) REVERT: A 95 PHE cc_start: 0.7617 (t80) cc_final: 0.7363 (t80) REVERT: A 117 PHE cc_start: 0.8925 (t80) cc_final: 0.8495 (t80) REVERT: A 168 PHE cc_start: 0.7653 (t80) cc_final: 0.7200 (t80) REVERT: A 218 GLN cc_start: 0.7853 (tt0) cc_final: 0.7563 (mm-40) REVERT: A 329 ASP cc_start: 0.7535 (t0) cc_final: 0.7237 (t0) REVERT: A 347 ARG cc_start: 0.7415 (ttp80) cc_final: 0.6805 (ttm110) REVERT: A 348 GLN cc_start: 0.8985 (mt0) cc_final: 0.8415 (mt0) REVERT: A 351 GLU cc_start: 0.8949 (mp0) cc_final: 0.8469 (mp0) REVERT: B 122 LEU cc_start: 0.9624 (mm) cc_final: 0.9371 (mm) REVERT: B 192 ARG cc_start: 0.9186 (tpp-160) cc_final: 0.8781 (mmm160) REVERT: B 215 ILE cc_start: 0.9021 (mm) cc_final: 0.8604 (pt) REVERT: B 249 ILE cc_start: 0.9069 (tp) cc_final: 0.8834 (tp) REVERT: B 330 TYR cc_start: 0.7112 (m-80) cc_final: 0.5897 (m-80) REVERT: B 351 GLU cc_start: 0.7468 (mp0) cc_final: 0.6856 (mp0) REVERT: C 201 ARG cc_start: 0.6430 (mmt180) cc_final: 0.5878 (mmt180) REVERT: C 352 ASP cc_start: 0.7018 (t70) cc_final: 0.6570 (t70) REVERT: D 43 ASN cc_start: 0.6217 (m-40) cc_final: 0.5853 (p0) REVERT: D 222 LYS cc_start: 0.8798 (tptp) cc_final: 0.8515 (tptp) REVERT: D 255 LEU cc_start: 0.8284 (mt) cc_final: 0.7788 (mt) REVERT: D 299 GLN cc_start: 0.8654 (tp40) cc_final: 0.8405 (tp-100) REVERT: D 351 GLU cc_start: 0.7490 (pp20) cc_final: 0.7201 (pp20) REVERT: D 352 ASP cc_start: 0.7917 (p0) cc_final: 0.7262 (p0) REVERT: E 42 ILE cc_start: 0.9017 (tt) cc_final: 0.8724 (tp) REVERT: E 51 TRP cc_start: 0.4377 (t60) cc_final: 0.3801 (t60) REVERT: E 74 ARG cc_start: 0.9281 (ttp-110) cc_final: 0.8876 (ttp-110) REVERT: E 148 ILE cc_start: 0.9343 (mm) cc_final: 0.9128 (mm) REVERT: E 160 HIS cc_start: 0.7888 (m90) cc_final: 0.7404 (m90) REVERT: E 176 VAL cc_start: 0.9382 (t) cc_final: 0.9171 (p) REVERT: E 181 MET cc_start: 0.8749 (mmp) cc_final: 0.8445 (mmm) REVERT: E 219 GLN cc_start: 0.7581 (tm-30) cc_final: 0.7278 (tm-30) REVERT: E 363 PHE cc_start: 0.9461 (t80) cc_final: 0.8989 (t80) REVERT: E 374 GLN cc_start: 0.8595 (mm110) cc_final: 0.7579 (mm-40) REVERT: E 427 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8058 (tp40) REVERT: E 546 MET cc_start: 0.8563 (mmt) cc_final: 0.8131 (mmp) REVERT: E 995 LYS cc_start: 0.6926 (pttm) cc_final: 0.6491 (pttm) REVERT: E 1024 HIS cc_start: 0.7227 (m90) cc_final: 0.6850 (m90) REVERT: E 1189 LEU cc_start: 0.8965 (mp) cc_final: 0.8639 (mp) REVERT: E 1235 ASN cc_start: 0.9529 (m-40) cc_final: 0.9178 (m-40) REVERT: E 1249 GLU cc_start: 0.8236 (tt0) cc_final: 0.7659 (tt0) outliers start: 1 outliers final: 1 residues processed: 679 average time/residue: 0.1026 time to fit residues: 110.5164 Evaluate side-chains 624 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 623 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 62 optimal weight: 20.0000 chunk 232 optimal weight: 30.0000 chunk 133 optimal weight: 40.0000 chunk 221 optimal weight: 40.0000 chunk 183 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 239 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 70 HIS B 97 HIS C 128 GLN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN D 277 HIS D 299 GLN ** E1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.126890 restraints weight = 40646.