Starting phenix.real_space_refine on Thu Mar 5 11:52:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u1q_26303/03_2026/7u1q_26303.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u1q_26303/03_2026/7u1q_26303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u1q_26303/03_2026/7u1q_26303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u1q_26303/03_2026/7u1q_26303.map" model { file = "/net/cci-nas-00/data/ceres_data/7u1q_26303/03_2026/7u1q_26303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u1q_26303/03_2026/7u1q_26303.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 1 8.98 5 P 31 5.49 5 S 112 5.16 5 C 13591 2.51 5 N 3557 2.21 5 O 3721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21013 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2608 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 16, 'TRANS': 344} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 14, 'TYR:plan': 2, 'ASP:plan': 10, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 157 Chain: "B" Number of atoms: 2511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2511 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 13, 'TRANS': 319} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASP:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 78 Chain: "C" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2461 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 13, 'TRANS': 318} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 4, 'GLN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 7, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 107 Chain: "D" Number of atoms: 2512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2512 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 13, 'TRANS': 317} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 7, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 67 Chain: "E" Number of atoms: 10040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1434, 10040 Classifications: {'peptide': 1434} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 371} Link IDs: {'PTRANS': 48, 'TRANS': 1385} Chain breaks: 4 Unresolved non-hydrogen bonds: 1306 Unresolved non-hydrogen angles: 1637 Unresolved non-hydrogen dihedrals: 1045 Unresolved non-hydrogen chiralities: 132 Planarities with less than four sites: {'GLN:plan1': 23, 'HIS:plan': 6, 'PHE:plan': 18, 'GLU:plan': 37, 'ASN:plan1': 7, 'ARG:plan': 30, 'ASP:plan': 34, 'TYR:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 696 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 122 Unusual residues: {' K': 1, 'ATP': 1, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'ATP': 1, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'ATP': 1, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'ATP': 1, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 368 Unusual residues: {'ATP': 1, 'BJX': 1, 'POV': 1, 'PTY': 5} Classifications: {'peptide': 2, 'undetermined': 8} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 4.83, per 1000 atoms: 0.23 Number of scatterers: 21013 At special positions: 0 Unit cell: (164.065, 104.5, 144.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 1 19.00 S 112 16.00 P 31 15.00 O 3721 8.00 N 3557 7.00 C 13591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 26 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG F 1 " - " ASN E 10 " Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 1.1 seconds 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5272 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 34 sheets defined 53.0% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 22 through 28 removed outlier: 4.142A pdb=" N TYR A 26 " --> pdb=" O THR A 22 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 66 removed outlier: 3.651A pdb=" N VAL A 64 " --> pdb=" O PHE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 97 Processing helix chain 'A' and resid 116 through 129 Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.746A pdb=" N ILE A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 179 removed outlier: 4.028A pdb=" N GLU A 179 " --> pdb=" O HIS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 58 through 66 removed outlier: 3.772A pdb=" N THR B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 98 Processing helix chain 'B' and resid 116 through 129 Processing helix chain 'B' and resid 142 through 172 removed outlier: 4.029A pdb=" N ILE B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 179 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 345 through 362 Processing helix chain 'C' and resid 53 through 58 removed outlier: 3.519A pdb=" N ASP C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 66 removed outlier: 3.674A pdb=" N THR C 62 " --> pdb=" O ASP C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 98 Processing helix chain 'C' and resid 116 through 129 Processing helix chain 'C' and resid 142 through 172 removed outlier: 3.930A pdb=" N ILE C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 180 Processing helix chain 'C' and resid 265 through 270 removed outlier: 4.044A pdb=" N ASP C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.946A pdb=" N LEU C 275 " --> pdb=" O PRO C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 333 No H-bonds generated for 'chain 'C' and resid 331 through 333' Processing helix chain 'C' and resid 345 through 361 Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 67 through 98 Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 142 through 172 removed outlier: 3.863A pdb=" N ILE D 146 " --> pdb=" O CYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 removed outlier: 3.623A pdb=" N GLU D 179 " --> pdb=" O HIS D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 270 removed outlier: 4.135A pdb=" N ASP D 269 " --> pdb=" O PRO D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 345 through 360 Processing helix chain 'E' and resid 8 through 13 removed outlier: 4.099A pdb=" N ALA E 13 " --> pdb=" O GLU E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 24 Processing helix chain 'E' and resid 26 through 55 Proline residue: E 35 - end of helix removed outlier: 4.025A pdb=" N PHE E 41 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Proline residue: E 45 - end of helix removed outlier: 3.688A pdb=" N SER E 55 " --> pdb=" O TRP E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 96 removed outlier: 4.086A pdb=" N VAL E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 106 Processing helix chain 'E' and resid 107 through 130 removed outlier: 3.743A pdb=" N MET E 115 " --> pdb=" O GLY E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 135 Processing helix chain 'E' and resid 136 through 160 Processing helix chain 'E' and resid 166 through 194 removed outlier: 3.602A pdb=" N CYS E 170 " --> pdb=" O GLN E 166 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE E 190 " --> pdb=" O GLU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 212 removed outlier: 3.826A pdb=" N ASP E 212 " --> pdb=" O GLU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 227 removed outlier: 3.540A pdb=" N LYS E 227 " --> pdb=" O LEU E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 243 removed outlier: 4.217A pdb=" N PHE E 236 " --> pdb=" O TRP E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 277 Processing helix chain 'E' and resid 283 through 314 removed outlier: 5.654A pdb=" N ARG E 297 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ARG E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU E 301 " --> pdb=" O ARG E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 328 removed outlier: 3.612A pdb=" N LEU E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 352 removed outlier: 3.895A pdb=" N LEU E 352 " --> pdb=" O SER E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 401 removed outlier: 4.476A pdb=" N GLN E 374 " --> pdb=" O ARG E 370 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR E 396 " --> pdb=" O GLN E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 413 through 456 removed outlier: 3.998A pdb=" N THR E 425 " --> pdb=" O VAL E 421 " (cutoff:3.500A) Proline residue: E 436 - end of helix removed outlier: 3.697A pdb=" N TRP E 439 " --> pdb=" O CYS E 435 " (cutoff:3.500A) Proline residue: E 442 - end of helix Processing helix chain 'E' and resid 457 through 505 removed outlier: 3.613A pdb=" N LEU E 461 " --> pdb=" O GLY E 457 " (cutoff:3.500A) Proline residue: E 472 - end of helix removed outlier: 3.784A pdb=" N GLY E 505 " --> pdb=" O GLU E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 512 Processing helix chain 'E' and resid 514 through 564 removed outlier: 4.403A pdb=" N PHE E 518 " --> pdb=" O TRP E 514 " (cutoff:3.500A) Proline residue: E 551 - end of helix Processing helix chain 'E' and resid 572 through 614 removed outlier: 3.842A pdb=" N ALA E 578 " --> pdb=" O SER E 574 " (cutoff:3.500A) Proline residue: E 589 - end of helix removed outlier: 3.886A pdb=" N LEU E 592 " --> pdb=" O THR E 588 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER E 594 " --> pdb=" O LEU E 590 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N SER E 595 " --> pdb=" O PHE E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 719 through 728 