Starting phenix.real_space_refine on Fri Nov 17 07:11:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1e_26299/11_2023/7u1e_26299_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1e_26299/11_2023/7u1e_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_26299/11_2023/7u1e_26299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1e_26299/11_2023/7u1e_26299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1e_26299/11_2023/7u1e_26299_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1e_26299/11_2023/7u1e_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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 chiralities: 1 Time building chain proxies: 10.32, 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: 7.41 Conformation dependent library (CDL) restraints added in 4.2 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: 4.62 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: 6.64 Time building geometry restraints manager: 7.91 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 - 17.68: 10146 17.68 - 35.35: 495 35.35 - 53.03: 93 53.03 - 70.71: 10 70.71 - 88.38: 5 Dihedral angle restraints: 10749 sinusoidal: 2803 harmonic: 7946 Sorted by residual: dihedral pdb=" N PHE B 315 " pdb=" CA PHE B 315 " pdb=" CB PHE B 315 " pdb=" CG PHE B 315 " ideal model delta sinusoidal sigma weight residual -60.00 -118.98 58.98 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA GLN A 57 " pdb=" CB GLN A 57 " pdb=" CG GLN A 57 " pdb=" CD GLN A 57 " ideal model delta sinusoidal sigma weight residual -60.00 -118.87 58.87 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LEU A 349 " pdb=" CA LEU A 349 " pdb=" CB LEU A 349 " pdb=" CG LEU A 349 " ideal model delta sinusoidal sigma weight residual -60.00 -117.45 57.45 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 10746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1943 0.029 - 0.057: 747 0.057 - 0.086: 252 0.086 - 0.114: 194 0.114 - 0.143: 24 Chirality restraints: 3160 Sorted by residual: chirality pdb=" CB THR C 214 " pdb=" CA THR C 214 " pdb=" OG1 THR C 214 " pdb=" CG2 THR C 214 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA ILE A 189 " pdb=" N ILE A 189 " pdb=" C ILE A 189 " pdb=" CB ILE A 189 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA ILE B 283 " pdb=" N ILE B 283 " pdb=" C ILE B 283 " pdb=" CB ILE B 283 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 3157 not shown) Planarity restraints: 3340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 101 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO A 102 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 339 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO A 340 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 340 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 340 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E1198 " -0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO E1199 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO E1199 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO E1199 " -0.016 5.00e-02 4.00e+02 ... (remaining 3337 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 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: 0.030 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: 1.420 Check model and map are aligned: 0.290 Set scattering table: 0.160 Process input model: 51.630 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.090 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.720 ------------------------------------------------------------------------------- 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 : 11.182 88.382 5568 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 *********************** 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 : 2.065 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 outliers start: 36 outliers final: 9 residues processed: 771 average time/residue: 0.2850 time to fit residues: 338.7158 Evaluate side-chains 635 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 626 time to evaluate : 1.869 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1927 time to fit residues: 5.5806 ------------------------------------------------------------------------------- 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: 20.0000 chunk 70 optimal weight: 0.9990 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: 1.7812 ------------------------------------------------------------------------------- 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** 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 E1235 ASN ** E1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18779 Z= 0.166 Angle : 0.525 8.284 25875 Z= 0.274 Chirality : 0.044 0.244 3160 Planarity : 0.004 0.075 3339 Dihedral : 4.067 67.302 2865 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.60 % Allowed : 4.32 % Favored : 95.08 % 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: 1.20 (0.14), residues: 1354 sheet: -1.43 (0.31), residues: 267 loop : -2.19 (0.17), residues: 1100 *********************** 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 723 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 715 time to evaluate : 1.967 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 outliers start: 8 outliers final: 0 residues processed: 716 average time/residue: 0.2693 time to fit residues: 302.5554 Evaluate side-chains 618 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 618 time to evaluate : 1.879 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4865 ------------------------------------------------------------------------------- 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: 9.9990 chunk 204 optimal weight: 20.0000 chunk 167 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 246 optimal weight: 0.9980 chunk 266 optimal weight: 6.9990 chunk 219 optimal weight: 50.0000 chunk 244 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 197 optimal weight: 30.