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.129995 restraints weight = 25015.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.132127 restraints weight = 17079.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133546 restraints weight = 12713.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.134600 restraints weight = 10188.947| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 18785 Z= 0.224 Angle : 0.660 8.094 25888 Z= 0.354 Chirality : 0.047 0.279 3160 Planarity : 0.005 0.088 3339 Dihedral : 5.072 56.868 2865 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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: 0.08 (0.16), residues: 2721 helix: 1.50 (0.14), residues: 1375 sheet: -1.11 (0.32), residues: 276 loop : -1.57 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 221 TYR 0.030 0.002 TYR E 230 PHE 0.056 0.003 PHE E 433 TRP 0.067 0.002 TRP C 83 HIS 0.010 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.22 (18779) covalent geometry : angle 0.65910 / 0.35 (25875) SS BOND : bond 0.00461 / 0.24 ( 5) SS BOND : angle 1.92666 / 1.15 ( 10) hydrogen bonds : bond 0.04196 / 2.82 ( 1185) hydrogen bonds : angle 4.53909 / 3.28 ( 3453) link_NAG-ASN : bond 0.00123 / 0.06 ( 1) link_NAG-ASN : angle 0.62014 / 0.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 665 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7116 (t0) cc_final: 0.6149 (t0) REVERT: A 117 PHE cc_start: 0.8969 (t80) cc_final: 0.8506 (t80) REVERT: A 122 LEU cc_start: 0.9293 (mt) cc_final: 0.9075 (mt) REVERT: A 168 PHE cc_start: 0.7625 (t80) cc_final: 0.7077 (t80) REVERT: A 218 GLN cc_start: 0.7904 (tt0) cc_final: 0.7619 (mm-40) REVERT: A 258 TYR cc_start: 0.8475 (p90) cc_final: 0.8232 (p90) REVERT: A 269 ASP cc_start: 0.6260 (m-30) cc_final: 0.6016 (m-30) REVERT: A 329 ASP cc_start: 0.7435 (t0) cc_final: 0.7102 (t0) REVERT: A 347 ARG cc_start: 0.7721 (ttp80) cc_final: 0.7520 (ttm110) REVERT: A 348 GLN cc_start: 0.9000 (mt0) cc_final: 0.8484 (mt0) REVERT: A 351 GLU cc_start: 0.9068 (mp0) cc_final: 0.8631 (mp0) REVERT: B 83 TRP cc_start: 0.8924 (m-10) cc_final: 0.8557 (m-10) REVERT: B 128 GLN cc_start: 0.8241 (tt0) cc_final: 0.7414 (tm-30) REVERT: B 215 ILE cc_start: 0.9001 (mm) cc_final: 0.8593 (pt) REVERT: B 249 ILE cc_start: 0.9078 (tp) cc_final: 0.8829 (tp) REVERT: B 330 TYR cc_start: 0.7682 (m-80) cc_final: 0.7479 (m-80) REVERT: B 333 PHE cc_start: 0.8177 (m-10) cc_final: 0.7764 (m-10) REVERT: B 351 GLU cc_start: 0.7557 (mp0) cc_final: 0.6844 (mp0) REVERT: C 78 SER cc_start: 0.7984 (p) cc_final: 0.7756 (p) REVERT: C 201 ARG cc_start: 0.6537 (mmt180) cc_final: 0.5947 (mmt180) REVERT: C 330 TYR cc_start: 0.8392 (m-80) cc_final: 0.7649 (m-10) REVERT: C 352 ASP cc_start: 0.6703 (t70) cc_final: 0.6400 (t70) REVERT: D 43 ASN cc_start: 0.6619 (m-40) cc_final: 0.6414 (m-40) REVERT: D 147 LEU cc_start: 0.9487 (tp) cc_final: 