Processing helix chain 'E' and resid 784 through 790 Processing helix chain 'E' and resid 795 through 806 Processing helix chain 'E' and resid 807 through 812 removed outlier: 3.851A pdb=" N ASP E 811 " --> pdb=" O SER E 807 " (cutoff:3.500A) Processing helix chain 'E' and resid 817 through 820 Processing helix chain 'E' and resid 831 through 846 removed outlier: 4.267A pdb=" N GLN E 846 " --> pdb=" O ARG E 842 " (cutoff:3.500A) Processing helix chain 'E' and resid 862 through 880 removed outlier: 3.697A pdb=" N ASP E 879 " --> pdb=" O GLU E 875 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP E 880 " --> pdb=" O LEU E 876 " (cutoff:3.500A) Processing helix chain 'E' and resid 913 through 921 removed outlier: 3.831A pdb=" N PHE E 917 " --> pdb=" O THR E 913 " (cutoff:3.500A) Processing helix chain 'E' and resid 987 through 993 Processing helix chain 'E' and resid 996 through 1009 removed outlier: 3.723A pdb=" N SER E1006 " --> pdb=" O THR E1002 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER E1007 " --> pdb=" O LYS E1003 " (cutoff:3.500A) Processing helix chain 'E' and resid 1011 through 1042 removed outlier: 3.954A pdb=" N PHE E1018 " --> pdb=" O SER E1014 " (cutoff:3.500A) Processing helix chain 'E' and resid 1064 through 1107 Processing helix chain 'E' and resid 1109 through 1116 removed outlier: 3.754A pdb=" N PHE E1113 " --> pdb=" O PRO E1109 " (cutoff:3.500A) Processing helix chain 'E' and resid 1119 through 1135 removed outlier: 4.557A pdb=" N ASP E1128 " --> pdb=" O ARG E1124 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1135 through 1161 Processing helix chain 'E' and resid 1163 through 1210 removed outlier: 3.865A pdb=" N ALA E1167 " --> pdb=" O VAL E1163 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 3.831A pdb=" N ASP E1188 " --> pdb=" O VAL E1184 " (cutoff:3.500A) Proline residue: E1199 - end of helix Processing helix chain 'E' and resid 1210 through 1217 Processing helix chain 'E' and resid 1219 through 1275 removed outlier: 3.819A pdb=" N PHE E1223 " --> pdb=" O TYR E1219 " (cutoff:3.500A) Processing helix chain 'E' and resid 1277 through 1319 removed outlier: 3.835A pdb=" N VAL E1281 " --> pdb=" O SER E1277 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N MET E1290 " --> pdb=" O THR E1286 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER E1292 " --> pdb=" O ALA E1288 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASN E1293 " --> pdb=" O LEU E1289 " (cutoff:3.500A) Processing helix chain 'E' and resid 1384 through 1393 Processing helix chain 'E' and resid 1411 through 1413 No H-bonds generated for 'chain 'E' and resid 1411 through 1413' Processing helix chain 'E' and resid 1414 through 1419 Processing helix chain 'E' and resid 1435 through 1441 Processing helix chain 'E' and resid 1450 through 1458 Processing helix chain 'E' and resid 1460 through 1466 removed outlier: 4.277A pdb=" N VAL E1464 " --> pdb=" O LEU E1460 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS E1465 " --> pdb=" O LYS E1461 " (cutoff:3.500A) Processing helix chain 'E' and resid 1485 through 1498 Processing helix chain 'E' and resid 1512 through 1530 Processing helix chain 'E' and resid 1539 through 1545 Processing helix chain 'E' and resid 1564 through 1570 removed outlier: 3.618A pdb=" N SER E1568 " --> pdb=" O GLU E1564 " (cutoff:3.500A) Processing helix chain 'E' and resid 1570 through 1578 removed outlier: 3.514A pdb=" N PHE E1574 " --> pdb=" O LYS E1570 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE E1577 " --> pdb=" O VAL E1573 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL E1578 " --> pdb=" O PHE E1574 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.722A pdb=" N VAL B 328 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA4, first strand: chain 'A' and resid 259 through 260 removed outlier: 3.588A pdb=" N HIS A 259 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 236 through 237 removed outlier: 5.938A pdb=" N SER A 212 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL A 290 " --> pdb=" O SER A 212 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 287 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 236 through 237 removed outlier: 5.938A pdb=" N SER A 212 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL A 290 " --> pdb=" O SER A 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AA8, first strand: chain 'A' and resid 313 through 315 Processing sheet with id=AA9, first strand: chain 'A' and resid 319 through 321 removed outlier: 6.664A pdb=" N TYR A 326 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LYS D 47 " --> pdb=" O TYR A 326 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL A 328 " --> pdb=" O LYS D 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 36 through 37 Processing sheet with id=AB2, first strand: chain 'B' and resid 44 through 47 removed outlier: 7.072A pdb=" N ALA B 45 " --> pdb=" O VAL C 328 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB4, first strand: chain 'B' and resid 259 through 260 removed outlier: 3.740A pdb=" N ARG B 195 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 234 through 237 removed outlier: 3.820A pdb=" N ALA B 213 " --> pdb=" O ILE B 249 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 234 through 237 removed outlier: 5.283A pdb=" N SER B 212 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL B 290 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 313 through 315 Processing sheet with id=AB8, first strand: chain 'C' and resid 44 through 47 removed outlier: 3.667A pdb=" N ALA C 45 " --> pdb=" O TYR D 326 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D 328 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 181 through 183 removed outlier: 3.595A pdb=" N VAL C 202 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 259 through 260 removed outlier: 6.334A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 210 through 211 Processing sheet with id=AC3, first strand: chain 'C' and resid 219 through 224 removed outlier: 6.073A pdb=" N VAL C 219 " --> pdb=" O GLN C 235 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN C 235 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ARG C 221 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU C 233 " --> pdb=" O ARG C 221 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 313 through 315 Processing sheet with id=AC5, first strand: chain 'D' and resid 36 through 37 removed outlier: 5.186A pdb=" N ASN D 41 " --> pdb=" O SER D 37 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 182 through 183 removed outlier: 3.512A pdb=" N VAL D 202 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 259 through 260 Processing sheet with id=AC8, first strand: chain 'D' and resid 231 through 238 removed outlier: 5.037A pdb=" N THR D 223 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N SER D 212 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL D 290 " --> pdb=" O SER D 212 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR D 214 " --> pdb=" O GLU D 288 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 313 through 315 Processing sheet with id=AD1, first strand: chain 'E' and resid 685 through 687 removed outlier: 6.723A pdb=" N PHE E 685 " --> pdb=" O VAL E 733 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 710 through 711 removed outlier: 6.894A pdb=" N MET E 710 " --> pdb=" O ILE E 901 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N MET E 903 " --> pdb=" O MET E 710 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE E 900 " --> pdb=" O GLU E 911 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU E 911 " --> pdb=" O ILE E 900 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ALA E 902 " --> pdb=" O GLN E 909 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 771 through 772 removed outlier: 6.588A pdb=" N ALA E 771 " --> pdb=" O PHE E 852 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 782 through 783 Processing sheet with id=AD5, first strand: chain 'E' and resid 1351 through 1352 Processing sheet with id=AD6, first strand: chain 'E' and resid 1404 through 1405 Processing sheet with id=AD7, first strand: chain 'E' and resid 1551 through 1553 removed outlier: 5.502A pdb=" N LYS E1553 " --> pdb=" O ILE E1557 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE E1557 " --> pdb=" O LYS E1553 " (cutoff:3.500A) 1173 hydrogen bonds defined for protein. 