Starting phenix.real_space_refine on Sun Mar 17 16:44:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1e_26299/03_2024/7u1e_26299_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1e_26299/03_2024/7u1e_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1e_26299/03_2024/7u1e_26299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1e_26299/03_2024/7u1e_26299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1e_26299/03_2024/7u1e_26299_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1e_26299/03_2024/7u1e_26299_updated.pdb" } resolution = 4.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: {'GLN:plan1': 2, 'ARG:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 11, 'ASP:plan': 9} 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: {'GLN:plan1': 4, 'HIS:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 7} 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: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 7} 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: {'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 10, 'ARG:plan': 9} 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: {'GLN:plan1': 39, 'ASP:plan': 48, 'TYR:plan': 4, 'ASN:plan1': 27, 'TRP:plan': 5, 'HIS:plan': 11, 'PHE:plan': 22, 'GLU:plan': 52, 'ARG:plan': 40} 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.22, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 6.38 Conformation dependent library (CDL) restraints added in 3.5 seconds 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... running ksdssp... Secondary structure from input PDB file: 81 helices and 16 sheets defined 49.7% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.40 Creating SS restraints... Processing helix chain 'A' and resid 56 through 65 Processing helix chain 'A' and resid 68 through 97 removed outlier: 3.538A pdb=" N HIS A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 143 through 177 removed outlier: 3.661A pdb=" N ALA A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 removed outlier: 4.109A pdb=" N ASP A 269 " --> pdb=" O PRO A 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 269' Processing helix chain 'A' and resid 272 through 275 Processing helix chain 'A' and resid 331 through 334 removed outlier: 3.852A pdb=" N GLY A 334 " --> pdb=" O SER A 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 331 through 334' Processing helix chain 'A' and resid 346 through 357 Processing helix chain 'B' and resid 56 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 68 through 96 Processing helix chain 'B' and resid 117 through 127 Processing helix chain 'B' and resid 143 through 173 removed outlier: 3.788A pdb=" N ALA B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 269 removed outlier: 4.383A pdb=" N ASP B 269 " --> pdb=" O PRO B 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 269' Processing helix chain 'B' and resid 272 through 274 No H-bonds generated for 'chain 'B' and resid 272 through 274' Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 346 through 357 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 56 through 63 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 68 through 97 removed outlier: 3.853A pdb=" N HIS C 97 " --> pdb=" O ILE C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 143 through 173 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 266 through 269 removed outlier: 3.817A pdb=" N ASP C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 269' Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 346 through 357 Processing helix chain 'D' and resid 56 through 64 Processing helix chain 'D' and resid 68 through 96 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 145 through 176 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 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 346 through 357 removed outlier: 3.695A pdb=" N ASP D 350 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 15 removed outlier: 5.527A pdb=" N ALA E 14 " --> pdb=" O ASN E 10 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TYR E 15 " --> pdb=" O HIS E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 50 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 71 through 98 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) Processing helix chain 'E' and resid 104 through 106 No H-bonds generated for 'chain 'E' and resid 104 through 106' Processing helix chain 'E' and resid 108 through 128 Processing helix chain 'E' and resid 135 through 160 removed outlier: 3.896A pdb=" N ALA E 138 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR E 144 " --> pdb=" O ILE E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 193 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 208 through 211 No H-bonds generated for 'chain 'E' and resid 208 through 211' Processing helix chain 'E' and resid 224 through 229 Processing helix chain 'E' and resid 231 through 242 removed outlier: 3.627A pdb=" N ALA E 235 " --> pdb=" O TRP E 232 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA E 240 " --> pdb=" O ILE E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 276 Processing helix chain 'E' and resid 284 through 328 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 348 through 351 No H-bonds generated for 'chain 'E' and resid 348 through 351' Processing helix chain 'E' and resid 355 through 401 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 407 through 455 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 458 through 504 removed outlier: 3.804A pdb=" N LEU E 470 " --> pdb=" O VAL E 466 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA E 471 " --> pdb=" O ILE E 467 " (cutoff:3.500A) Proline residue: E 472 - end of helix removed outlier: 3.634A pdb=" N GLU E 494 " --> pdb=" O GLU E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 512 removed outlier: 3.806A pdb=" N TYR E 512 " --> pdb=" O LEU E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 565 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 573 through 614 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 719 through 727 Processing helix chain 'E' and resid 784 through 789 Processing helix chain 'E' and resid 796 through 806 Processing helix chain 'E' and resid 808 through 814 Processing helix chain 'E' and resid 832 through 846 Processing helix chain 'E' and resid 856 through 860 Processing helix chain 'E' and resid 863 through 880 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 894 through 897 No H-bonds generated for 'chain 'E' and resid 894 through 897' Processing helix chain 'E' and resid 914 through 919 removed outlier: 3.797A pdb=" N GLN E 918 " --> pdb=" O LEU E 914 " (cutoff:3.500A) Processing helix chain 'E' and resid 923 through 927 Processing helix chain 'E' and resid 981 through 993 Processing helix chain 'E' and resid 997 through 1008 Processing helix chain 'E' and resid 1010 through 1043 Processing helix chain 'E' and resid 1061 through 1107 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) removed outlier: 3.985A pdb=" N LEU E1107 " --> pdb=" O ASN E1103 " (cutoff:3.500A) Processing helix chain 'E' and resid 1110 through 1115 removed outlier: 3.523A pdb=" N GLU E1114 " --> pdb=" O MET E1110 " (cutoff:3.500A) Processing helix chain 'E' and resid 1118 through 1134 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 1136 through 1160 Processing helix chain 'E' and resid 1162 through 1209 removed outlier: 3.823A pdb=" N LEU E1165 " --> pdb=" O