0.9284 (tp) REVERT: D 222 LYS cc_start: 0.8890 (tptp) cc_final: 0.8624 (tptp) REVERT: D 255 LEU cc_start: 0.8397 (mt) cc_final: 0.8004 (mt) REVERT: D 258 TYR cc_start: 0.8477 (p90) cc_final: 0.8212 (p90) REVERT: D 351 GLU cc_start: 0.7556 (pp20) cc_final: 0.7262 (pp20) REVERT: E 39 LEU cc_start: 0.9099 (tp) cc_final: 0.8690 (tp) REVERT: E 42 ILE cc_start: 0.9150 (tt) cc_final: 0.8842 (tp) REVERT: E 74 ARG cc_start: 0.9344 (ttp-110) cc_final: 0.9119 (ttp-110) REVERT: E 142 TYR cc_start: 0.8591 (t80) cc_final: 0.7896 (t80) REVERT: E 160 HIS cc_start: 0.7766 (m90) cc_final: 0.7462 (m90) REVERT: E 176 VAL cc_start: 0.9358 (t) cc_final: 0.9139 (p) REVERT: E 181 MET cc_start: 0.8769 (mmp) cc_final: 0.8467 (mmm) REVERT: E 363 PHE cc_start: 0.9605 (t80) cc_final: 0.9134 (t80) REVERT: E 427 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8129 (tp40) REVERT: E 546 MET cc_start: 0.8695 (mmt) cc_final: 0.8193 (mmp) REVERT: E 995 LYS cc_start: 0.6270 (pttm) cc_final: 0.5675 (pttm) REVERT: E 1126 SER cc_start: 0.9069 (t) cc_final: 0.8837 (p) REVERT: E 1230 TYR cc_start: 0.8045 (m-80) cc_final: 0.7816 (m-80) REVERT: E 1231 THR cc_start: 0.9419 (p) cc_final: 0.9184 (p) REVERT: E 1235 ASN cc_start: 0.9565 (m-40) cc_final: 0.9152 (m-40) REVERT: E 1249 GLU cc_start: 0.7982 (tt0) cc_final: 0.7373 (tt0) REVERT: E 1300 ARG cc_start: 0.9205 (mmt90) cc_final: 0.9005 (mmt90) outliers start: 0 outliers final: 0 residues processed: 665 average time/residue: 0.1026 time to fit residues: 108.1776 Evaluate side-chains 601 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 601 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 164 optimal weight: 7.9990 chunk 214 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 219 optimal weight: 40.0000 chunk 78 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 217 optimal weight: 20.0000 chunk 95 optimal weight: 7.9990 chunk 120 optimal weight: 0.0050 chunk 62 optimal weight: 0.9990 overall best weight: 4.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 70 HIS C 128 GLN C 160 ASN C 216 HIS C 235 GLN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN D 153 ASN D 299 GLN ** E1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.155438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.130104 restraints weight = 40980.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.133287 restraints weight = 25202.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.135471 restraints weight = 17240.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.136863 restraints weight = 12856.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.137995 restraints weight = 10382.622| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 18785 Z= 0.148 Angle : 0.623 14.402 25888 Z= 0.325 Chirality : 0.046 0.297 3160 Planarity : 0.004 0.073 3339 Dihedral : 4.936 59.547 2865 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.07 % Allowed : 0.52 % Favored : 99.40 % 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: 0.21 (0.17), residues: 2721 helix: 1.61 (0.14), residues: 1381 