3402 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3459 1.32 - 1.45: 5455 1.45 - 1.57: 12296 1.57 - 1.69: 59 1.69 - 1.81: 174 Bond restraints: 21443 Sorted by residual: bond pdb=" C16 BJX E1603 " pdb=" N1 BJX E1603 " ideal model delta sigma weight residual 1.344 1.478 -0.134 2.00e-02 2.50e+03 4.49e+01 bond pdb=" N BJX E1603 " pdb=" C6 BJX E1603 " ideal model delta sigma weight residual 1.412 1.509 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C5 BJX E1603 " pdb=" N1 BJX E1603 " ideal model delta sigma weight residual 1.446 1.542 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C5 BJX E1603 " pdb=" C7 BJX E1603 " ideal model delta sigma weight residual 1.518 1.607 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C21 BJX E1603 " pdb=" O1 BJX E1603 " ideal model delta sigma weight residual 1.347 1.425 -0.078 2.00e-02 2.50e+03 1.53e+01 ... (remaining 21438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 28783 1.98 - 3.96: 343 3.96 - 5.94: 70 5.94 - 7.92: 21 7.92 - 9.90: 5 Bond angle restraints: 29222 Sorted by residual: angle pdb=" C17 BJX E1603 " pdb=" C16 BJX E1603 " pdb=" N1 BJX E1603 " ideal model delta sigma weight residual 113.90 122.77 -8.87 3.00e+00 1.11e-01 8.75e+00 angle pdb=" C16 BJX E1603 " pdb=" N1 BJX E1603 " pdb=" C5 BJX E1603 " ideal model delta sigma weight residual 123.13 131.64 -8.51 3.00e+00 1.11e-01 8.04e+00 angle pdb=" N GLN E 219 " pdb=" CA GLN E 219 " pdb=" C GLN E 219 " ideal model delta sigma weight residual 109.81 115.50 -5.69 2.21e+00 2.05e-01 6.63e+00 angle pdb=" CA LEU A 191 " pdb=" CB LEU A 191 " pdb=" CG LEU A 191 " ideal model delta sigma weight residual 116.30 124.72 -8.42 3.50e+00 8.16e-02 5.79e+00 angle pdb=" O2 BJX E1603 " pdb=" C24 BJX E1603 " pdb=" O3 BJX E1603 " ideal model delta sigma weight residual 126.98 119.81 7.17 3.00e+00 1.11e-01 5.71e+00 ... (remaining 29217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.77: 12482 34.77 - 69.53: 352 69.53 - 104.30: 54 104.30 - 139.06: 25 139.06 - 173.83: 23 Dihedral angle restraints: 12936 sinusoidal: 4830 harmonic: 8106 Sorted by residual: dihedral pdb=" C17 P5S D 402 " pdb=" C20 P5S D 402 " pdb=" C21 P5S D 402 " pdb=" C22 P5S D 402 " ideal model delta sinusoidal sigma weight residual 71.45 -102.38 173.83 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C21 P5S D 402 " pdb=" C22 P5S D 402 " pdb=" C23 P5S D 402 " pdb=" C24 P5S D 402 " ideal model delta sinusoidal sigma weight residual 295.37 122.41 172.96 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C17 P5S E1610 " pdb=" C20 P5S E1610 " pdb=" C21 P5S E1610 " pdb=" C22 P5S E1610 " ideal model delta sinusoidal sigma weight residual 71.45 -101.43 172.88 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3162 0.074 - 0.147: 325 0.147 - 0.221: 3 0.221 - 0.294: 5 0.294 - 0.368: 2 Chirality restraints: 3497 Sorted by residual: chirality pdb=" C2 P5S B 403 " pdb=" C1 P5S B 403 " pdb=" C3 P5S B 403 " pdb=" O37 P5S B 403 " both_signs ideal model delta sigma weight residual False 2.59 2.23 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" C2 P5S E1610 " pdb=" C1 P5S E1610 " pdb=" C3 P5S E1610 " pdb=" O37 P5S E1610 " both_signs ideal model delta sigma weight residual False 2.59 2.29 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C2 P5S A 403 " pdb=" C1 P5S A 403 " pdb=" C3 P5S A 403 " pdb=" O37 P5S A 403 " both_signs ideal model delta sigma weight residual False 2.59 2.33 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 3494 not shown) Planarity restraints: 3592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 265 " -0.039 5.00e-02 4.00e+02 5.91e-02 5.58e+00 pdb=" N PRO B 266 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 266 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 266 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 588 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO E 589 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO E 589 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 589 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E1335 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO E1336 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO E1336 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E1336 " -0.028 5.00e-02 4.00e+02 ... (remaining 3589 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 5518 2.81 - 3.39: 23721 3.39 - 3.98: 37838 3.98 - 4.56: 51200 4.56 - 5.14: 76338 Nonbonded interactions: 194615 Sorted by model distance: nonbonded pdb=" OD1 ASP C 329 " pdb=" OG SER C 331 " model vdw 2.228 3.040 nonbonded pdb=" O VAL A 138 " pdb=" NH2 ARG B 136 " model vdw 2.237 3.120 nonbonded pdb=" O SER B 116 " pdb=" OG SER B 119 " model vdw 2.241 3.040 nonbonded pdb=" NH1 ARG D 177 " pdb=" OG SER D 208 " model vdw 2.241 3.120 nonbonded pdb=" NH1 ARG B 177 " pdb=" OG SER B 208 " model vdw 2.253 3.120 ... (remaining 194610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 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 nam \ e CA or name C or name O or name CB )) or resid 60 through 175 or (resid 176 and \ (name N or name CA or name C or name O or name CB )) or resid 177 through 205 o \ r (resid 206 through 207 and (name N or name CA or name C or name O or name CB ) \ ) or resid 208 through 261 or (resid 262 through 265 and (name N or name CA or n \ ame C or name O or name CB )) or resid 266 through 285 or (resid 286 and (name N \ or name CA or name C or name O or name CB )) or resid 287 or (resid 288 and (na \ me N or name CA or name C or name O or name CB )) or resid 289 through 290 or (r \ esid 291 and (name N or name CA or name C or name O or name CB )) or resid 292 t \ hrough 320 or (resid 321 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 n \ ame C or name O or name CB )) or resid 330 through 331 or (resid 332 and (name N \ or name CA or name C or name O or name CB )) or resid 333 through 348 or (resid \ 349 through 360 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and ((resid 30 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 46 or (resid 47 and (name N or na \ me CA or name C or name O or name CB )) or resid 48 through 51 or (resid 52 and \ (name N or name CA or name C or name O or name CB )) or resid 53 or (resid 54 th \ rough 59 and (name N or name CA or name C or name O or name CB )) or resid 60 th \ rough 64 or (resid 65 and (name N or name CA or name C or name O or name CB )) o \ r resid 66 through 98 or (resid 99 and (name N or name CA or name C or name O or \ name CB )) or resid 100 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )) or resid 127 through 175 or (resid 176 and (name N o \ r name CA or name C or name O or name CB )) or resid 177 through 259 or (resid 2 \ 60 and (name N or name CA or name C or name O or name CB )) or resid 261 or (res \ id 262 through 265 and (name N or name CA or name C or name O or name CB )) or r \ esid 266 through 273 or (resid 274 through 275 and (name N or name CA or name C \ or name O or name CB )) or resid 276 or (resid 277 and (name N or name CA or nam \ e C or name O or name CB )) or resid 278 through 279 or (resid 280 through 281 a \ nd (name N or name CA or name C or name O or name CB )) or resid 282 through 285 \ or (resid 286 and (name N or name CA or name C or name O or name CB )) or resid \ 287 or (resid 288 and (name N or name CA or name C or name O or name CB )) or r \ esid 289 through 290 or (resid 291 and (name N or name CA or name C or name O or \ name CB )) or resid 292 through 304 or (resid 305 through 306 and (name N or na \ me CA or name C or name O or name CB )) or resid 307 through 331 or (resid 332 a \ nd (name N or name CA or name C or name O or name CB )) or resid 333 through 335 \ or (resid 336 through 337 and (name N or name CA or name C or name O or name CB \ )) or resid 338 or (resid 339 and (name N or name CA or name C or name O or nam \ e CB )) or resid 340 or (resid 341 and (name N or name CA or name C or name O or \ name CB )) or resid 342 through 347 or (resid 348 through 360 and (name N or na \ me CA or name C or name O or name CB )))) selection = (chain 'C' and ((resid 30 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 58 or (resid 59 and (name N or na \ me CA or name C or name O or name CB )) or resid 60 through 98 or (resid 99 and \ (name N or name CA or name C or name O or name CB )) or resid 100 through 125 or \ (resid 126 and (name N or name CA or name C or name O or name CB )) or resid 12 \ 7 through 205 or (resid 206 through 207 and (name N or name CA or name C or name \ O or name CB )) or resid 208 through 243 or (resid 244 and (name N or name CA o \ r name C or name O or name CB )) or resid 245 through 259 or (resid 260 and (nam \ e N or name CA or name C or name O or name CB )) or resid 261 through 273 or (re \ sid 274 through 275 and (name N or name CA or name C or name O or name CB )) or \ resid 276 or (resid 277 and (name N or name CA or name C or name O or name CB )) \ or resid 278 through 279 or (resid 280 through 281 and (name N or name CA or na \ me C or name O or name CB )) or resid 282 through 304 or (resid 305 through 306 \ and (name N or name CA or name C or name O or name CB )) or resid 307 through 32 \ 0 or (resid 321 through 323 and (name N or name CA or name C or name O or name C \ B )) 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 through 331 or (resid 332 and (name N or name \ CA or name C or name O or name CB )) or resid 333 through 335 or (resid 336 thro \ ugh 337 and (name N or name CA or name C or name O or name CB )) or resid 338 or \ (resid 339 and (name N or name CA or name C or name O or name CB )) or resid 34 \ 0 or (resid 341 and (name N or name CA or name C or name O or name CB )) or resi \ d 342 through 360)) selection = (chain 'D' and ((resid 30 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 46 or (resid 47 and (name N or na \ me CA or name C or name O or name CB )) or resid 48 through 50 or (resid 51 thro \ ugh 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 125 or (resid 126 and (name