PRO E1162 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU E1169 " --> pdb=" O VAL E1166 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 4.202A pdb=" N VAL E1173 " --> pdb=" O PRO E1170 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL E1174 " --> pdb=" O LEU E1171 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS E1175 " --> pdb=" O ALA E1172 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL E1184 " --> pdb=" O TYR E1181 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG E1187 " --> pdb=" O VAL E1184 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP E1188 " --> pdb=" O ALA E1185 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU E1192 " --> pdb=" O LEU E1189 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU E1198 " --> pdb=" O THR E1195 " (cutoff:3.500A) Proline residue: E1199 - end of helix removed outlier: 3.574A pdb=" N THR E1207 " --> pdb=" O PHE E1204 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL E1208 " --> pdb=" O ALA E1205 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU E1209 " --> pdb=" O GLU E1206 " (cutoff:3.500A) Processing helix chain 'E' and resid 1211 through 1217 Processing helix chain 'E' and resid 1220 through 1274 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 1278 through 1320 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) Processing helix chain 'E' and resid 1332 through 1335 No H-bonds generated for 'chain 'E' and resid 1332 through 1335' Processing helix chain 'E' and resid 1387 through 1391 removed outlier: 3.906A pdb=" N ALA E1391 " --> pdb=" O SER E1387 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1387 through 1391' Processing helix chain 'E' and resid 1415 through 1420 Processing helix chain 'E' and resid 1436 through 1441 Processing helix chain 'E' and resid 1448 through 1458 removed outlier: 3.740A pdb=" N ILE E1457 " --> pdb=" O GLU E1453 " (cutoff:3.500A) Processing helix chain 'E' and resid 1461 through 1466 Processing helix chain 'E' and resid 1476 through 1478 No H-bonds generated for 'chain 'E' and resid 1476 through 1478' Processing helix chain 'E' and resid 1484 through 1498 removed outlier: 3.750A pdb=" N GLN E1488 " --> pdb=" O GLN E1484 " (cutoff:3.500A) Processing helix chain 'E' and resid 1513 through 1530 Processing helix chain 'E' and resid 1540 through 1543 No H-bonds generated for 'chain 'E' and resid 1540 through 1543' Processing helix chain 'E' and resid 1564 through 1569 Processing helix chain 'E' and resid 1574 through 1577 Processing sheet with id= A, 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= B, first strand: chain 'A' and resid 188 through 192 Processing sheet with id= C, first strand: chain 'A' and resid 234 through 237 Processing sheet with id= D, 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= E, first strand: chain 'B' and resid 181 through 183 Processing sheet with id= F, first strand: chain 'B' and resid 188 through 192 removed outlier: 3.718A pdb=" N VAL B 188 " --> pdb=" O MET B 199 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 234 through 236 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= H, 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= I, first strand: chain 'C' and resid 188 through 192 removed outlier: 3.961A pdb=" N VAL C 188 " --> pdb=" O MET C 199 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET C 199 " --> pdb=" O VAL C 188 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 281 through 287 removed outlier: 4.219A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG C 221 " --> pdb=" O HIS C 234 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 200 through 202 Processing sheet with id= L, first strand: chain 'D' and resid 234 through 238 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= M, first strand: chain 'D' and resid 223 through 225 removed outlier: 4.185A pdb=" N VAL D 231 " --> pdb=" O THR D 223 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 225 " --> pdb=" O GLU D 229 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU D 229 " --> pdb=" O SER D 225 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 319 through 321 Processing sheet with id= O, first strand: chain 'E' and resid 850 through 854 removed outlier: 7.729A pdb=" N THR E 883 " --> pdb=" O VAL E 851 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N LEU E 853 " --> pdb=" O THR E 883 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL E 885 " --> pdb=" O LEU E 853 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'E' and resid 1534 through 1537 removed outlier: 6.045A pdb=" N ILE E1375 " --> pdb=" O THR E1535 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ALA E1537 " --> pdb=" O ILE E1375 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE E1377 " --> pdb=" O ALA E1537 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU E1548 " --> pdb=" O GLY E1376 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N CYS E1378 " --> pdb=" O LEU E1548 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N MET E1550 " --> pdb=" O CYS E1378 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N LYS E1553 " --> pdb=" O ILE E1557 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE E1557 " --> pdb=" O LYS E1553 " (cutoff:3.500A) 1037 hydrogen bonds defined for protein. 2877 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: 6.43 Time building geometry restraints manager: 7.09 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: 100.49 - 108.38: 953 108.38 - 116.26: 11566 116.26 - 124.15: 12909 124.15 - 132.03: 394 132.03 - 139.92: 53 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 - 17.80: 10214 17.80 - 35.59: 525 35.59 - 53.39: 134 53.39 - 71.18: 42 71.18 - 88.98: 10 Dihedral angle restraints: 10925 sinusoidal: 2979 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 10922 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: 3588 2.77 - 3.30: 18802 3.30 - 3.84: 30105 3.84 - 4.37: 30639 4.37 - 4.90: 53479 Nonbonded interactions: 136613 Sorted by model distance: nonbonded pdb=" O SER B 116 " pdb=" OG SER B 119 " model vdw 2.240 2.440 nonbonded pdb=" OG1 THR A 139 " pdb=" OE1 GLU A 140 " model vdw 2.242 2.440 nonbonded pdb=" O GLY B 156 " pdb=" ND2 ASN B 160 " model vdw 2.253 2.520 nonbonded pdb=" O GLY D 156 " pdb=" ND2 ASN D 160 " model vdw 2.299 2.520 nonbonded pdb=" O ASN D 48 " pdb=" N6 ATP D 401 " model vdw 2.307 2.520 ... (remaining 136608 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.300 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 48.760 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 18779 Z= 0.101 Angle : 0.423 6.033 25875 Z= 0.215 Chirality : 0.041 0.143 3160 Planarity : 0.003 0.038 3339 Dihedral : 12.906 88.979 5744 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.36 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (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 TRP 0.009 0.001 TRP A 90 HIS 0.006 0.000 HIS C 276 PHE 0.011 0.001 PHE E 221 TYR 0.006 0.001 TYR D 268 ARG 0.002 0.000 ARG D 50 *********************** 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 fitting. rotamer outliers: 36 poor density : 758 time to evaluate : 1.781 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: 0.6084 (m-10) cc_final: 0.5453 (m-10) REVERT: A 234 HIS cc_start: 0.7073 (t-170) cc_final: 0.6795 (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: 0.7666 (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: 0.6144 (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: 