sheet: -1.04 (0.33), residues: 269 loop : -1.54 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 221 TYR 0.028 0.002 TYR E1219 PHE 0.042 0.002 PHE E 433 TRP 0.071 0.002 TRP C 83 HIS 0.005 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (18779) covalent geometry : angle 0.62207 / 0.32 (25875) SS BOND : bond 0.00367 / 0.19 ( 5) SS BOND : angle 2.00811 / 1.18 ( 10) hydrogen bonds : bond 0.03878 / 2.59 ( 1185) hydrogen bonds : angle 4.32588 / 3.12 ( 3453) link_NAG-ASN : bond 0.00141 / 0.07 ( 1) link_NAG-ASN : angle 0.96810 / 0.57 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 693 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7026 (t0) cc_final: 0.6058 (t0) REVERT: A 117 PHE cc_start: 0.8809 (t80) cc_final: 0.8357 (t80) REVERT: A 122 LEU cc_start: 0.9306 (mt) cc_final: 0.9083 (mt) REVERT: A 168 PHE cc_start: 0.7615 (t80) cc_final: 0.7118 (t80) REVERT: A 218 GLN cc_start: 0.7933 (tt0) cc_final: 0.7606 (mm-40) REVERT: A 329 ASP cc_start: 0.7545 (t0) cc_final: 0.7206 (t0) REVERT: A 347 ARG cc_start: 0.7534 (ttp80) cc_final: 0.7094 (ttp-170) REVERT: A 348 GLN cc_start: 0.8959 (mt0) cc_final: 0.8362 (mt0) REVERT: A 351 GLU cc_start: 0.9051 (mp0) cc_final: 0.8614 (mp0) REVERT: B 122 LEU cc_start: 0.9537 (mm) cc_final: 0.9259 (mm) REVERT: B 128 GLN cc_start: 0.8081 (tt0) cc_final: 0.7544 (tm-30) REVERT: B 164 LEU cc_start: 0.9274 (tt) cc_final: 0.9033 (tt) REVERT: B 205 LEU cc_start: 0.8223 (mt) cc_final: 0.8018 (mt) REVERT: B 215 ILE cc_start: 0.8991 (mm) cc_final: 0.8597 (pt) REVERT: B 249 ILE cc_start: 0.9083 (tp) cc_final: 0.8826 (tp) REVERT: B 330 TYR cc_start: 0.7016 (m-80) cc_final: 0.5944 (m-80) REVERT: B 333 PHE cc_start: 0.8124 (m-10) cc_final: 0.7863 (m-10) REVERT: B 351 GLU cc_start: 0.7774 (mp0) cc_final: 0.7182 (mp0) REVERT: C 160 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.8900 (t0) REVERT: C 201 ARG cc_start: 0.6488 (mmt180) cc_final: 0.5849 (mmt180) REVERT: C 330 TYR cc_start: 0.8257 (m-80) cc_final: 0.7607 (m-10) REVERT: C 352 ASP cc_start: 0.6652 (t70) cc_final: 0.6339 (t70) REVERT: D 43 ASN cc_start: 0.6565 (m-40) cc_final: 0.6152 (p0) REVERT: D 222 LYS cc_start: 0.8880 (tptp) cc_final: 0.8579 (tptp) REVERT: D 255 LEU cc_start: 0.8027 (mt) cc_final: 0.7659 (mt) REVERT: D 258 TYR cc_start: 0.8499 (p90) cc_final: 0.8214 (p90) REVERT: D 299 GLN cc_start: 0.8683 (tp40) cc_final: 0.8443 (tp-100) REVERT: D 351 GLU cc_start: 0.7354 (pp20) cc_final: 0.7138 (pp20) REVERT: E 39 LEU cc_start: 0.9084 (tp) cc_final: 0.8766 (tp) REVERT: E 42 ILE cc_start: 0.9119 (tt) cc_final: 0.8794 (tp) REVERT: E 142 TYR cc_start: 0.8535 (t80) cc_final: 0.7907 (t80) REVERT: E 148 ILE cc_start: 0.9289 (mm) cc_final: 0.9049 (mm) REVERT: E 160 HIS cc_start: 0.7864 (m90) cc_final: 0.7503 (m90) REVERT: E 176 VAL cc_start: 0.9422 (t) cc_final: 0.9179 (p) REVERT: E 181 MET cc_start: 0.8736 (mmp) cc_final: 0.8498 (mmm) REVERT: E 219 GLN cc_start: 0.7621 (tm-30) cc_final: 0.7270 (tm-30) REVERT: E 363 PHE cc_start: 0.9578 (t80) cc_final: 0.9204 (t80) REVERT: E 377 TYR cc_start: 0.8722 (m-10) cc_final: 