N or name CA or name C or name O or \ name CB )) or resid 127 through 175 or (resid 176 and (name N or name CA or nam \ e C or name O or name CB )) or resid 177 through 205 or (resid 206 through 207 a \ nd (name N or name CA or name C or name O or name CB )) or resid 208 through 243 \ or (resid 244 and (name N or name CA or name C or name O or name CB )) or resid \ 245 through 258 or (resid 259 through 260 and (name N or name CA or name C or n \ ame O or name CB )) or resid 261 or (resid 262 through 265 and (name N or name C \ A or name C or name O or name CB )) or resid 266 through 273 or (resid 274 throu \ gh 275 and (name N or name CA or name C or name O or name CB )) or resid 276 or \ (resid 277 and (name N or name CA or name C or name O or name CB )) or resid 278 \ through 279 or (resid 280 through 281 and (name N or name CA or name C or name \ O or name CB )) or resid 282 through 285 or (resid 286 and (name N or name CA or \ name C or name O or name CB )) or resid 287 or (resid 288 and (name N or name C \ A or name C or name O or name CB )) or resid 289 through 290 or (resid 291 and ( \ name N or name CA or name C or name O or name CB )) or resid 292 through 304 or \ (resid 305 through 306 and (name N or name CA or name C or name O or name CB )) \ or resid 307 through 320 or (resid 321 through 323 and (name N or name CA or nam \ e C or name O or name CB )) or resid 324 through 328 or (resid 329 and (name N o \ r name CA or name C or name O or name CB )) or resid 330 through 335 or (resid 3 \ 36 through 337 and (name N or name CA or name C or name O or name CB )) or resid \ 338 or (resid 339 and (name N or name CA or name C or name O or name CB )) or r \ esid 340 or (resid 341 and (name N or name CA or name C or name O or name CB )) \ or resid 342 through 360)) } 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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.280 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.134 21450 Z= 0.147 Angle : 0.582 9.895 29238 Z= 0.271 Chirality : 0.043 0.368 3497 Planarity : 0.004 0.059 3591 Dihedral : 19.076 173.828 7649 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.16), residues: 2773 helix: 0.89 (0.14), residues: 1340 sheet: -2.96 (0.30), residues: 246 loop : -2.19 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 248 TYR 0.016 0.001 TYR E 230 PHE 0.020 0.001 PHE D 168 TRP 0.016 0.001 TRP E 998 HIS 0.003 0.000 HIS E1024 Details of bonding type rmsd covalent geometry : bond 0.00299 (21443) covalent geometry : angle 0.57990 (29222) SS BOND : bond 0.00109 ( 5) SS BOND : angle 0.85904 ( 10) hydrogen bonds : bond 0.16158 ( 1161) hydrogen bonds : angle 6.43000 ( 3402) link_BETA1-4 : bond 0.00750 ( 1) link_BETA1-4 : angle 3.83400 ( 3) link_NAG-ASN : bond 0.00118 ( 1) link_NAG-ASN : angle 2.39561 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 755 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8403 (m110) cc_final: 0.8120 (m110) REVERT: A 67 LYS cc_start: 0.8391 (mppt) cc_final: 0.8130 (mppt) REVERT: A 93 ILE cc_start: 0.9286 (tt) cc_final: 0.9029 (mp) REVERT: A 314 ARG cc_start: 0.7393 (ptp-170) cc_final: 0.7114 (ptm-80) REVERT: B 77 MET cc_start: 0.6654 (mmm) cc_final: 0.5964 (tmm) REVERT: B 88 MET cc_start: 0.7162 (tpp) cc_final: 0.6909 (tpp) REVERT: B 158 MET cc_start: 0.7577 (mmm) cc_final: 0.7040 (mmm) REVERT: B 180 THR cc_start: 0.8702 (p) cc_final: 0.8402 (p) REVERT: B 221 ARG cc_start: 0.7718 (ttm-80) cc_final: 0.7377 (mtp-110) REVERT: B 311 TRP cc_start: 0.8859 (t-100) cc_final: 0.8506 (t-100) REVERT: C 77 MET cc_start: 0.6759 (mmm) cc_final: 0.5943 (tmm) REVERT: C 86 PHE cc_start: 0.7928 (m-80) cc_final: 0.7383 (m-80) REVERT: D 43 ASN cc_start: 0.8733 (t0) cc_final: 0.8531 (t0) REVERT: D 67 LYS cc_start: 0.7988 (mppt) cc_final: 0.7438 (mtmt) REVERT: D 158 MET cc_start: 0.8032 (mmm) cc_final: 0.7725 (tpp) REVERT: D 240 MET cc_start: 0.8293 (ttp) cc_final: 0.8084 (ttp) REVERT: E 17 VAL cc_start: 0.8299 (m) cc_final: 0.7750 (t) REVERT: E 42 ILE cc_start: 0.8671 (tt) cc_final: 0.8437 (tt) REVERT: E 82 LEU cc_start: 0.9088 (mp) cc_final: 0.8813 (mt) REVERT: E 134 LYS cc_start: 0.8740 (mttt) cc_final: 0.8326 (mtpt) REVERT: E 158 TYR cc_start: 0.6343 (t80) cc_final: 0.5986 (t80) REVERT: E 230 TYR cc_start: 0.8596 (m-80) cc_final: 0.7672 (m-80) REVERT: E 232 TRP cc_start: 0.8494 (p-90) cc_final: 0.8257 (p-90) REVERT: E 252 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7935 (pttp) REVERT: E 264 GLN cc_start: 0.8017 (mm110) cc_final: 0.7701 (tp-100) REVERT: E 289 ARG cc_start: 0.5863 (mpt-90) cc_final: 0.5055 (tpt-90) REVERT: E 323 ILE cc_start: 0.8943 (mt) cc_final: 0.8708 (mt) REVERT: E 547 ASN cc_start: 0.8925 (t0) cc_final: 0.8695 (m-40) REVERT: E 604 LEU cc_start: 0.8797 (mt) cc_final: 0.8588 (mt) REVERT: E 708 LEU cc_start: 0.6151 (tt) cc_final: 0.5622 (mp) REVERT: E 807 SER cc_start: 0.8301 (m) cc_final: 0.7516 (p) REVERT: E 1012 LEU cc_start: 0.7117 (mt) cc_final: 0.6912 (tp) REVERT: E 1234 ASN cc_start: 0.8723 (t0) cc_final: 0.8456 (t0) outliers start: 0 outliers final: 0 residues processed: 755 average time/residue: 0.1462 time to fit residues: 171.0777 Evaluate side-chains 593 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 593 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 0.0170 chunk 215 optimal weight: 50.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 20.0000 chunk 111 optimal weight: 8.9990 overall best weight: 4.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 279 GLN B 173 GLN C 335 ASN D 247 ASN D 276 HIS ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN E 282 GLN E 584 HIS E 817 HIS E 846 GLN E1245 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.198996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.172600 restraints weight = 27131.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.175792 restraints weight = 14963.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.178126 restraints weight = 9899.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.179545 restraints weight = 6969.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.179697 restraints weight = 6064.547| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21450 Z= 0.193 Angle : 0.672 11.454 29238 Z= 0.340 Chirality : 0.047 0.416 3497 Planarity : 0.005 0.053 3591 Dihedral : 20.899 177.646 3783 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.16 % Allowed : 14.58 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.16), residues: 2773 helix: 1.28 (0.14), residues: 1364 sheet: -2.52 (0.32), residues: 220 loop : -2.00 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 54 TYR 0.014 0.002 TYR B 268 PHE 0.023 0.002 PHE C 75 TRP 0.015 0.002 TRP A 83 HIS 0.007 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00435 (21443) covalent geometry : angle 0.66918 (29222) SS BOND : bond 0.00640 ( 5) SS BOND : angle 1.88627 ( 10) hydrogen bonds : bond 0.05113 ( 1161) hydrogen bonds : angle 4.87296 ( 3402) link_BETA1-4 : bond 0.01126 ( 1) link_BETA1-4 : angle 4.53249 ( 3) link_NAG-ASN : bond 0.00588 ( 1) link_NAG-ASN : angle 2.68880 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 615 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8494 (m110) cc_final: 0.8194 (m110) REVERT: A 93 ILE cc_start: 0.9170 (tt) cc_final: 0.8916 (mp) REVERT: A 200 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8882 (tt) REVERT: A 314 ARG cc_start: 0.7403 (ptp-170) cc_final: 0.7093 (ptm-80) REVERT: B 77 MET cc_start: 0.6767 (mmm) cc_final: 0.5985 (tmm) REVERT: B 88 MET cc_start: 0.7204 (tpp) cc_final: 0.6976 (tpp) REVERT: B 311 TRP cc_start: 0.9078 (t-100) cc_final: 0.8630 (t-100) REVERT: B 313 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.8003 (mt0) REVERT: C 77 MET cc_start: 0.6747 (mmm) cc_final: 0.5557 (tmm) REVERT: C 347 ARG cc_start: 0.8738 (ttm-80) cc_final: 0.8522 (ttm-80) REVERT: D 58 ASP cc_start: 0.7556 (t0) cc_final: 0.7238 (t0) REVERT: D 67 LYS cc_start: 0.8087 (mppt) cc_final: 0.7479 (mtmt) REVERT: D 90 TRP cc_start: 0.8500 (m100) cc_final: 0.8033 (m100) REVERT: D 112 THR cc_start: 0.8894 (p) cc_final: 0.8652 (t) REVERT: D 158 MET cc_start: 0.8081 (mmm) cc_final: 0.7864 (tpp) REVERT: D 240 MET cc_start: 0.8390 (ttp) cc_final: 0.8184 (ttp) REVERT: D 304 TYR cc_start: 0.8517 (m-80) cc_final: 0.8098 (m-10) REVERT: E 38 PHE cc_start: 0.7568 (t80) cc_final: 0.7331 (t80) REVERT: E 39 LEU cc_start: 0.8992 (tt) cc_final: 0.8652 (tp) REVERT: E 130 SER cc_start: 0.7888 (OUTLIER) cc_final: 0.7601 (p) REVERT: E 134 LYS cc_start: 0.8806 (mttt) cc_final: 0.8403 (tttp) REVERT: E 158 TYR cc_start: 0.6531 (t80) cc_final: 0.5952 (t80) REVERT: E 176 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.8171 (t) REVERT: E 230 TYR cc_start: 0.8630 (m-80) cc_final: 0.7663 (m-80) REVERT: E 247 LEU cc_start: 0.8979 (mt) cc_final: 0.8696 (mt) REVERT: E 252 LYS cc_start: 0.8352 (ttmt) cc_final: 0.8031 (pttp) REVERT: E 264 GLN cc_start: 0.8115 (mm110) cc_final: 0.7734 (tp-100) REVERT: E 429 MET cc_start: 0.8643 (ttp) cc_final: 0.8284 (ttt) REVERT: E 441 MET cc_start: 0.7901 (mtt) cc_final: 0.7559 (mtm) REVERT: E 604 LEU cc_start: 0.8747 (mt) cc_final: 0.8485 (mt) REVERT: E 883 THR cc_start: 0.5824 (m) cc_final: 0.5408 (p) REVERT: E 1073 SER cc_start: 0.8429 (m) cc_final: 0.8147 (p) REVERT: E 1154 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8074 (mm) REVERT: E 1209 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7501 (mm-30) REVERT: E 1269 SER cc_start: 0.8953 (t) cc_final: 0.8679 (m) outliers start: 98 outliers final: 58 residues processed: 656 average time/residue: 0.1356 time to fit residues: 140.6998 Evaluate side-chains 637 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 574 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 259 HIS Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1151 VAL Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1277 SER Chi-restraints excluded: chain E residue 1286 THR Chi-restraints excluded: chain E residue 1425 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 58 optimal weight: 5.9990 chunk 221 optimal weight: 20.0000 chunk 240 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 212 optimal weight: 8.9990 chunk 148 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 GLN B 313 GLN C 128 GLN C 335 ASN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 HIS D 299 GLN E 562 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.195245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.169141 restraints weight = 27240.