0.6507 (t70) REVERT: D 44 VAL cc_start: 0.8485 (m) cc_final: 0.7341 (p) REVERT: D 76 THR cc_start: 0.9065 (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: 0.7877 (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: 0.8545 (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: 0.7312 (mt0) cc_final: 0.6558 (mt0) REVERT: D 351 GLU cc_start: 0.8011 (pp20) cc_final: 0.7715 (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: 0.7685 (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: 0.7499 (pt) REVERT: E 219 GLN cc_start: 0.7301 (tm-30) cc_final: 0.6667 (tm-30) REVERT: E 265 ARG cc_start: 0.9003 (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: 0.8054 (mm110) REVERT: E 377 TYR cc_start: 0.7947 (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: 0.6941 (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: 0.8688 (m-40) cc_final: 0.8449 (m-40) REVERT: E 1306 GLU cc_start: 0.7982 (tp30) cc_final: 0.7131 (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: 0.2784 time to fit residues: 328.9629 Evaluate side-chains 656 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 641 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 228 optimal weight: 10.0000 chunk 205 optimal weight: 0.0030 chunk 113 optimal weight: 30.0000 chunk 70 optimal weight: 2.9990 chunk 138 optimal weight: 20.0000 chunk 109 optimal weight: 30.0000 chunk 212 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 158 optimal weight: 0.8980 chunk 246 optimal weight: 0.0070 overall best weight: 2.1812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 234 HIS ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN C 160 ASN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN D 216 HIS D 299 GLN ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18779 Z= 0.171 Angle : 0.519 8.026 25875 Z= 0.273 Chirality : 0.044 0.157 3160 Planarity : 0.004 0.053 3339 Dihedral : 8.827 89.895 3041 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.45 % Allowed : 3.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 2721 helix: 1.21 (0.14), residues: 1354 sheet: -1.49 (0.30), residues: 280 loop : -2.20 (0.17), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 83 HIS 0.013 0.001 HIS C 259 PHE 0.029 0.002 PHE B 315 TYR 0.020 0.001 TYR E1294 ARG 0.004 0.000 ARG C 221 *********************** 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 726 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 720 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.7960 (m-80) cc_final: 0.7677 (m-80) REVERT: A 117 PHE cc_start: 0.8536 (t80) cc_final: 0.8136 (t80) REVERT: A 162 ILE cc_start: 0.9350 (mm) cc_final: 0.9138 (mm) REVERT: A 168 PHE cc_start: 0.7747 (t80) cc_final: 0.7426 (t80) REVERT: A 218 GLN cc_start: 0.7864 (mt0) cc_final: 0.7446 (tp40) REVERT: A 329 ASP cc_start: 0.7466 (t0) cc_final: 0.6944 (t0) REVERT: A 348 GLN cc_start: 0.8886 (mt0) cc_final: 0.8391 (mt0) REVERT: A 351 GLU cc_start: 0.8775 (mp0) cc_final: 0.8413 (mp0) REVERT: B 75 PHE cc_start: 0.7965 (m-10) cc_final: 0.7544 (m-80) REVERT: B 76 THR cc_start: 0.8968 (m) cc_final: 0.8763 (m) REVERT: B 88 MET cc_start: 0.8357 (tpp) cc_final: 0.7534 (tpp) REVERT: B 168 PHE cc_start: 0.8175 (m-80) cc_final: 0.7699 (m-80) REVERT: B 185 LYS cc_start: 0.5881 (mttp) cc_final: 0.5377 (mttm) REVERT: B 191 LEU cc_start: 0.9136 (mt) cc_final: 0.8883 (mt) REVERT: B 330 TYR cc_start: 0.7177 (m-80) cc_final: 0.6645 (m-80) REVERT: B 351 GLU cc_start: 0.7200 (mp0) cc_final: 0.6998 (mp0) REVERT: C 91 TRP cc_start: 0.6633 (t60) cc_final: 0.6172 (t60) REVERT: C 114 ILE cc_start: 0.8500 (mm) cc_final: 0.7083 (tp) REVERT: C 207 LYS cc_start: 0.7807 (mmmt) cc_final: 0.7501 (mmmt) REVERT: C 276 HIS cc_start: 0.8758 (p-80) cc_final: 0.8556 (p-80) REVERT: C 352 ASP cc_start: 0.6959 (t70) cc_final: 0.6312 (t70) REVERT: D 43 ASN cc_start: 0.6064 (m-40) cc_final: 0.5755 (p0) REVERT: D 76 THR cc_start: 0.9133 (m) cc_final: 0.8931 (m) REVERT: D 88 MET cc_start: 0.8722 (mmm) cc_final: 0.8271 (mmm) REVERT: D 122 LEU cc_start: 0.9169 (mt) cc_final: 0.8853 (mt) REVERT: D 136 ARG cc_start: 0.8826 (mpp80) cc_final: 0.8435 (mpp80) REVERT: D 147 LEU cc_start: 0.9593 (tp) cc_final: 0.9367 (tp) REVERT: D 153 ASN cc_start: 0.9441 (m-40) cc_final: 0.8904 (m-40) REVERT: D 255 LEU cc_start: 0.8548 (mt) cc_final: 0.8145 (mt) REVERT: D 258 TYR cc_start: 0.8505 (p90) cc_final: 0.8265 (p90) REVERT: D 313 GLN cc_start: 0.5572 (pp30) cc_final: 0.5238 (pp30) REVERT: D 348 GLN cc_start: 0.7035 (mt0) cc_final: 0.6150 (mt0) REVERT: D 351 GLU cc_start: 0.8272 (pp20) cc_final: 0.8041 (pp20) REVERT: D 352 ASP cc_start: 0.7770 (p0) cc_final: 0.6996 (p0) REVERT: E 112 MET cc_start: 0.8031 (mmp) cc_final: 0.7783 (mmp) REVERT: E 135 LEU cc_start: 0.9341 (mm) cc_final: 0.8987 (mm) REVERT: E 142 TYR cc_start: 0.8502 (t80) cc_final: 0.7802 (t80) REVERT: E 159 ASP cc_start: 0.7806 (t70) cc_final: 0.7601 (t0) REVERT: E 179 TYR cc_start: 0.8861 (m-80) cc_final: 0.8633 (m-80) REVERT: E 181 MET cc_start: 0.8634 (mmp) cc_final: 0.8289 (mmm) REVERT: E 219 GLN cc_start: 0.7484 (tm-30) cc_final: 0.6533 (tm-30) REVERT: E 306 ARG cc_start: 0.8406 (tpt-90) cc_final: 0.7856 (tpt-90) REVERT: E 374 GLN cc_start: 0.8576 (mm110) cc_final: 0.8012 (mm-40) REVERT: E 377 TYR cc_start: 0.8049 (m-10) cc_final: 0.7662 (m-10) REVERT: E 395 ILE cc_start: 0.9257 (mp) cc_final: 0.9042 (tp) REVERT: E 432 PHE cc_start: 0.8129 (t80) cc_final: 0.7548 (t80) REVERT: E 437 ASN cc_start: 0.9121 (t0) cc_final: 0.8400 (m-40) REVERT: E 582 LEU cc_start: 0.9511 (mt) cc_final: 0.9284 (mt) REVERT: E 614 LEU cc_start: 0.8401 (tp) cc_final: 0.8126 (tp) REVERT: E 834 GLN cc_start: 0.8916 (mt0) cc_final: 0.8662 (mt0) REVERT: E 995 LYS cc_start: 0.6812 (pttm) cc_final: 0.5997 (pttm) REVERT: E 1024 HIS cc_start: 0.7460 (m90) cc_final: 0.7076 (m90) REVERT: E 1148 LEU cc_start: 0.8946 (mp) cc_final: 0.8618 (mp) REVERT: E 1189 LEU cc_start: 0.9243 (mt) cc_final: 0.8970 (mt) REVERT: E 1231 THR cc_start: 0.8946 (p) cc_final: 0.8660 (p) REVERT: E 1235 ASN cc_start: 0.9303 (m-40) cc_final: 0.8516 (m-40) REVERT: E 1236 ILE cc_start: 0.8202 (tt) cc_final: 0.7860 (tt) REVERT: E 1314 ARG cc_start: 0.8775 (ptp-170) cc_final: 0.8479 (ptp-170) outliers start: 6 outliers final: 0 residues processed: 721 average time/residue: 0.2615 time to fit residues: 294.3114 Evaluate side-chains 628 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 628 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 136 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 204 optimal weight: 20.0000 chunk 167 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 246 optimal weight: 10.0000 chunk 266 optimal weight: 50.0000 chunk 219 optimal weight: 40.0000 chunk 244 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 197 optimal weight: 20.0000 overall best weight: 9.