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 264 ASN C 299 GLN C 348 GLN ** D 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS E 401 HIS E 775 GLN E 817 HIS E1225 GLN E1235 ASN ** E1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18779 Z= 0.224 Angle : 0.553 11.670 25875 Z= 0.295 Chirality : 0.044 0.213 3160 Planarity : 0.004 0.049 3339 Dihedral : 4.322 62.952 2865 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.37 % Allowed : 4.40 % Favored : 95.23 % 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: 1.42 (0.14), residues: 1358 sheet: -1.45 (0.30), residues: 292 loop : -1.84 (0.18), residues: 1071 *********************** 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 698 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 693 time to evaluate : 1.835 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 outliers start: 5 outliers final: 1 residues processed: 693 average time/residue: 0.2829 time to fit residues: 305.4510 Evaluate side-chains 605 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 604 time to evaluate : 2.051 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1543 time to fit residues: 3.0132 ------------------------------------------------------------------------------- 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: 7.9990 chunk 185 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 27 optimal weight: 40.0000 chunk 117 optimal weight: 20.0000 chunk 165 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 261 optimal weight: 50.0000 chunk 129 optimal weight: 7.9990 chunk 234 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 overall best weight: 6.7788 ------------------------------------------------------------------------------- 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 335 ASN B 70 HIS ** 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 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS D 279 GLN ** D 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS E 437 ASN E1225 GLN ** E1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 18779 Z= 0.288 Angle : 0.604 11.672 25875 Z= 0.322 Chirality : 0.045 0.173 3160 Planarity : 0.004 0.048 3339 Dihedral : 4.755 62.647 2865 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.30 % Allowed : 4.32 % Favored : 95.38 % 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: -0.15 (0.16), residues: 2721 helix: 1.39 (0.14), residues: 1358 sheet: -1.31 (0.31), residues: 275 loop : -1.73 (0.18), residues: 1088 *********************** 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 677 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 673 time to evaluate : 2.008 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 outliers start: 4 outliers final: 0 residues processed: 674 average time/residue: 0.2737 time to fit residues: 289.1919 Evaluate side-chains 590 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 590 time to evaluate : 1.894 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5697 ------------------------------------------------------------------------------- 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: 9.9990 chunk 3 optimal weight: 10.0000 chunk 195 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 chunk 223 optimal weight: 40.0000 chunk 181 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 133 optimal weight: 40.0000 chunk 235 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 overall best weight: 7.9588 ------------------------------------------------------------------------------- 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 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 HIS ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN ** D 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 18779 Z= 0.318 Angle : 0.629 12.510 25875 Z= 0.336 Chirality : 0.046 0.234 3160 Planarity : 0.005 0.041 3339 Dihedral : 4.966 65.714 2865 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % 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: -0.23 (0.16), residues: 2721 helix: 1.28 (0.14), residues: 1356 sheet: -1.15 (0.31), residues: 270 loop : -1.76 (0.18), residues: 1095 *********************** 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 663 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 662 time to evaluate : 2.138 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 outliers start: 1 outliers final: 0 residues processed: 662 average time/residue: 0.2745 time to fit residues: 285.5609 Evaluate side-chains 588 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 588 time to evaluate : 2.122 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9286 ------------------------------------------------------------------------------- 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: 0.0670 chunk 235 optimal weight: 20.0000 chunk 51 optimal weight: 0.0000 chunk 153 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 262 optimal weight: 30.0000 chunk 217 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 chunk 21 optimal weight: 0.5980 chunk 86 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 overall best weight: 6.1330 ------------------------------------------------------------------------------- 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** ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN C 193 HIS C 259 HIS C 348 GLN D 216 HIS ** D 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7708 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 18779 Z= 0.269 Angle : 0.599 10.619 25875 Z= 0.317 Chirality : 0.045 0.237 3160 Planarity : 0.004 0.033 3339 Dihedral : 4.931 65.084 2865 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % 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: -0.10 (0.16), residues: 2721 helix: 1.33 (0.14), residues: 1370 sheet: -1.02 (0.33), residues: 252 loop : -1.67 (0.19), residues: 1099 *********************** 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 672 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 671 time to evaluate : 2.055 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 outliers start: 1 outliers final: 0 residues processed: 671 average time/residue: 0.2768 time to fit residues: 291.4740 Evaluate side-chains 583 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 583 time to evaluate : 2.137 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8573 ------------------------------------------------------------------------------- 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: 0.0670 chunk 29 optimal weight: 50.0000 chunk 149 optimal weight: 9.9990 chunk 191 optimal weight: 50.0000 chunk 148 optimal weight: 20.0000 chunk 220 optimal weight: 20.0000 chunk 146 optimal weight: 20.0000 chunk 261 optimal weight: 50.0000 chunk 163 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 overall best weight: 6.