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.172796 restraints weight = 15721.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.174292 restraints weight = 10367.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.176196 restraints weight = 7879.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.176523 restraints weight = 6362.950| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21450 Z= 0.194 Angle : 0.653 10.293 29238 Z= 0.330 Chirality : 0.047 0.390 3497 Planarity : 0.005 0.051 3591 Dihedral : 19.514 175.477 3783 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 5.95 % Allowed : 16.58 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.16), residues: 2773 helix: 1.51 (0.14), residues: 1346 sheet: -2.48 (0.32), residues: 232 loop : -1.83 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 370 TYR 0.021 0.002 TYR C 326 PHE 0.024 0.002 PHE C 95 TRP 0.014 0.002 TRP E 232 HIS 0.007 0.001 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00432 (21443) covalent geometry : angle 0.65018 (29222) SS BOND : bond 0.02110 ( 5) SS BOND : angle 1.72634 ( 10) hydrogen bonds : bond 0.04840 ( 1161) hydrogen bonds : angle 4.59510 ( 3402) link_BETA1-4 : bond 0.01517 ( 1) link_BETA1-4 : angle 4.66260 ( 3) link_NAG-ASN : bond 0.00577 ( 1) link_NAG-ASN : angle 2.55356 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 588 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8527 (m110) cc_final: 0.8185 (m110) REVERT: A 84 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8568 (tt) REVERT: A 93 ILE cc_start: 0.9147 (tt) cc_final: 0.8876 (mp) REVERT: A 200 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8963 (tt) REVERT: B 39 LYS cc_start: 0.8577 (mttp) cc_final: 0.8325 (mmmt) REVERT: B 77 MET cc_start: 0.6797 (mmm) cc_final: 0.6050 (tmm) REVERT: B 235 GLN cc_start: 0.8735 (mt0) cc_final: 0.8496 (mt0) REVERT: B 278 HIS cc_start: 0.7173 (m90) cc_final: 0.6879 (m90) REVERT: B 304 TYR cc_start: 0.8521 (m-80) cc_final: 0.8309 (m-10) REVERT: B 313 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7965 (mt0) REVERT: C 77 MET cc_start: 0.6707 (mmm) cc_final: 0.5745 (tmm) REVERT: C 347 ARG cc_start: 0.8733 (ttm-80) cc_final: 0.8498 (ttm-80) REVERT: D 58 ASP cc_start: 0.7604 (t0) cc_final: 0.7179 (t0) REVERT: D 67 LYS cc_start: 0.8180 (mppt) cc_final: 0.7571 (mtmt) REVERT: D 90 TRP cc_start: 0.8511 (m100) cc_final: 0.8239 (m100) REVERT: D 112 THR cc_start: 0.8857 (p) cc_final: 0.8651 (t) REVERT: D 158 MET cc_start: 0.8058 (mmm) cc_final: 0.7853 (tpp) REVERT: D 173 GLN cc_start: 0.8368 (mm-40) cc_final: 0.7847 (mt0) REVERT: D 177 ARG cc_start: 0.8601 (tpt170) cc_final: 0.8345 (tpt170) REVERT: D 186 HIS cc_start: 0.7358 (p-80) cc_final: 0.7021 (p90) REVERT: D 212 SER cc_start: 0.9026 (m) cc_final: 0.8799 (t) REVERT: D 276 HIS cc_start: 0.7528 (p-80) cc_final: 0.7145 (p-80) REVERT: D 304 TYR cc_start: 0.8468 (m-80) cc_final: 0.8160 (m-80) REVERT: E 39 LEU cc_start: 0.9021 (tt) cc_final: 0.8772 (tp) REVERT: E 81 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7353 (pp) REVERT: E 134 LYS cc_start: 0.8779 (mttt) cc_final: 0.8534 (mttm) REVERT: E 230 TYR cc_start: 0.8610 (m-80) cc_final: 0.7660 (m-80) REVERT: E 264 GLN cc_start: 0.8019 (mm110) cc_final: 0.7694 (tp-100) REVERT: E 506 MET cc_start: 0.7159 (tpt) cc_final: 0.6949 (tpt) REVERT: E 604 LEU cc_start: 0.8716 (mt) cc_final: 0.8455 (mt) REVERT: E 883 THR cc_start: 0.5992 (m) cc_final: 0.5597 (p) REVERT: E 1073 SER cc_start: 0.8378 (m) cc_final: 0.8125 (p) REVERT: E 1154 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8058 (mm) REVERT: E 1269 SER cc_start: 0.9022 (t) cc_final: 0.8756 (m) outliers start: 113 outliers final: 72 residues processed: 637 average time/residue: 0.1349 time to fit residues: 136.0570 Evaluate side-chains 630 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 553 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1151 VAL Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1207 THR Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1252 MET Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1277 SER Chi-restraints excluded: chain E residue 1416 HIS Chi-restraints excluded: chain E residue 1425 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 130 optimal weight: 9.9990 chunk 255 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 144 optimal weight: 20.0000 chunk 148 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 266 optimal weight: 30.0000 chunk 264 optimal weight: 40.0000 chunk 112 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN D 175 HIS ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN E 273 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.182308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.154111 restraints weight = 28194.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.157806 restraints weight = 15408.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.160306 restraints weight = 10075.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.161904 restraints weight = 7491.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.163103 restraints weight = 6079.542| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21450 Z= 0.171 Angle : 0.640 9.956 29238 Z= 0.317 Chirality : 0.046 0.374 3497 Planarity : 0.004 0.049 3591 Dihedral : 18.799 178.663 3783 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 5.79 % Allowed : 18.05 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.16), residues: 2773 helix: 1.71 (0.14), residues: 1330 sheet: -2.28 (0.32), residues: 237 loop : -1.81 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 192 TYR 0.021 0.002 TYR E 772 PHE 0.020 0.002 PHE C 95 TRP 0.013 0.001 TRP D 83 HIS 0.010 0.001 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00379 (21443) covalent geometry : angle 0.63679 (29222) SS BOND : bond 0.00889 ( 5) SS BOND : angle 1.29363 ( 10) hydrogen bonds : bond 0.04525 ( 1161) hydrogen bonds : angle 4.44438 ( 3402) link_BETA1-4 : bond 0.01802 ( 1) link_BETA1-4 : angle 4.90833 ( 3) link_NAG-ASN : bond 0.00570 ( 1) link_NAG-ASN : angle 2.54062 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 578 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7266 (mtt-85) cc_final: 0.6980 (mtt-85) REVERT: A 48 ASN cc_start: 0.8497 (m110) cc_final: 0.8165 (m110) REVERT: A 84 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8569 (tt) REVERT: A 93 ILE cc_start: 0.9127 (tt) cc_final: 0.8839 (mp) REVERT: A 149 LEU cc_start: 0.9228 (tp) cc_final: 0.8880 (tt) REVERT: A 200 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8885 (tt) REVERT: A 292 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6557 (pp20) REVERT: B 39 LYS cc_start: 0.8618 (mttp) cc_final: 0.8371 (mmmt) REVERT: B 169 MET cc_start: 0.8000 (mtm) cc_final: 0.7639 (mtp) REVERT: B 173 GLN cc_start: 0.8499 (mm110) cc_final: 0.8286 (tt0) REVERT: B 278 HIS cc_start: 0.7216 (m90) cc_final: 0.6988 (m90) REVERT: B 304 TYR cc_start: 0.8522 (m-80) cc_final: 0.8259 (m-10) REVERT: B 338 LYS cc_start: 0.8044 (mmtm) cc_final: 0.7738 (mptt) REVERT: C 77 MET cc_start: 0.6785 (mmm) cc_final: 0.5776 (tmm) REVERT: C 347 ARG cc_start: 0.8702 (ttm-80) cc_final: 0.8496 (ttm-80) REVERT: D 58 ASP cc_start: 0.7760 (t0) cc_final: 0.7235 (t0) REVERT: D 67 LYS cc_start: 0.8303 (mppt) cc_final: 0.7767 (mtmt) REVERT: D 112 THR cc_start: 0.8867 (p) cc_final: 0.8635 (t) REVERT: D 152 GLN cc_start: 0.9288 (tp40) cc_final: 0.8737 (tp40) REVERT: D 158 MET cc_start: 0.8058 (mmm) cc_final: 0.7847 (tpp) REVERT: D 173 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7676 (mt0) REVERT: D 177 ARG cc_start: 0.8553 (tpt170) cc_final: 0.8290 (tpt170) REVERT: D 186 HIS cc_start: 0.7363 (p-80) cc_final: 0.7023 (p90) REVERT: E 39 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8840 (tp) REVERT: E 176 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8259 (t) REVERT: E 230 TYR cc_start: 0.8594 (m-80) cc_final: 0.7702 (m-80) REVERT: E 