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 GLN A 218 GLN A 235 GLN ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN C 299 GLN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN E 105 HIS E 401 HIS E 775 GLN ** E1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 18779 Z= 0.387 Angle : 0.672 8.943 25875 Z= 0.364 Chirality : 0.046 0.159 3160 Planarity : 0.005 0.052 3339 Dihedral : 8.778 86.899 3041 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.37 % Allowed : 5.81 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.16), residues: 2721 helix: 1.12 (0.14), residues: 1359 sheet: -1.53 (0.30), residues: 289 loop : -1.95 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 83 HIS 0.012 0.002 HIS E1024 PHE 0.041 0.003 PHE D 86 TYR 0.025 0.002 TYR E1294 ARG 0.009 0.001 ARG E 74 *********************** 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 684 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 679 time to evaluate : 2.073 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 122 LEU cc_start: 0.9161 (mt) cc_final: 0.8932 (mt) REVERT: A 160 ASN cc_start: 0.8567 (t0) cc_final: 0.8327 (t0) REVERT: A 168 PHE cc_start: 0.7873 (t80) cc_final: 0.7358 (t80) REVERT: A 218 GLN cc_start: 0.8173 (tt0) cc_final: 0.7786 (mm-40) REVERT: A 329 ASP cc_start: 0.7406 (t0) cc_final: 0.6980 (t0) REVERT: A 348 GLN cc_start: 0.8991 (mt0) cc_final: 0.8513 (mt0) REVERT: A 350 ASP cc_start: 0.8687 (t0) cc_final: 0.8474 (t0) REVERT: A 351 GLU cc_start: 0.8864 (mp0) cc_final: 0.8365 (mp0) REVERT: B 88 MET cc_start: 0.8435 (tpp) cc_final: 0.7677 (tpp) REVERT: B 168 PHE cc_start: 0.8109 (m-80) cc_final: 0.7487 (m-80) REVERT: B 185 LYS cc_start: 0.6292 (mttp) cc_final: 0.5908 (mttm) REVERT: B 205 LEU cc_start: 0.8400 (mt) cc_final: 0.8184 (mt) REVERT: B 330 TYR cc_start: 0.6948 (m-80) cc_final: 0.6009 (m-80) REVERT: B 335 ASN cc_start: 0.9165 (t0) cc_final: 0.8938 (t0) REVERT: B 351 GLU cc_start: 0.7081 (mp0) cc_final: 0.6830 (mp0) REVERT: C 154 ILE cc_start: 0.8735 (mt) cc_final: 0.8448 (mt) REVERT: C 207 LYS cc_start: 0.7266 (mmmt) cc_final: 0.6806 (mmmt) REVERT: C 330 TYR cc_start: 0.8818 (m-80) cc_final: 0.8505 (m-10) REVERT: C 352 ASP cc_start: 0.7016 (t70) cc_final: 0.6428 (t70) REVERT: D 43 ASN cc_start: 0.6293 (m-40) cc_final: 0.6036 (m-40) REVERT: D 73 LEU cc_start: 0.8135 (tt) cc_final: 0.7789 (tt) REVERT: D 91 TRP cc_start: 0.8447 (t60) cc_final: 0.8207 (t60) REVERT: D 149 LEU cc_start: 0.9478 (tt) cc_final: 0.9067 (tt) REVERT: D 153 ASN cc_start: 0.9570 (m-40) cc_final: 0.8966 (m110) REVERT: D 215 ILE cc_start: 0.8801 (mt) cc_final: 0.8514 (mt) REVERT: D 255 LEU cc_start: 0.8677 (mt) cc_final: 0.8270 (mt) REVERT: D 351 GLU cc_start: 0.8313 (pp20) cc_final: 0.7847 (pp20) REVERT: E 83 PHE cc_start: 0.9337 (t80) cc_final: 0.9103 (t80) REVERT: E 112 MET cc_start: 0.8179 (mmp) cc_final: 0.7919 (mmp) REVERT: E 135 LEU cc_start: 0.9261 (mm) cc_final: 0.9018 (mm) REVERT: E 142 TYR cc_start: 0.8832 (t80) cc_final: 0.8141 (t80) REVERT: E 176 VAL cc_start: 0.9432 (t) cc_final: 0.9206 (p) REVERT: E 179 TYR cc_start: 0.9212 (m-80) cc_final: 0.8889 (m-80) REVERT: E 181 MET cc_start: 0.8582 (mmp) cc_final: 0.8361 (mmm) REVERT: E 183 LEU cc_start: 0.9063 (mm) cc_final: 0.8825 (mm) REVERT: E 186 GLU cc_start: 0.7830 (tp30) cc_final: 0.7625 (tp30) REVERT: E 219 GLN cc_start: 0.7370 (tm-30) cc_final: 0.6591 (tm-30) REVERT: E 230 TYR cc_start: 0.9195 (m-80) cc_final: 0.8920 (m-10) REVERT: E 266 LEU cc_start: 0.9345 (tp) cc_final: 0.8766 (tp) REVERT: E 270 PHE cc_start: 0.8870 (m-80) cc_final: 0.8476 (m-80) REVERT: E 306 ARG cc_start: 0.8753 (tpt-90) cc_final: 0.8397 (tpt-90) REVERT: E 374 GLN cc_start: 0.9039 (mm110) cc_final: 0.7891 (mm110) REVERT: E 377 TYR cc_start: 0.8473 (m-10) cc_final: 0.8100 (m-10) REVERT: E 383 THR cc_start: 0.9346 (p) cc_final: 0.9062 (p) REVERT: E 395 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.9068 (mp) REVERT: E 427 GLN cc_start: 0.8520 (mt0) cc_final: 0.8286 (tt0) REVERT: E 432 PHE cc_start: 0.8467 (t80) cc_final: 0.7303 (t80) REVERT: E 433 PHE cc_start: 0.8066 (m-80) cc_final: 0.7681 (m-80) REVERT: E 437 ASN cc_start: 0.8961 (t0) cc_final: 0.8435 (m110) REVERT: E 582 LEU cc_start: 0.9550 (mt) cc_final: 0.9309 (mt) REVERT: E 609 LYS cc_start: 0.9109 (ptmt) cc_final: 0.8719 (ptmm) REVERT: E 995 LYS cc_start: 0.6972 (pttm) cc_final: 0.5848 (pttm) REVERT: E 1024 HIS cc_start: 0.7561 (m90) cc_final: 0.5900 (m90) REVERT: E 1136 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8499 (tp) REVERT: E 1145 ARG cc_start: 0.8652 (tpp-160) cc_final: 0.8390 (tpp-160) REVERT: E 1148 LEU cc_start: 0.8992 (mp) cc_final: 0.8761 (mp) REVERT: E 1231 THR cc_start: 0.9228 (p) cc_final: 0.8785 (t) REVERT: E 1235 ASN cc_start: 0.9490 (m-40) cc_final: 0.8480 (m-40) REVERT: E 1249 GLU cc_start: 0.7579 (tt0) cc_final: 0.7290 (tt0) REVERT: E 1314 ARG cc_start: 0.8978 (ptp-170) cc_final: 0.8769 (ptp-170) outliers start: 5 outliers final: 1 residues processed: 679 average time/residue: 0.2693 time to fit residues: 285.4696 Evaluate side-chains 614 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 611 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 243 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 27 optimal weight: 40.0000 chunk 117 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 247 optimal weight: 0.0770 chunk 261 optimal weight: 50.0000 chunk 129 optimal weight: 20.0000 chunk 234 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN D 216 HIS ** E1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 18779 Z= 0.233 Angle : 0.555 7.260 25875 Z= 0.295 Chirality : 0.044 0.184 3160 Planarity : 0.004 0.049 3339 Dihedral : 8.482 82.289 3041 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.30 % Allowed : 4.10 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2721 helix: 1.39 (0.14), residues: 1356 sheet: -1.28 (0.31), residues: 278 loop : -1.78 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP E 514 HIS 0.009 0.001 HIS E1024 PHE 0.028 0.002 PHE D 86 TYR 0.025 0.002 TYR E 539 ARG 0.005 0.000 ARG C 221 *********************** 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 675 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 671 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 PHE cc_start: 0.8713 (t80) cc_final: 0.8338 (t80) REVERT: A 122 LEU cc_start: 0.9180 (mt) cc_final: 0.8878 (mt) REVERT: A 168 PHE cc_start: 0.7876 (t80) cc_final: 0.7538 (t80) REVERT: A 218 GLN cc_start: 0.7963 (tt0) cc_final: 0.7635 (mm-40) REVERT: A 329 ASP cc_start: 0.7138 (t0) cc_final: 0.6708 (t0) REVERT: A 348 GLN cc_start: 0.8965 (mt0) cc_final: 0.8467 (mt0) REVERT: A 351 GLU cc_start: 0.8767 (mp0) cc_final: 0.8339 (mp0) REVERT: B 75 PHE cc_start: 0.8239 (m-10) cc_final: 0.7989 (m-80) REVERT: B 88 MET cc_start: 0.8386 (tpp) cc_final: 0.7627 (tpp) REVERT: B 168 PHE cc_start: 0.8233 (m-80) cc_final: 0.7790 (m-80) REVERT: B 185 LYS cc_start: 0.6062 (mttp) cc_final: 0.5617 (mttm) REVERT: B 192 ARG cc_start: 0.9220 (tpp-160) cc_final: 0.8972 (mmm160) REVERT: B 205 LEU cc_start: 0.8456 (mt) cc_final: 0.8224 (mt) REVERT: B 215 ILE cc_start: 0.9103 (mm) cc_final: 0.8800 (pt) REVERT: B 258 TYR cc_start: 0.8820 (p90) cc_final: 0.8206 (p90) REVERT: B 330 TYR cc_start: 0.7038 (m-80) cc_final: 0.6093 (m-80) REVERT: B 351 GLU cc_start: 0.7205 (mp0) cc_final: 0.6871 (mp0) REVERT: C 71 THR cc_start: 0.8658 (p) cc_final: 0.8316 (p) REVERT: C 78 SER cc_start: 0.7721 (p) cc_final: 0.7431 (p) REVERT: C 131 ILE cc_start: 0.8645 (mt) cc_final: 0.8425 (mt) REVERT: C 192 ARG cc_start: 0.9065 (tpt-90) cc_final: 0.8486 (mmm-85) REVERT: C 207 LYS cc_start: 0.7275 (mmmt) cc_final: 0.6807 (mmmt) REVERT: C 333 PHE cc_start: 0.8283 (t80) cc_final: 0.8082 (t80) REVERT: C 352 ASP cc_start: 0.6859 (t70) cc_final: 0.6185 (t70) REVERT: D 43 ASN cc_start: 0.6332 (m-40) cc_final: 0.6065 (m-40) REVERT: D 73 LEU cc_start: 0.8020 (tt) cc_final: 0.7701 (tt) REVERT: D 84 LEU cc_start: 0.9106 (mp) cc_final: 0.8882 (mp) REVERT: D 149 LEU cc_start: 0.9427 (tt) cc_final: 0.9124 (tt) REVERT: D 153 ASN cc_start: 