0.8353 (m-80) REVERT: E 427 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8139 (tp40) REVERT: E 539 TYR cc_start: 0.8414 (m-10) cc_final: 0.7990 (m-80) REVERT: E 546 MET cc_start: 0.8589 (mmt) cc_final: 0.8208 (mmp) REVERT: E 1024 HIS cc_start: 0.6693 (m90) cc_final: 0.6480 (m90) REVERT: E 1164 PHE cc_start: 0.9183 (t80) cc_final: 0.8960 (t80) REVERT: E 1189 LEU cc_start: 0.8978 (mp) cc_final: 0.8700 (mp) REVERT: E 1230 TYR cc_start: 0.7998 (m-80) cc_final: 0.7766 (m-80) REVERT: E 1231 THR cc_start: 0.9608 (p) cc_final: 0.9403 (p) REVERT: E 1235 ASN cc_start: 0.9454 (m-40) cc_final: 0.9157 (m-40) REVERT: E 1249 GLU cc_start: 0.7937 (tt0) cc_final: 0.7266 (tt0) REVERT: E 1253 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8116 (mt-10) outliers start: 1 outliers final: 0 residues processed: 693 average time/residue: 0.1039 time to fit residues: 115.1151 Evaluate side-chains 623 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 622 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 238 optimal weight: 8.9990 chunk 197 optimal weight: 8.9990 chunk 123 optimal weight: 20.0000 chunk 232 optimal weight: 30.0000 chunk 182 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 117 optimal weight: 0.3980 chunk 152 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 59 optimal weight: 30.0000 chunk 97 optimal weight: 40.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 ASN C 235 GLN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN D 153 ASN D 277 HIS ** E1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.155860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.130720 restraints weight = 40948.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133947 restraints weight = 25168.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.136148 restraints weight = 17150.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.137634 restraints weight = 12732.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138757 restraints weight = 10177.368| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18785 Z= 0.140 Angle : 0.607 8.845 25888 Z= 0.316 Chirality : 0.046 0.276 3160 Planarity : 0.004 0.065 3339 Dihedral : 4.849 57.718 2865 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 0.29 (0.17), residues: 2721 helix: 1.68 (0.14), residues: 1381 sheet: -1.01 (0.33), residues: 269 loop : -1.51 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 221 TYR 0.028 0.002 TYR E1219 PHE 0.043 0.002 PHE E 433 TRP 0.079 0.002 TRP C 83 HIS 0.011 0.001 HIS D 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (18779) covalent geometry : angle 0.60572 / 0.32 (25875) SS BOND : bond 0.00257 / 0.12 ( 5) SS BOND : angle 1.94384 / 1.17 ( 10) hydrogen bonds : bond 0.03784 / 2.54 ( 1185) hydrogen bonds : angle 4.24559 / 3.06 ( 3453) link_NAG-ASN : bond 0.00197 / 0.10 ( 1) link_NAG-ASN : angle 0.98565 / 0.61 ( 3) =============================================================================== Job complete usr+sys time: 2996.95 seconds wall clock time: 52 minutes 15.77 seconds (3135.77 seconds total)