264 GLN cc_start: 0.7986 (mm110) cc_final: 0.7732 (tp-100) REVERT: E 289 ARG cc_start: 0.7329 (ttm170) cc_final: 0.7117 (ttp-170) REVERT: E 358 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8659 (mt) REVERT: E 429 MET cc_start: 0.8446 (ttp) cc_final: 0.8072 (ttt) REVERT: E 506 MET cc_start: 0.7216 (tpt) cc_final: 0.7015 (tpt) REVERT: E 604 LEU cc_start: 0.8683 (mt) cc_final: 0.8428 (mt) REVERT: E 775 GLN cc_start: 0.8437 (tp40) cc_final: 0.8146 (tp40) REVERT: E 1073 SER cc_start: 0.8314 (m) cc_final: 0.8090 (p) REVERT: E 1209 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7694 (mm-30) REVERT: E 1269 SER cc_start: 0.9005 (t) cc_final: 0.8740 (m) outliers start: 110 outliers final: 88 residues processed: 629 average time/residue: 0.1338 time to fit residues: 133.8975 Evaluate side-chains 648 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 554 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 259 HIS Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 788 ILE Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1151 VAL Chi-restraints excluded: chain E residue 1207 THR Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1252 MET Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1277 SER Chi-restraints excluded: chain E residue 1286 THR Chi-restraints excluded: chain E residue 1416 HIS Chi-restraints excluded: chain E residue 1425 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 39 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 184 optimal weight: 30.0000 chunk 29 optimal weight: 8.9990 chunk 248 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 190 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 245 optimal weight: 6.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 GLN B 313 GLN C 235 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN E 273 GLN E1191 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.190865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.164589 restraints weight = 27358.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.168172 restraints weight = 15856.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.169804 restraints weight = 10535.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.171472 restraints weight = 7827.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.171934 restraints weight = 6432.993| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 21450 Z= 0.204 Angle : 0.670 11.586 29238 Z= 0.332 Chirality : 0.046 0.386 3497 Planarity : 0.004 0.052 3591 Dihedral : 18.214 178.852 3783 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 6.47 % Allowed : 19.37 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.16), residues: 2773 helix: 1.65 (0.14), residues: 1333 sheet: -2.25 (0.32), residues: 237 loop : -1.84 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 314 TYR 0.022 0.002 TYR E 772 PHE 0.022 0.002 PHE C 75 TRP 0.015 0.002 TRP D 83 HIS 0.011 0.001 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00459 (21443) covalent geometry : angle 0.66673 (29222) SS BOND : bond 0.00434 ( 5) SS BOND : angle 1.71920 ( 10) hydrogen bonds : bond 0.04557 ( 1161) hydrogen bonds : angle 4.46983 ( 3402) link_BETA1-4 : bond 0.01710 ( 1) link_BETA1-4 : angle 4.94478 ( 3) link_NAG-ASN : bond 0.00615 ( 1) link_NAG-ASN : angle 2.53014 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 554 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8507 (m110) cc_final: 0.8185 (m110) REVERT: A 84 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8616 (tt) REVERT: A 93 ILE cc_start: 0.9141 (tt) cc_final: 0.8886 (mt) REVERT: A 185 LYS cc_start: 0.6014 (mttt) cc_final: 0.5627 (mmtt) REVERT: A 200 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8969 (tt) REVERT: A 292 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6423 (pp20) REVERT: A 314 ARG cc_start: 0.7853 (ptp90) cc_final: 0.7355 (ptp90) REVERT: B 125 ILE cc_start: 0.9475 (mm) cc_final: 0.9134 (mt) REVERT: B 169 MET cc_start: 0.8009 (mtm) cc_final: 0.7663 (mtp) REVERT: B 177 ARG cc_start: 0.8382 (tpt170) cc_final: 0.8090 (tpt170) REVERT: B 304 TYR cc_start: 0.8531 (m-80) cc_final: 0.8287 (m-10) REVERT: C 67 LYS cc_start: 0.8566 (mttt) cc_final: 0.8366 (mtpt) REVERT: C 77 MET cc_start: 0.6790 (mmm) cc_final: 0.5787 (tmm) REVERT: D 58 ASP cc_start: 0.7835 (t0) cc_final: 0.7301 (t0) REVERT: D 67 LYS cc_start: 0.8276 (mppt) cc_final: 0.7721 (mtmt) REVERT: D 112 THR cc_start: 0.8887 (p) cc_final: 0.8674 (t) REVERT: D 158 MET cc_start: 0.8027 (mmm) cc_final: 0.7616 (tpp) REVERT: D 173 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7816 (mt0) REVERT: D 186 HIS cc_start: 0.7391 (p-80) cc_final: 0.7007 (p90) REVERT: E 36 HIS cc_start: 0.8102 (m-70) cc_final: 0.7894 (m170) REVERT: E 39 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8864 (tp) REVERT: E 40 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8420 (mt) REVERT: E 176 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8253 (t) REVERT: E 230 TYR cc_start: 0.8673 (m-80) cc_final: 0.7770 (m-80) REVERT: E 273 GLN cc_start: 0.6462 (OUTLIER) cc_final: 0.6158 (tp40) REVERT: E 289 ARG cc_start: 0.7232 (ttm170) cc_final: 0.5185 (tpt-90) REVERT: E 358 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8723 (mt) REVERT: E 437 ASN cc_start: 0.7998 (m-40) cc_final: 0.7725 (t0) REVERT: E 506 MET cc_start: 0.7112 (tpt) cc_final: 0.6852 (tpt) REVERT: E 604 LEU cc_start: 0.8623 (mt) cc_final: 0.8336 (mt) REVERT: E 1073 SER cc_start: 0.8343 (m) cc_final: 0.8099 (p) REVERT: E 1154 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8061 (mm) REVERT: E 1209 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7723 (mm-30) REVERT: E 1269 SER cc_start: 0.9029 (t) cc_final: 0.8737 (m) outliers start: 123 outliers final: 93 residues processed: 616 average time/residue: 0.1380 time to fit residues: 135.9642 Evaluate side-chains 649 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 547 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 259 HIS Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 265 ARG Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 788 ILE Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1151 VAL Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1173 VAL Chi-restraints excluded: chain E residue 1207 THR Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1252 MET Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1277 SER Chi-restraints excluded: chain E residue 1286 THR Chi-restraints excluded: chain E residue 1416 HIS Chi-restraints excluded: chain E residue 1425 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 60 optimal weight: 1.9990 chunk 239 optimal weight: 6.9990 chunk 232 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 258 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN E1234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.182882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.154261 restraints weight = 28198.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.157956 restraints weight = 15449.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.160470 restraints weight = 10156.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.162066 restraints weight = 7566.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.163264 restraints weight = 6153.424| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21450 Z= 0.171 Angle : 0.646 11.801 29238 Z= 0.318 Chirality : 0.046 0.368 3497 Planarity : 0.004 0.050 3591 Dihedral : 17.619 177.489 3783 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 6.47 % Allowed : 20.26 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.16), residues: 2773 helix: 1.77 (0.14), residues: 1334 sheet: -2.17 (0.33), residues: 233 loop : -1.77 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 325 TYR 0.025 0.001 TYR E 772 PHE 0.020 0.002 PHE C 75 TRP 0.016 0.001 TRP D 83 HIS 0.009 0.001 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00380 (21443) covalent geometry : angle 0.64355 (29222) SS BOND : bond 0.00348 ( 5) SS BOND : angle 1.45837 ( 10) hydrogen bonds : bond 0.04395 ( 1161) hydrogen bonds : angle 4.36384 ( 3402) link_BETA1-4 : bond 0.02122 ( 1) link_BETA1-4 : angle 4.85797 ( 3) link_NAG-ASN : bond 0.00505 ( 1) link_NAG-ASN : angle 2.31769 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 566 time to evaluate : 0.751 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: A 34 ARG cc_start: 0.7239 (mtt-85) cc_final: 0.6995 (mtt-85) REVERT: A 48 ASN cc_start: 0.8488 (m110) cc_final: 0.8096 (m110) REVERT: A 84 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8579 (tt) REVERT: A 93 ILE cc_start: 0.9125 (tt) cc_final: 0.8876 (mt) REVERT: A 200 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8964 (tt) REVERT: A 292 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6219 (pp20) REVERT: A 325 ARG cc_start: 0.7765 (ptm-80) cc_final: 0.7477 (ptm-80) REVERT: B 77 MET cc_start: 0.6681 (mmm) cc_final: 0.5640 (mtp) REVERT: B 125 ILE cc_start: 0.9445 (mm) cc_final: 0.9183 (mt) REVERT: B 169 MET cc_start: 0.8029 (mtm) cc_final: 0.7682 (mtp) REVERT: B 177 ARG cc_start: 0.8370 (tpt170) cc_final: 0.8133 (tpt170) REVERT: B 311 TRP cc_start: 0.9118 (t-100) cc_final: 0.8597 (t60) REVERT: C 67 LYS cc_start: 0.8567 (mttt) cc_final: 0.8353 (mtpt) REVERT: C 77 MET cc_start: 0.6857 (mmm) cc_final: 0.5869 (tmm) REVERT: C 182 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8283 (mm) REVERT: C 258 TYR cc_start: 0.9010 (p90) cc_final: 0.8785 (p90) REVERT: D 58 ASP cc_start: 0.7783 (t0) cc_final: 0.7221 (t0) REVERT: D 67 LYS cc_start: 0.8262 (mppt) cc_final: 0.7627 (mtmt) REVERT: D 112 THR cc_start: 0.8910 (p) cc_final: 0.8686 (t) REVERT: D 152 GLN cc_start: 0.9310 (tp40) cc_final: 0.8683 (tp40) REVERT: D 158 MET cc_start: 0.8058 (mmm) cc_final: 0.7855 (tpp) REVERT: D 173 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7732 (mt0) REVERT: D 177 ARG cc_start: 0.8325 (tpt170) cc_final: 0.7953 (tpt170) REVERT: D 186 HIS cc_start: 0.7347 (p-80) cc_final: 0.7009 (p90) REVERT: D 251 LEU cc_start: 0.8304 (tp) cc_final: 0.8069 (tt) REVERT: E 40 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8426 (mt) REVERT: E 44 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.7504 (t80) REVERT: E 176 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8327 (t) REVERT: E 230 TYR cc_start: 0.8628 (m-80) cc_final: 0.7715 (m-80) REVERT: E 289 ARG cc_start: 0.7248 (ttm170) cc_final: 0.6764 (ttm-80) REVERT: E 437 ASN cc_start: 0.7969 (m-40) cc_final: 0.7647 (t0) REVERT: E 506 MET cc_start: 0.7047 (tpt) cc_final: 0.6754 (tpt) REVERT: E 547 ASN cc_start: 0.8946 (t0) cc_final: 0.8617 (t0) REVERT: E 604 LEU cc_start: 0.8636 (mt) cc_final: 0.8360 (mt) REVERT: E 1073 SER cc_start: 0.8374 (m) cc_final: 0.8117 (p) REVERT: E 1154 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8002 (mm) REVERT: E 1209 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7790 (mm-30) REVERT: E 1269 SER cc_start: 0.8965 (t) cc_final: 0.8649 (m) outliers start: 123 outliers final: 90 residues processed: 631 average time/residue: 0.1329 time to fit residues: 134.2380 Evaluate side-chains 645 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 547 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 265 ARG Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 788 ILE Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1151 VAL Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1207 THR Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1252 MET Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1277 SER Chi-restraints excluded: chain E residue 1286 THR Chi-restraints excluded: chain E residue 1416 HIS Chi-restraints excluded: chain E residue 1425 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 187 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 27 optimal weight: 0.0670 chunk 122 optimal weight: 5.9990 chunk 267 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 179 optimal weight: 8.9990 chunk 125 optimal weight: 0.4980 chunk 126 optimal weight: 7.9990 chunk 264 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 overall best weight: 3.7124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 GLN C 173 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.195252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.168874 restraints weight = 26996.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.171899 restraints weight = 14761.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.173932 restraints weight = 9773.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.176095 restraints weight = 6977.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.176281 restraints weight = 5671.848| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21450 Z= 0.169 Angle : 0.652 13.062 29238 Z= 0.318 Chirality : 0.046 0.368 3497 Planarity : 0.004 0.050 3591 Dihedral : 17.101 177.199 3783 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 5.79 % Allowed : 21.68 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.16), residues: 2773 helix: 1.80 (0.14), residues: 1339 sheet: -2.02 (0.33), residues: 238 loop : -1.72 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 16 TYR 0.025 0.001 TYR E 772 PHE 0.020 0.002 PHE C 75 TRP 0.018 0.001 TRP D 83 HIS 0.010 0.001 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00375 (21443) covalent geometry : angle 0.64957 (29222) SS BOND : bond 0.00711 ( 5) SS BOND : angle 1.25470 ( 10) hydrogen bonds : bond 0.04340 ( 1161) hydrogen bonds : angle 4.33486 ( 3402) link_BETA1-4 : bond 0.01877 ( 1) link_BETA1-4 : angle 4.83978 ( 3) link_NAG-ASN : bond 0.00502 ( 1) link_NAG-ASN : angle 2.21477 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 558 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7223 (mtt-85) cc_final: 0.6969 (mtt-85) REVERT: A 48 ASN cc_start: 0.8464 (m110) cc_final: 0.8078 (m110) REVERT: A 84 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8586 (tt) REVERT: A 93 ILE cc_start: 0.9105 (tt) cc_final: 0.8853 (mt) REVERT: A 200 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8949 (tt) REVERT: A 292 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6112 (pp20) REVERT: B 77 MET cc_start: 0.6633 (mmm) cc_final: 0.5875 (tmm) REVERT: B 125 ILE cc_start: 0.9447 (mm) cc_final: 0.9151 (mt) REVERT: B 169 MET cc_start: 0.8035 (mtm) cc_final: 0.7697 (mtp) REVERT: B 177 ARG cc_start: 0.8354 (tpt170) cc_final: 0.8125 (tpt170) REVERT: B 311 TRP cc_start: 0.9101 (t-100) cc_final: 0.8588 (t60) REVERT: C 77 MET cc_start: 0.6819 (mmm) cc_final: 0.5849 (tmm) REVERT: C 182 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8241 (mm) REVERT: C 258 TYR cc_start: 0.9117 (p90) cc_final: 0.8896 (p90) REVERT: D 58 ASP cc_start: 0.7730 (t0) cc_final: 0.7155 (t0) REVERT: D 67 LYS cc_start: 0.8218 (mppt) cc_final: 0.7567 (mtmt) REVERT: D 112 THR cc_start: 0.8934 (p) cc_final: 0.8713 (t) REVERT: D 152 GLN cc_start: 0.9295 (tp40) cc_final: 0.8618 (tp40) REVERT: D 158 MET cc_start: 0.8064 (mmm) cc_final: 0.7634 (tpp) REVERT: D 173 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7733 (mt0) REVERT: D 177 ARG cc_start: 0.8445 (tpt170) cc_final: 0.8078 (tpt170) REVERT: E 44 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.7529 (t80) REVERT: E 176 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8321 (t) REVERT: E 230 TYR cc_start: 0.8667 (m-80) cc_final: 0.7726 (m-80) REVERT: E 437 ASN cc_start: 0.7947 (m-40) cc_final: 0.7626 (t0) REVERT: E 506 MET cc_start: 0.7008 (tpt) cc_final: 0.6676 (tpt) REVERT: E 547 ASN cc_start: 0.8922 (t0) cc_final: 0.8606 (t0) REVERT: E 604 LEU cc_start: 0.8638 (mt) cc_final: 0.8351 (mt) REVERT: E 1073 SER cc_start: 0.8421 (m) cc_final: 0.8150 (p) REVERT: E 1154 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7992 (mm) REVERT: E 1209 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7802 (mm-30) REVERT: E 1219 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.7312 (t80) outliers start: 110 outliers final: 87 residues processed: 613 average time/residue: 0.1327 time to fit residues: 129.7097 Evaluate side-chains 635 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 540 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 265 ARG Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain E residue 788 ILE Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1151 VAL Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1207 THR Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1252 MET Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1277 SER Chi-restraints excluded: chain E residue 1286 THR Chi-restraints excluded: chain E residue 1416 HIS Chi-restraints excluded: chain E residue 1425 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 16 optimal weight: 8.9990 chunk 250 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 224 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 258 optimal weight: 20.0000 chunk 73 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 335 ASN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.191908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.165023 restraints weight = 27187.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.168503 restraints weight = 15308.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.170840 restraints weight = 10183.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.172209 restraints weight = 7593.