0.9533 (m-40) cc_final: 0.8929 (m-40) REVERT: D 255 LEU cc_start: 0.8592 (mt) cc_final: 0.8121 (mt) REVERT: E 135 LEU cc_start: 0.9215 (mm) cc_final: 0.8997 (mm) REVERT: E 142 TYR cc_start: 0.8668 (t80) cc_final: 0.8063 (t80) REVERT: E 179 TYR cc_start: 0.9130 (m-80) cc_final: 0.8804 (m-80) REVERT: E 219 GLN cc_start: 0.7373 (tm-30) cc_final: 0.7158 (tm-30) REVERT: E 230 TYR cc_start: 0.9167 (m-80) cc_final: 0.8875 (m-10) REVERT: E 306 ARG cc_start: 0.8460 (tpt-90) cc_final: 0.8056 (tpt-90) REVERT: E 366 LEU cc_start: 0.9487 (mt) cc_final: 0.9272 (mt) REVERT: E 373 LEU cc_start: 0.9589 (tt) cc_final: 0.9340 (tt) REVERT: E 374 GLN cc_start: 0.9193 (mm110) cc_final: 0.8357 (mm110) REVERT: E 383 THR cc_start: 0.9282 (p) cc_final: 0.8975 (p) REVERT: E 392 GLN cc_start: 0.9357 (mt0) cc_final: 0.9110 (mt0) REVERT: E 400 MET cc_start: 0.8305 (ttm) cc_final: 0.7947 (ttp) REVERT: E 432 PHE cc_start: 0.8672 (t80) cc_final: 0.7418 (t80) REVERT: E 437 ASN cc_start: 0.9350 (t0) cc_final: 0.9067 (m110) REVERT: E 995 LYS cc_start: 0.6770 (pttm) cc_final: 0.6402 (pttm) REVERT: E 1024 HIS cc_start: 0.7231 (m90) cc_final: 0.6887 (m90) REVERT: E 1148 LEU cc_start: 0.8933 (mp) cc_final: 0.8699 (mp) REVERT: E 1231 THR cc_start: 0.9280 (p) cc_final: 0.8974 (p) REVERT: E 1235 ASN cc_start: 0.9510 (m-40) cc_final: 0.9040 (m-40) REVERT: E 1249 GLU cc_start: 0.7795 (tt0) cc_final: 0.7380 (tt0) REVERT: E 1314 ARG cc_start: 0.8941 (ptp-170) cc_final: 0.8277 (ptp-170) REVERT: E 1354 TYR cc_start: 0.7284 (t80) cc_final: 0.6973 (t80) outliers start: 4 outliers final: 0 residues processed: 671 average time/residue: 0.2602 time to fit residues: 272.9420 Evaluate side-chains 614 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 614 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 218 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 195 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 181 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 133 optimal weight: 30.0000 chunk 235 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN C 259 HIS ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN D 216 HIS ** E1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18779 Z= 0.271 Angle : 0.587 7.766 25875 Z= 0.314 Chirality : 0.045 0.174 3160 Planarity : 0.004 0.043 3339 Dihedral : 8.416 83.969 3041 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.07 % Allowed : 4.25 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2721 helix: 1.32 (0.14), residues: 1359 sheet: -1.31 (0.31), residues: 277 loop : -1.66 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP C 83 HIS 0.009 0.001 HIS E1098 PHE 0.040 0.002 PHE C 168 TYR 0.031 0.002 TYR E1294 ARG 0.006 0.001 ARG C 221 *********************** 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 665 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 664 time to evaluate : 2.216 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 117 PHE cc_start: 0.8340 (t80) cc_final: 0.8022 (t80) REVERT: A 122 LEU cc_start: 0.9208 (mt) cc_final: 0.8919 (mt) REVERT: A 168 PHE cc_start: 0.7810 (t80) cc_final: 0.7363 (t80) REVERT: A 329 ASP cc_start: 0.7141 (t0) cc_final: 0.6729 (t0) REVERT: A 348 GLN cc_start: 0.8993 (mt0) cc_final: 0.8423 (mt0) REVERT: A 351 GLU cc_start: 0.9042 (mp0) cc_final: 0.8723 (mp0) REVERT: B 75 PHE cc_start: 0.8217 (m-10) cc_final: 0.7972 (m-80) REVERT: B 168 PHE cc_start: 0.8108 (m-80) cc_final: 0.7801 (m-80) REVERT: B 205 LEU cc_start: 0.8497 (mt) cc_final: 0.8171 (mt) REVERT: B 330 TYR cc_start: 0.6984 (m-80) cc_final: 0.6012 (m-80) REVERT: B 335 ASN cc_start: 0.9158 (t0) cc_final: 0.8859 (t0) REVERT: B 351 GLU cc_start: 0.7209 (mp0) cc_final: 0.6858 (mp0) REVERT: C 39 LYS cc_start: 0.9110 (mmtm) cc_final: 0.8692 (mmmt) REVERT: C 71 THR cc_start: 0.8644 (p) cc_final: 0.8350 (p) REVERT: C 154 ILE cc_start: 0.8780 (mt) cc_final: 0.8552 (mt) REVERT: C 192 ARG cc_start: 0.9262 (tpt-90) cc_final: 0.8850 (tpt-90) REVERT: C 207 LYS cc_start: 0.7028 (mmmt) cc_final: 0.6630 (mmmt) REVERT: C 325 ARG cc_start: 0.7916 (tpp80) cc_final: 0.7622 (tpp80) REVERT: C 333 PHE cc_start: 0.8435 (t80) cc_final: 0.8213 (t80) REVERT: C 352 ASP cc_start: 0.6853 (t70) cc_final: 0.6325 (t70) REVERT: D 43 ASN cc_start: 0.6376 (m-40) cc_final: 0.6133 (m-40) REVERT: D 147 LEU cc_start: 0.9559 (tp) cc_final: 0.9342 (tp) REVERT: D 149 LEU cc_start: 0.9442 (tt) cc_final: 0.9092 (tt) REVERT: D 153 ASN cc_start: 0.9492 (m-40) cc_final: 0.8883 (m-40) REVERT: D 198 PHE cc_start: 0.7992 (t80) cc_final: 0.7791 (t80) REVERT: D 255 LEU cc_start: 0.8656 (mt) cc_final: 0.8329 (mt) REVERT: D 263 SER cc_start: 0.8694 (t) cc_final: 0.8483 (p) REVERT: D 351 GLU cc_start: 0.7965 (pp20) cc_final: 0.7635 (pp20) REVERT: E 35 PRO cc_start: 0.9240 (Cg_exo) cc_final: 0.8815 (Cg_endo) REVERT: E 142 TYR cc_start: 0.8668 (t80) cc_final: 0.8197 (t80) REVERT: E 181 MET cc_start: 0.8835 (mmp) cc_final: 0.8479 (mmm) REVERT: E 219 GLN cc_start: 0.7452 (tm-30) cc_final: 0.7168 (tm-30) REVERT: E 230 TYR cc_start: 0.9173 (m-80) cc_final: 0.8897 (m-80) REVERT: E 306 ARG cc_start: 0.8498 (tpt-90) cc_final: 0.8097 (tpt-90) REVERT: E 366 LEU cc_start: 0.9527 (mt) cc_final: 0.9289 (mt) REVERT: E 383 THR cc_start: 0.9230 (p) cc_final: 0.8911 (p) REVERT: E 395 ILE cc_start: 0.9326 (mp) cc_final: 0.9087 (tp) REVERT: E 424 ASP cc_start: 0.7852 (t0) cc_final: 0.7632 (t0) REVERT: E 432 PHE cc_start: 0.8633 (t80) cc_final: 0.7885 (t80) REVERT: E 437 ASN cc_start: 0.9273 (t0) cc_final: 0.9063 (m110) REVERT: E 539 TYR cc_start: 0.8445 (m-80) cc_final: 0.8159 (m-80) REVERT: E 1024 HIS cc_start: 0.7218 (m90) cc_final: 0.6870 (m90) REVERT: E 1148 LEU cc_start: 0.8972 (mp) cc_final: 0.8742 (mp) REVERT: E 1197 GLN cc_start: 0.8837 (pt0) cc_final: 0.8567 (pt0) REVERT: E 1231 THR cc_start: 0.9298 (p) cc_final: 0.9001 (p) REVERT: E 1235 ASN cc_start: 0.9538 (m-40) cc_final: 0.9096 (m-40) REVERT: E 1314 ARG cc_start: 0.8946 (ptp-170) cc_final: 0.8221 (ptp-170) REVERT: E 1354 TYR cc_start: 0.7477 (t80) cc_final: 0.7188 (t80) outliers start: 1 outliers final: 1 residues processed: 664 average time/residue: 0.2687 time to fit residues: 277.0296 Evaluate side-chains 605 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 604 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 88 optimal weight: 0.8980 chunk 235 optimal weight: 20.0000 chunk 51 optimal weight: 0.7980 chunk 153 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 262 optimal weight: 30.0000 chunk 217 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 21 optimal weight: 30.0000 chunk 86 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 128 GLN ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN E 401 HIS ** E 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18779 Z= 0.273 Angle : 0.594 8.178 25875 Z= 0.315 Chirality : 0.045 0.156 3160 Planarity : 0.004 0.047 3339 Dihedral : 8.307 84.091 3041 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.17), residues: 2721 helix: 1.36 (0.14), residues: 1362 sheet: -1.19 (0.32), residues: 265 loop : -1.63 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 83 HIS 0.016 0.001 HIS E1098 PHE 0.032 0.002 PHE D 86 TYR 0.027 0.002 TYR E1294 ARG 0.007 0.001 ARG C 221 *********************** 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 667 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 667 time to evaluate : 1.988 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 117 PHE cc_start: 0.8528 (t80) cc_final: 