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 160 ASN A 335 ASN ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN ** E 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18779 Z= 0.273 Angle : 0.618 11.695 25875 Z= 0.326 Chirality : 0.045 0.233 3160 Planarity : 0.004 0.038 3339 Dihedral : 4.989 63.323 2865 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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 (0.16), residues: 2721 helix: 1.33 (0.14), residues: 1370 sheet: -0.99 (0.33), residues: 252 loop : -1.63 (0.19), residues: 1099 *********************** 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 658 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 658 time to evaluate : 2.198 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 outliers start: 0 outliers final: 0 residues processed: 658 average time/residue: 0.2798 time to fit residues: 289.4228 Evaluate side-chains 579 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 579 time to evaluate : 1.943 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6721 ------------------------------------------------------------------------------- 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: 7.9990 chunk 104 optimal weight: 20.0000 chunk 156 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 51 optimal weight: 0.6980 chunk 50 optimal weight: 30.0000 chunk 166 optimal weight: 20.0000 chunk 177 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 205 optimal weight: 0.8980 overall best weight: 4.7186 ------------------------------------------------------------------------------- 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 70 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 HIS C 348 GLN ** D 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 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: 0.7694 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18779 Z= 0.235 Angle : 0.603 13.109 25875 Z= 0.314 Chirality : 0.045 0.263 3160 Planarity : 0.004 0.082 3339 Dihedral : 4.938 61.975 2865 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.17), residues: 2721 helix: 1.38 (0.14), residues: 1372 sheet: -1.02 (0.32), residues: 264 loop : -1.57 (0.19), residues: 1085 *********************** 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 679 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 679 time to evaluate : 2.199 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 outliers start: 0 outliers final: 0 residues processed: 679 average time/residue: 0.2677 time to fit residues: 288.8734 Evaluate side-chains 595 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 595 time to evaluate : 2.064 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8311 ------------------------------------------------------------------------------- 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: 7.9990 chunk 250 optimal weight: 8.9990 chunk 228 optimal weight: 6.9990 chunk 243 optimal weight: 6.9990 chunk 146 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 191 optimal weight: 50.0000 chunk 74 optimal weight: 0.9990 chunk 219 optimal weight: 40.0000 chunk 230 optimal weight: 0.8980 chunk 242 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 HIS C 348 GLN ** E 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18779 Z= 0.181 Angle : 0.591 13.880 25875 Z= 0.302 Chirality : 0.044 0.246 3160 Planarity : 0.004 0.067 3339 Dihedral : 4.730 61.231 2865 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: 0.14 (0.17), residues: 2721 helix: 1.47 (0.14), residues: 1374 sheet: -0.76 (0.34), residues: 251 loop : -1.52 (0.19), residues: 1096 *********************** 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 676 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 676 time to evaluate : 2.189 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 outliers start: 0 outliers final: 0 residues processed: 676 average time/residue: 0.2825 time to fit residues: 302.8215 Evaluate side-chains 606 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 606 time to evaluate : 2.007 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7118 ------------------------------------------------------------------------------- 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: 1.9990 chunk 157 optimal weight: 10.0000 chunk 122 optimal weight: 0.0670 chunk 178 optimal weight: 8.9990 chunk 269 optimal weight: 50.0000 chunk 248 optimal weight: 50.0000 chunk 214 optimal weight: 4.9990 chunk 22 optimal weight: 30.0000 chunk 166 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 HIS C 348 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18779 Z= 0.227 Angle : 0.604 11.240 25875 Z= 0.313 Chirality : 0.045 0.236 3160 Planarity : 0.004 0.065 3339 Dihedral : 4.810 61.193 2865 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 0.14 (0.17), residues: 2721 helix: 1.47 (0.14), residues: 1371 sheet: -0.79 (0.33), residues: 256 loop : -1.50 (0.19), residues: 1094 ********************** 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 665 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 665 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 outliers start: 0 outliers final: 0 residues processed: 665 average time/residue: 0.2798 time to fit residues: 292.9856 Evaluate side-chains 600 residues out of total 2389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 600 time to evaluate : 1.977 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7672 ------------------------------------------------------------------------------- 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: 9.9990 chunk 229 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 198 optimal weight: 50.0000 chunk 31 optimal weight: 30.0000 chunk 59 optimal weight: 50.0000 chunk 215 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 221 optimal weight: 30.0000 chunk 27 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 160 ASN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 HIS C 348 GLN ** D 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.153347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.127966 restraints weight = 41914.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.130959 restraints weight = 26222.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.133088 restraints weight = 18189.983| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18779 Z= 0.292 Angle : 0.645 11.545 25875 Z= 0.339 Chirality : 0.046 0.217 3160 Planarity : 0.005 0.065 3339 Dihedral : 5.074 60.713 2865 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: 1.31 (0.14), residues: 1370 sheet: -0.79 (0.33), residues: 264 loop : -1.49 (0.19), residues: 1087 =============================================================================== Job complete usr+sys time: 4947.98 seconds wall clock time: 92 minutes 15.33 seconds (5535.33 seconds total)