0.8122 (t80) REVERT: A 122 LEU cc_start: 0.9255 (mt) cc_final: 0.8963 (mt) REVERT: A 168 PHE cc_start: 0.7700 (t80) cc_final: 0.7262 (t80) REVERT: A 218 GLN cc_start: 0.8340 (tp40) cc_final: 0.7511 (mm-40) REVERT: A 329 ASP cc_start: 0.7149 (t0) cc_final: 0.6748 (t0) REVERT: A 348 GLN cc_start: 0.9102 (mt0) cc_final: 0.8494 (mt0) REVERT: A 351 GLU cc_start: 0.8828 (mp0) cc_final: 0.8458 (mp0) REVERT: B 112 THR cc_start: 0.8189 (p) cc_final: 0.7699 (t) REVERT: B 168 PHE cc_start: 0.8041 (m-80) cc_final: 0.7836 (m-80) REVERT: B 205 LEU cc_start: 0.8492 (mt) cc_final: 0.8183 (mt) REVERT: B 215 ILE cc_start: 0.8987 (mm) cc_final: 0.8634 (pt) REVERT: B 249 ILE cc_start: 0.9017 (tp) cc_final: 0.8802 (tp) REVERT: B 282 GLU cc_start: 0.7323 (tm-30) cc_final: 0.6997 (tm-30) REVERT: B 330 TYR cc_start: 0.6704 (m-80) cc_final: 0.5532 (m-80) REVERT: B 351 GLU cc_start: 0.7211 (mp0) cc_final: 0.6838 (mp0) REVERT: C 39 LYS cc_start: 0.9159 (mmtm) cc_final: 0.8732 (mmmt) REVERT: C 78 SER cc_start: 0.7833 (p) cc_final: 0.7524 (p) REVERT: C 154 ILE cc_start: 0.8787 (mt) cc_final: 0.8582 (mt) REVERT: C 192 ARG cc_start: 0.9291 (tpt-90) cc_final: 0.8923 (mmm-85) REVERT: C 207 LYS cc_start: 0.6938 (mmmt) cc_final: 0.6470 (mmmt) REVERT: C 325 ARG cc_start: 0.7918 (tpp80) cc_final: 0.7647 (tpp80) REVERT: C 333 PHE cc_start: 0.8646 (t80) cc_final: 0.8289 (t80) REVERT: C 352 ASP cc_start: 0.6821 (t70) cc_final: 0.6287 (t70) REVERT: D 43 ASN cc_start: 0.6462 (m-40) cc_final: 0.6203 (m-40) REVERT: D 84 LEU cc_start: 0.9139 (mp) cc_final: 0.8879 (mp) REVERT: D 149 LEU cc_start: 0.9437 (tt) cc_final: 0.9084 (tt) REVERT: D 153 ASN cc_start: 0.9510 (m-40) cc_final: 0.8943 (m-40) REVERT: D 222 LYS cc_start: 0.8715 (tptp) cc_final: 0.8430 (tptp) REVERT: D 255 LEU cc_start: 0.8625 (mt) cc_final: 0.8128 (mt) REVERT: D 258 TYR cc_start: 0.8646 (p90) cc_final: 0.8389 (p90) REVERT: D 351 GLU cc_start: 0.7981 (pp20) cc_final: 0.7635 (pp20) REVERT: E 39 LEU cc_start: 0.9051 (tp) cc_final: 0.8829 (tp) REVERT: E 142 TYR cc_start: 0.8707 (t80) cc_final: 0.8100 (t80) REVERT: E 181 MET cc_start: 0.8779 (mmp) cc_final: 0.8511 (mmm) REVERT: E 230 TYR cc_start: 0.9175 (m-80) cc_final: 0.8803 (m-80) REVERT: E 306 ARG cc_start: 0.8818 (tpt-90) cc_final: 0.8284 (tpt-90) REVERT: E 366 LEU cc_start: 0.9526 (mt) cc_final: 0.9227 (mt) REVERT: E 395 ILE cc_start: 0.9343 (mp) cc_final: 0.9070 (tp) REVERT: E 437 ASN cc_start: 0.9287 (t0) cc_final: 0.9070 (m-40) REVERT: E 1024 HIS cc_start: 0.7108 (m90) cc_final: 0.6832 (m90) REVERT: E 1148 LEU cc_start: 0.8966 (mp) cc_final: 0.8726 (mp) REVERT: E 1197 GLN cc_start: 0.8869 (pt0) cc_final: 0.8598 (pt0) REVERT: E 1231 THR cc_start: 0.9315 (p) cc_final: 0.8996 (p) REVERT: E 1235 ASN cc_start: 0.9555 (m-40) cc_final: 0.9117 (m-40) REVERT: E 1253 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8510 (mt-10) REVERT: E 1354 TYR cc_start: 0.7309 (t80) cc_final: 0.7063 (t80) outliers start: 0 outliers final: 0 residues processed: 667 average time/residue: 0.2665 time to fit residues: 278.6653 Evaluate side-chains 607 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 607 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 252 optimal weight: 2.9990 chunk 29 optimal weight: 50.0000 chunk 149 optimal weight: 30.0000 chunk 191 optimal weight: 50.0000 chunk 148 optimal weight: 40.0000 chunk 220 optimal weight: 20.0000 chunk 146 optimal weight: 8.9990 chunk 261 optimal weight: 50.0000 chunk 163 optimal weight: 0.9990 chunk 159 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 218 GLN A 335 ASN B 70 HIS ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN D 216 HIS E 105 HIS ** E 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18779 Z= 0.249 Angle : 0.592 7.912 25875 Z= 0.313 Chirality : 0.045 0.166 3160 Planarity : 0.004 0.057 3339 Dihedral : 8.162 84.220 3041 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.17), residues: 2721 helix: 1.38 (0.14), residues: 1361 sheet: -1.18 (0.32), residues: 262 loop : -1.61 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 83 HIS 0.007 0.001 HIS E1024 PHE 0.029 0.002 PHE C 168 TYR 0.023 0.002 TYR E1294 ARG 0.009 0.001 ARG A 347 *********************** 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 665 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 665 time to evaluate : 1.974 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 48 ASN cc_start: 0.6896 (t0) cc_final: 0.5917 (t0) REVERT: A 117 PHE cc_start: 0.8711 (t80) cc_final: 0.8313 (t80) REVERT: A 122 LEU cc_start: 0.9237 (mt) cc_final: 0.8969 (mt) REVERT: A 168 PHE cc_start: 0.7655 (t80) cc_final: 0.7271 (t80) REVERT: A 218 GLN cc_start: 0.8393 (tp-100) cc_final: 0.7575 (mm-40) REVERT: A 258 TYR cc_start: 0.8478 (p90) cc_final: 0.7850 (p90) REVERT: A 329 ASP cc_start: 0.7182 (t0) cc_final: 0.6789 (t0) REVERT: A 348 GLN cc_start: 0.9030 (mt0) cc_final: 0.8509 (mt0) REVERT: A 351 GLU cc_start: 0.8803 (mp0) cc_final: 0.8165 (mp0) REVERT: B 75 PHE cc_start: 0.7491 (m-80) cc_final: 0.7261 (m-80) REVERT: B 112 THR cc_start: 0.8108 (p) cc_final: 0.7738 (t) REVERT: B 192 ARG cc_start: 0.9177 (tpp-160) cc_final: 0.8914 (mmm160) REVERT: B 205 LEU cc_start: 0.8484 (mt) cc_final: 0.8173 (mt) REVERT: B 215 ILE cc_start: 0.9015 (mm) cc_final: 0.8673 (pt) REVERT: B 249 ILE cc_start: 0.9037 (tp) cc_final: 0.8791 (tp) REVERT: B 330 TYR cc_start: 0.6793 (m-80) cc_final: 0.5484 (m-80) REVERT: B 335 ASN cc_start: 0.9123 (t0) cc_final: 0.8922 (t0) REVERT: B 351 GLU cc_start: 0.7235 (mp0) cc_final: 0.6842 (mp0) REVERT: C 39 LYS cc_start: 0.9177 (mmtm) cc_final: 0.8757 (mmmt) REVERT: C 192 ARG cc_start: 0.9311 (tpt-90) cc_final: 0.8931 (mmm-85) REVERT: C 207 LYS cc_start: 0.6920 (mmmt) cc_final: 0.6461 (mmmt) REVERT: C 325 ARG cc_start: 0.7875 (tpp80) cc_final: 0.7649 (tpp80) REVERT: C 333 PHE cc_start: 0.8673 (t80) cc_final: 0.8273 (t80) REVERT: C 352 ASP cc_start: 0.6692 (t70) cc_final: 0.6191 (t70) REVERT: D 43 ASN cc_start: 0.6472 (m-40) cc_final: 0.6207 (m-40) REVERT: D 222 LYS cc_start: 0.8706 (tptp) cc_final: 0.8439 (tptp) REVERT: D 255 LEU cc_start: 0.8575 (mt) cc_final: 0.8111 (mt) REVERT: D 258 TYR cc_start: 0.8649 (p90) cc_final: 0.8392 (p90) REVERT: D 351 GLU cc_start: 0.7977 (pp20) cc_final: 0.7619 (pp20) REVERT: E 35 PRO cc_start: 0.9231 (Cg_exo) cc_final: 0.8827 (Cg_endo) REVERT: E 39 LEU cc_start: 0.9021 (tp) cc_final: 0.8784 (tp) REVERT: E 142 TYR cc_start: 0.8763 (t80) cc_final: 0.8305 (t80) REVERT: E 181 MET cc_start: 0.8731 (mmp) cc_final: 0.8420 (mmm) REVERT: E 218 LEU cc_start: 0.7932 (pt) cc_final: 0.7689 (pt) REVERT: E 219 GLN cc_start: 0.7399 (tm-30) cc_final: 0.6783 (tm-30) REVERT: E 230 TYR cc_start: 0.9171 (m-80) cc_final: 0.8798 (m-80) REVERT: E 306 ARG cc_start: 0.8525 (tpt-90) cc_final: 0.8105 (tpt-90) REVERT: E 366 LEU cc_start: 0.9540 (mt) cc_final: 0.9260 (mt) REVERT: E 377 TYR cc_start: 0.8434 (m-10) cc_final: 0.8215 (m-80) REVERT: E 395 ILE cc_start: 0.9225 (mp) cc_final: 0.8969 (tp) REVERT: E 546 MET cc_start: 0.8264 (mmp) cc_final: 0.8027 (mmp) REVERT: E 1024 HIS cc_start: 0.7028 (m90) cc_final: 0.6808 (m90) REVERT: E 1148 LEU cc_start: 0.8891 (mp) cc_final: 0.8675 (mp) REVERT: E 1197 GLN cc_start: 0.8837 (pt0) cc_final: 0.8621 (pt0) REVERT: E 1231 THR cc_start: 0.9296 (p) cc_final: 0.8990 (p) REVERT: E 1235 ASN cc_start: 0.9560 (m-40) cc_final: 0.9173 (m-40) REVERT: E 1253 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8480 (mt-10) REVERT: E 1354 TYR cc_start: 0.7295 (t80) cc_final: 0.7081 (t80) outliers start: 0 outliers final: 0 residues processed: 665 average time/residue: 0.2625 time to fit residues: 273.6629 Evaluate side-chains 602 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 602 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 161 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 78 optimal weight: 30.0000 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 30.0000 chunk 166 optimal weight: 20.0000 chunk 177 optimal weight: 8.9990 chunk 129 optimal weight: 0.4980 chunk 24 optimal weight: 6.9990 chunk 205 optimal weight: 50.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 335 ASN ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN C 259 HIS C 348 GLN D 153 ASN D 299 GLN ** D 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS ** E 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 18779 Z= 0.229 Angle : 0.597 9.264 25875 Z= 0.311 Chirality : 0.045 0.215 3160 Planarity : 0.004 0.082 3339 Dihedral : 8.009 87.717 3041 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.17), residues: 2721 helix: 1.46 (0.14), residues: 1359 sheet: -1.25 (0.32), residues: 274 loop : -1.53 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 83 HIS 0.009 0.001 HIS B 259 PHE 0.027 0.002 PHE B 168 TYR 0.027 0.002 TYR E1294 ARG 0.008 0.001 ARG C 221 *********************** 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 662 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 661 time to evaluate : 1.984 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 48 ASN cc_start: 0.6935 (t0) cc_final: 0.5956 (t0) REVERT: A 68 TRP cc_start: 0.6809 (m100) cc_final: 0.6208 (m-10) REVERT: A 117 PHE cc_start: 0.8659 (t80) cc_final: 0.8279 (t80) REVERT: A 168 PHE cc_start: 0.7681 (t80) cc_final: 0.7265 (t80) REVERT: A 329 ASP cc_start: 0.7344 (t0) cc_final: 0.7052 (t0) REVERT: A 348 GLN cc_start: 0.9031 (mt0) cc_final: 0.8530 (mt0) REVERT: A 350 ASP cc_start: 0.8166 (t0) cc_final: 0.7895 (t0) REVERT: A 351 GLU cc_start: 0.8805 (mp0) cc_final: 0.8178 (mp0) REVERT: B 75 PHE cc_start: 0.7559 (m-80) cc_final: 0.7351 (m-80) REVERT: B 192 ARG cc_start: 0.9134 (tpp-160) cc_final: 0.8907 (mmm160) REVERT: B 205 LEU cc_start: 0.8445 (mt) cc_final: 0.8040 (mt) REVERT: B 215 ILE cc_start: 0.8983 (mm) cc_final: 0.8650 (pt) REVERT: B 249 ILE cc_start: 0.9061 (tp) cc_final: 0.8813 (tp) REVERT: B 282 GLU cc_start: 0.7320 (tm-30) cc_final: 0.7021 (tm-30) REVERT: B 330 TYR cc_start: 0.6659 (m-80) cc_final: 0.5448 (m-80) REVERT: B 351 GLU cc_start: 0.7285 (mp0) cc_final: 0.6843 (mp0) REVERT: C 39 LYS cc_start: 0.9193 (mmtm) cc_final: 0.8756 (mmmt) REVERT: C 78 SER cc_start: 0.7877 (p) cc_final: 0.7586 (p) REVERT: C 192 ARG cc_start: 0.9197 (tpt-90) cc_final: 0.8793 (mmm-85) REVERT: C 207 LYS cc_start: 0.6924 (mmmt) cc_final: 0.6447 (mmmt) REVERT: C 333 PHE cc_start: 0.8756 (t80) cc_final: 0.8311 (t80) REVERT: C 352 ASP cc_start: 0.6659 (t70) cc_final: 0.6164 (t70) REVERT: D 43 ASN cc_start: 0.6484 (m-40) cc_final: 0.6232 (m-40) REVERT: D 222 LYS cc_start: 0.8709 (tptp) cc_final: 0.8411 (tptp) REVERT: D 255 LEU cc_start: 0.8575 (mt) cc_final: 0.8061 (mt) REVERT: D 258 TYR cc_start: 0.8638 (p90) cc_final: 0.8392 (p90) REVERT: D 351 GLU cc_start: 0.7956 (pp20) cc_final: 0.7593 (pp20) REVERT: E 39 LEU cc_start: 0.9030 (tp) cc_final: 0.8814 (tp) REVERT: E 142 TYR cc_start: 0.8633 (t80) cc_final: 0.8088 (t80) REVERT: E 181 MET cc_start: 0.8729 (mmp) cc_final: 0.8421 (mmm) REVERT: E 230 TYR cc_start: 0.9154 (m-80) cc_final: 0.8760 (m-80) REVERT: E 377 TYR cc_start: 0.8589 (m-10) cc_final: 0.8380 (m-80) REVERT: E 527 ARG cc_start: 0.6875 (mmp80) cc_final: 0.6421 (mmp80) REVERT: E 546 MET cc_start: 0.8314 (mmp) cc_final: 0.8090 (mmp) REVERT: E 1024 HIS cc_start: 0.6876 (m90) cc_final: 0.6666 (m90) REVERT: E 1148 LEU cc_start: 0.8989 (mp) cc_final: 0.8747 (mp) REVERT: E 1231 THR cc_start: 0.9296 (p) cc_final: 0.8986 (p) REVERT: E 1235 ASN cc_start: 0.9537 (m-40) cc_final: 0.9150 (m-40) REVERT: E 1253 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8461 (mt-10) REVERT: E 1354 TYR cc_start: 0.7294 (t80) cc_final: 0.7080 (t80) outliers start: 1 outliers final: 1 residues processed: 661 average time/residue: 0.2633 time to fit residues: 272.9762 Evaluate side-chains 614 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 613 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 237 optimal weight: 20.0000 chunk 250 optimal weight: 20.0000 chunk 228 optimal weight: 7.9990 chunk 243 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 106 optimal weight: 0.0980 chunk 191 optimal weight: 50.0000 chunk 74 optimal weight: 6.9990 chunk 219 optimal weight: 30.0000 chunk 230 optimal weight: 30.0000 chunk 242 optimal weight: 3.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 218 GLN ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 HIS C 348 GLN D 216 HIS D 299 GLN D 335 ASN ** E 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18779 Z= 0.229 Angle : 0.598 7.890 25875 Z= 0.312 Chirality : 0.045 0.199 3160 Planarity : 0.004 0.071 3339 Dihedral : 7.880 86.595 3041 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 2721 helix: 1.46 (0.14), residues: 1356 sheet: -1.10 (0.32), residues: 265 loop : -1.53 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 83 HIS 0.011 0.001 HIS A 97 PHE 0.033 0.002 PHE C 168 TYR 0.028 0.002 TYR E1294 ARG 0.007 0.001 ARG C 221 *********************** 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 656 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 656 time to evaluate : 1.956 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: 0.6184 (t0) REVERT: A 68 TRP cc_start: 0.6705 (m100) cc_final: 0.6238 (m-10) REVERT: A 117 PHE cc_start: 0.8716 (t80) cc_final: 0.8315 (t80) REVERT: A 122 LEU cc_start: 0.9266 (mt) cc_final: 0.8988 (mt) REVERT: A 168 PHE cc_start: 0.7582 (t80) cc_final: 0.7057 (t80) REVERT: A 218 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7698 (mm-40) REVERT: A 329 ASP cc_start: 0.7353 (t0) cc_final: 0.7040 (t0) REVERT: A 348 GLN cc_start: 0.9017 (mt0) cc_final: 0.8569 (mt0) REVERT: A 351 GLU cc_start: 0.8883 (mp0) cc_final: 0.8471 (mp0) REVERT: B 192 ARG cc_start: 0.9140 (tpp-160) cc_final: 0.8906 (mmm160) REVERT: B 205 LEU cc_start: 0.8417 (mt) cc_final: 0.8024 (mt) REVERT: B 215 ILE cc_start: 0.9018 (mm) cc_final: 0.8662 (pt) REVERT: B 249 ILE cc_start: 0.9054 (tp) cc_final: 0.8789 (tp) REVERT: B 282 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6993 (tm-30) REVERT: B 330 TYR cc_start: 0.6562 (m-80) cc_final: 0.5913 (m-80) REVERT: B 351 GLU cc_start: 0.7289 (mp0) cc_final: 0.6823 (mp0) REVERT: C 39 LYS cc_start: 0.9209 (mmtm) cc_final: 0.8727 (mmmt) REVERT: C 78 SER cc_start: 0.7901 (p) cc_final: 0.7575 (p) REVERT: C 192 ARG cc_start: 0.9206 (tpt-90) cc_final: 0.8872 (mmm-85) REVERT: C 207 LYS cc_start: 0.6897 (mmmt) cc_final: 0.6422 (mmmt) REVERT: C 315 PHE cc_start: 0.8372 (m-80) cc_final: 0.8050 (m-80) REVERT: C 333 PHE cc_start: 0.8710 (t80) cc_final: 0.8238 (t80) REVERT: C 352 ASP cc_start: 0.6637 (t70) cc_final: 0.6139 (t70) REVERT: D 43 ASN cc_start: 0.6402 (m-40) cc_final: 0.6149 (m-40) REVERT: D 222 LYS cc_start: 0.8709 (tptp) cc_final: 0.8419 (tptp) REVERT: D 258 TYR cc_start: 0.8660 (p90) cc_final: 0.8386 (p90) REVERT: D 299 GLN cc_start: 0.8645 (tp40) cc_final: 0.8412 (tp-100) REVERT: D 351 GLU cc_start: 0.7947 (pp20) cc_final: 0.7562 (pp20) REVERT: E 35 PRO cc_start: 0.9222 (Cg_exo) cc_final: 0.8828 (Cg_endo) REVERT: E 142 TYR cc_start: 0.8634 (t80) cc_final: 0.8179 (t80) REVERT: E 181 MET cc_start: 0.8735 (mmp) cc_final: 0.8406 (mmm) REVERT: E 219 GLN cc_start: 0.7675 (tm-30) cc_final: 0.7160 (tm-30) REVERT: E 230 TYR cc_start: 0.9143 (m-80) cc_final: 0.8738 (m-80) REVERT: E 539 TYR cc_start: 0.8359 (m-80) cc_final: 0.7911 (m-80) REVERT: E 1147 THR cc_start: 0.9246 (m) cc_final: 0.8504 (m) REVERT: E 1148 LEU cc_start: 0.9027 (mp) cc_final: 0.8708 (mp) REVERT: E 1230 TYR cc_start: 0.7877 (m-80) cc_final: 0.7585 (m-80) REVERT: E 1231 THR cc_start: 0.9292 (p) cc_final: 0.8961 (p) REVERT: E 1235 ASN cc_start: 0.9558 (m-40) cc_final: 0.9175 (m-40) REVERT: E 1253 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8384 (mt-10) outliers start: 0 outliers final: 0 residues processed: 656 average time/residue: 0.2708 time to fit residues: 280.4909 Evaluate side-chains 607 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 607 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 159 optimal weight: 9.9990 chunk 257 optimal weight: 50.0000 chunk 157 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 178 optimal weight: 20.0000 chunk 269 optimal weight: 50.0000 chunk 248 optimal weight: 50.0000 chunk 214 optimal weight: 2.9990 chunk 22 optimal weight: 30.0000 chunk 166 optimal weight: 7.9990 chunk 131 optimal weight: 20.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 HIS B 97 HIS ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN C 259 HIS C 348 GLN D 153 ASN ** E 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 18779 Z= 0.319 Angle : 0.665 9.833 25875 Z= 0.352 Chirality : 0.046 0.226 3160 Planarity : 0.005 0.070 3339 Dihedral : 8.024 84.494 3041 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.07 % Allowed : 0.75 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 2721 helix: 1.20 (0.14), residues: 1358 sheet: -1.12 (0.32), residues: 262 loop : -1.61 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 83 HIS 0.009 0.001 HIS A 97 PHE 0.054 0.003 PHE E 433 TYR 0.027 0.002 TYR A 258 ARG 0.010 0.001 ARG A 347 ********************** 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 643 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 642 time to evaluate : 1.914 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 48 ASN cc_start: 0.6830 (t0) cc_final: 0.5946 (t0) REVERT: A 68 TRP cc_start: 0.6823 (m100) cc_final: 0.6255 (m-10) REVERT: A 117 PHE cc_start: 0.8611 (t80) cc_final: 0.8233 (t80) REVERT: A 122 LEU cc_start: 0.9291 (mt) cc_final: 0.8968 (mt) REVERT: A 155 VAL cc_start: 0.8782 (m) cc_final: 0.8062 (t) REVERT: A 168 PHE cc_start: 0.7697 (t80) cc_final: 0.7101 (t80) REVERT: A 218 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7580 (mm110) REVERT: A 329 ASP cc_start: 0.7334 (t0) cc_final: 0.7029 (t0) REVERT: A 348 GLN cc_start: 0.9022 (mt0) cc_final: 0.8464 (mt0) REVERT: A 351 GLU cc_start: 0.8924 (mp0) cc_final: 0.8487 (mp0) REVERT: B 131 ILE cc_start: 0.9618 (mt) cc_final: 0.9376 (mt) REVERT: B 133 PHE cc_start: 0.8433 (m-10) cc_final: 0.8217 (m-10) REVERT: B 192 ARG cc_start: 0.9172 (tpp-160) cc_final: 0.8914 (mmm160) REVERT: B 205 LEU cc_start: 0.8279 (mt) cc_final: 0.7758 (mt) REVERT: B 215 ILE cc_start: 0.9020 (mm) cc_final: 0.8652 (pt) REVERT: B 249 ILE cc_start: 0.9088 (tp) cc_final: 0.8830 (tp) REVERT: B 282 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6990 (tm-30) REVERT: B 330 TYR cc_start: 0.6972 (m-80) cc_final: 0.5688 (m-80) REVERT: B 333 PHE cc_start: 0.8052 (m-80) cc_final: 0.7823 (m-80) REVERT: B 351 GLU cc_start: 0.7280 (mp0) cc_final: 0.6813 (mp0) REVERT: C 39 LYS cc_start: 0.9108 (mmtm) cc_final: 0.8689 (mmmt) REVERT: C 78 SER cc_start: 0.8060 (p) cc_final: 0.7852 (p) REVERT: C 192 ARG cc_start: 0.9163 (tpt-90) cc_final: 0.8814 (mmm-85) REVERT: C 207 LYS cc_start: 0.6834 (mmmt) cc_final: 0.6385 (mmmt) REVERT: C 315 PHE cc_start: 0.8460 (m-80) cc_final: 0.8114 (m-80) REVERT: C 325 ARG cc_start: 0.7954 (tpp80) cc_final: 0.7721 (tpp80) REVERT: C 333 PHE cc_start: 0.8826 (t80) cc_final: 0.8623 (t80) REVERT: C 352 ASP cc_start: 0.6622 (t70) cc_final: 0.6143 (t70) REVERT: D 43 ASN cc_start: 0.6471 (m-40) cc_final: 0.6201 (m-40) REVERT: D 222 LYS cc_start: 0.8735 (tptp) cc_final: 0.8457 (tptp) REVERT: D 258 TYR cc_start: 0.8667 (p90) cc_final: 0.8377 (p90) REVERT: D 279 GLN cc_start: 0.7056 (tm-30) cc_final: 0.6608 (tp40) REVERT: D 299 GLN cc_start: 0.8636 (tp40) cc_final: 0.8425 (tp-100) REVERT: D 351 GLU cc_start: 0.8041 (pp20) cc_final: 0.7654 (pp20) REVERT: E 35 PRO cc_start: 0.9191 (Cg_exo) cc_final: 0.8865 (Cg_endo) REVERT: E 142 TYR cc_start: 0.8740 (t80) cc_final: 0.8311 (t80) REVERT: E 179 TYR cc_start: 0.9121 (m-80) cc_final: 0.8903 (m-80) REVERT: E 181 MET cc_start: 0.8854 (mmp) cc_final: 0.8543 (mmm) REVERT: E 219 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7717 (tm-30) REVERT: E 230 TYR cc_start: 0.9216 (m-80) cc_final: 0.8796 (m-80) REVERT: E 306 ARG cc_start: 0.8807 (tpt-90) cc_final: 0.8280 (tpt-90) REVERT: E 539 TYR cc_start: 0.8386 (m-80) cc_final: 0.7930 (m-80) REVERT: E 1024 HIS cc_start: 0.6616 (m90) cc_final: 0.5078 (m90) REVERT: E 1136 ILE cc_start: 0.8957 (mp) cc_final: 0.8684 (mp) REVERT: E 1145 ARG cc_start: 0.8173 (tpp-160) cc_final: 0.7651 (tpp-160) REVERT: E 1148 LEU cc_start: 0.9099 (mp) cc_final: 0.8828 (mp) REVERT: E 1230 TYR cc_start: 0.7966 (m-80) cc_final: 0.7643 (m-80) REVERT: E 1231 THR cc_start: 0.9276 (p) cc_final: 0.8966 (p) REVERT: E 1235 ASN cc_start: 0.9595 (m-40) cc_final: 0.9146 (m-40) REVERT: E 1292 SER cc_start: 0.8822 (p) cc_final: 0.8361 (t) outliers start: 1 outliers final: 1 residues processed: 642 average time/residue: 0.2667 time to fit residues: 271.0739 Evaluate side-chains 586 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 585 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 170 optimal weight: 8.9990 chunk 229 optimal weight: 0.8980 chunk 65 optimal weight: 20.0000 chunk 198 optimal weight: 0.8980 chunk 31 optimal weight: 30.0000 chunk 59 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 90 optimal weight: 0.7980 chunk 221 optimal weight: 40.0000 chunk 27 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 overall best weight: 2.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 HIS ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN D 216 HIS D 335 ASN E 427 GLN ** E 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1308 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.155954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.131389 restraints weight = 41310.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.134798 restraints weight = 25551.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.137121 restraints weight = 16178.620| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18779 Z= 0.185 Angle : 0.601 15.255 25875 Z= 0.306 Chirality : 0.045 0.224 3160 Planarity : 0.004 0.061 3339 Dihedral : 7.686 84.807 3041 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.17), residues: 2721 helix: 1.43 (0.14), residues: 1355 sheet: -0.98 (0.33), residues: 265 loop : -1.47 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 83 HIS 0.016 0.001 HIS E1098 PHE 0.043 0.002 PHE E 433 TYR 0.023 0.001 TYR E1294 ARG 0.009 0.001 ARG A 347 =============================================================================== Job complete usr+sys time: 4764.98 seconds wall clock time: 85 minutes 21.33 seconds (5121.33 seconds total)