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.173352 restraints weight = 6258.388| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21450 Z= 0.192 Angle : 0.676 13.915 29238 Z= 0.331 Chirality : 0.046 0.369 3497 Planarity : 0.004 0.051 3591 Dihedral : 16.641 176.704 3783 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.89 % Allowed : 21.74 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.16), residues: 2773 helix: 1.74 (0.14), residues: 1340 sheet: -2.11 (0.31), residues: 257 loop : -1.73 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 16 TYR 0.025 0.002 TYR E 772 PHE 0.021 0.002 PHE C 75 TRP 0.023 0.002 TRP D 83 HIS 0.006 0.001 HIS E1024 Details of bonding type rmsd covalent geometry : bond 0.00433 (21443) covalent geometry : angle 0.67369 (29222) SS BOND : bond 0.00476 ( 5) SS BOND : angle 1.21857 ( 10) hydrogen bonds : bond 0.04405 ( 1161) hydrogen bonds : angle 4.35643 ( 3402) link_BETA1-4 : bond 0.01712 ( 1) link_BETA1-4 : angle 4.87771 ( 3) link_NAG-ASN : bond 0.00560 ( 1) link_NAG-ASN : angle 2.27135 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 552 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7196 (mtt-85) cc_final: 0.6926 (mtt-85) REVERT: A 48 ASN cc_start: 0.8475 (m110) cc_final: 0.8087 (m110) REVERT: A 84 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8592 (tt) REVERT: A 93 ILE cc_start: 0.9116 (tt) cc_final: 0.8866 (mt) REVERT: A 200 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9013 (tt) REVERT: A 292 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6207 (pp20) REVERT: B 77 MET cc_start: 0.6614 (mmm) cc_final: 0.5948 (tmm) REVERT: B 125 ILE cc_start: 0.9437 (mm) cc_final: 0.9163 (mt) REVERT: B 169 MET cc_start: 0.8046 (mtm) cc_final: 0.7706 (mtp) REVERT: B 177 ARG cc_start: 0.8356 (tpt170) cc_final: 0.8145 (tpt170) REVERT: B 235 GLN cc_start: 0.8565 (mt0) cc_final: 0.8351 (mt0) REVERT: B 311 TRP cc_start: 0.9097 (t-100) cc_final: 0.8633 (t60) REVERT: C 77 MET cc_start: 0.6885 (mmm) cc_final: 0.5954 (tmm) REVERT: C 182 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8248 (mm) REVERT: C 258 TYR cc_start: 0.9141 (p90) cc_final: 0.8933 (p90) REVERT: D 58 ASP cc_start: 0.7770 (t0) cc_final: 0.7226 (t0) REVERT: D 67 LYS cc_start: 0.8222 (mppt) cc_final: 0.7563 (mtmt) REVERT: D 112 THR cc_start: 0.8963 (p) cc_final: 0.8739 (t) REVERT: D 152 GLN cc_start: 0.9327 (tp40) cc_final: 0.8647 (tp40) REVERT: D 158 MET cc_start: 0.8004 (mmm) cc_final: 0.7567 (tpp) REVERT: D 173 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7717 (mt0) REVERT: D 251 LEU cc_start: 0.8367 (tp) cc_final: 0.8065 (tt) REVERT: E 44 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7431 (t80) REVERT: E 48 PHE cc_start: 0.7896 (m-80) cc_final: 0.7385 (m-10) REVERT: E 176 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8331 (t) REVERT: E 230 TYR cc_start: 0.8700 (m-80) cc_final: 0.7756 (m-80) REVERT: E 273 GLN cc_start: 0.6690 (OUTLIER) cc_final: 0.6320 (tp40) REVERT: E 604 LEU cc_start: 0.8608 (mt) cc_final: 0.8318 (mt) REVERT: E 1073 SER cc_start: 0.8271 (m) cc_final: 0.8056 (p) REVERT: E 1104 ARG cc_start: 0.7244 (tpp80) cc_final: 0.6999 (tpt-90) REVERT: E 1154 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8056 (mm) REVERT: E 1209 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7770 (mm-30) REVERT: E 1219 TYR cc_start: 0.7786 (OUTLIER) cc_final: 0.7304 (t80) outliers start: 112 outliers final: 92 residues processed: 606 average time/residue: 0.1303 time to fit residues: 126.0953 Evaluate side-chains 645 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 544 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 265 ARG Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain E residue 788 ILE Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1151 VAL Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1173 VAL Chi-restraints excluded: chain E residue 1207 THR Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1252 MET Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1277 SER Chi-restraints excluded: chain E residue 1286 THR Chi-restraints excluded: chain E residue 1416 HIS Chi-restraints excluded: chain E residue 1425 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 114 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 230 optimal weight: 20.0000 chunk 204 optimal weight: 30.0000 chunk 65 optimal weight: 7.9990 chunk 261 optimal weight: 8.9990 chunk 214 optimal weight: 20.0000 chunk 138 optimal weight: 0.2980 chunk 168 optimal weight: 20.0000 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN ** E 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.191733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.165513 restraints weight = 27203.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.169004 restraints weight = 15592.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.170775 restraints weight = 10459.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.172347 restraints weight = 7712.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.172723 restraints weight = 6378.971| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21450 Z= 0.194 Angle : 0.687 13.500 29238 Z= 0.335 Chirality : 0.046 0.366 3497 Planarity : 0.004 0.051 3591 Dihedral : 16.386 176.748 3783 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 5.84 % Allowed : 22.53 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.16), residues: 2773 helix: 1.74 (0.14), residues: 1343 sheet: -2.06 (0.32), residues: 255 loop : -1.77 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 16 TYR 0.024 0.002 TYR E 772 PHE 0.022 0.002 PHE C 75 TRP 0.027 0.002 TRP D 83 HIS 0.006 0.001 HIS E1024 Details of bonding type rmsd covalent geometry : bond 0.00438 (21443) covalent geometry : angle 0.68497 (29222) SS BOND : bond 0.00609 ( 5) SS BOND : angle 1.20752 ( 10) hydrogen bonds : bond 0.04403 ( 1161) hydrogen bonds : angle 4.35905 ( 3402) link_BETA1-4 : bond 0.01763 ( 1) link_BETA1-4 : angle 4.84844 ( 3) link_NAG-ASN : bond 0.00560 ( 1) link_NAG-ASN : angle 2.21841 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 549 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8465 (m110) cc_final: 0.8067 (m110) REVERT: A 84 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8612 (tt) REVERT: A 93 ILE cc_start: 0.9091 (tt) cc_final: 0.8840 (mt) REVERT: A 200 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8997 (tt) REVERT: A 209 MET cc_start: 0.8324 (ttm) cc_final: 0.8104 (ttp) REVERT: A 292 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6179 (pp20) REVERT: A 314 ARG cc_start: 0.7702 (ptp90) cc_final: 0.6795 (ptp90) REVERT: B 77 MET cc_start: 0.6592 (mmm) cc_final: 0.5902 (tmm) REVERT: B 125 ILE cc_start: 0.9442 (mm) cc_final: 0.9162 (mt) REVERT: B 169 MET cc_start: 0.8080 (mtm) cc_final: 0.7715 (mtp) REVERT: B 177 ARG cc_start: 0.8346 (tpt170) cc_final: 0.8146 (tpt170) REVERT: B 199 MET cc_start: 0.8078 (mmm) cc_final: 0.7614 (mmm) REVERT: B 347 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.7566 (ttm-80) REVERT: C 77 MET cc_start: 0.6905 (mmm) cc_final: 0.5933 (tmm) REVERT: C 182 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8237 (mm) REVERT: D 58 ASP cc_start: 0.7756 (t0) cc_final: 0.7216 (t0) REVERT: D 67 LYS cc_start: 0.8179 (mppt) cc_final: 0.7517 (mtmt) REVERT: D 112 THR cc_start: 0.9021 (p) cc_final: 0.8800 (t) REVERT: D 152 GLN cc_start: 0.9313 (tp40) cc_final: 0.8617 (tp40) REVERT: D 158 MET cc_start: 0.8016 (mmm) cc_final: 0.7594 (tpp) REVERT: D 173 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7800 (mt0) REVERT: D 177 ARG cc_start: 0.8537 (tpt170) cc_final: 0.8270 (tpt170) REVERT: D 186 HIS cc_start: 0.7392 (p-80) cc_final: 0.7033 (p90) REVERT: D 251 LEU cc_start: 0.8298 (tp) cc_final: 0.8005 (tt) REVERT: E 44 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7484 (t80) REVERT: E 48 PHE cc_start: 0.7944 (m-80) cc_final: 0.7426 (m-10) REVERT: E 81 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7419 (pp) REVERT: E 158 TYR cc_start: 0.6835 (t80) cc_final: 0.5884 (t80) REVERT: E 176 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8335 (t) REVERT: E 230 TYR cc_start: 0.8712 (m-80) cc_final: 0.7737 (m-80) REVERT: E 506 MET cc_start: 0.7061 (tpt) cc_final: 0.6829 (tpt) REVERT: E 604 LEU cc_start: 0.8630 (mt) cc_final: 0.8330 (mt) REVERT: E 781 ASN cc_start: 0.8158 (p0) cc_final: 0.7693 (p0) REVERT: E 1073 SER cc_start: 0.8374 (m) cc_final: 0.8114 (p) REVERT: E 1104 ARG cc_start: 0.7256 (tpp80) cc_final: 0.7001 (tpt-90) REVERT: E 1154 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8035 (mm) REVERT: E 1183 ARG cc_start: 0.7913 (mtm110) cc_final: 0.7283 (mtm-85) REVERT: E 1209 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7752 (mm-30) REVERT: E 1219 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.7299 (t80) outliers start: 111 outliers final: 93 residues processed: 601 average time/residue: 0.1362 time to fit residues: 129.1076 Evaluate side-chains 639 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 537 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 265 ARG Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain E residue 788 ILE Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1151 VAL Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1173 VAL Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1207 THR Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1252 MET Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1269 SER Chi-restraints excluded: chain E residue 1277 SER Chi-restraints excluded: chain E residue 1286 THR Chi-restraints excluded: chain E residue 1416 HIS Chi-restraints excluded: chain E residue 1425 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 55 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 144 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 255 optimal weight: 8.9990 chunk 143 optimal weight: 0.9990 chunk 109 optimal weight: 0.0370 chunk 182 optimal weight: 8.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.184026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.155648 restraints weight = 28151.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.159493 restraints weight = 15094.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.162082 restraints weight = 9753.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.163779 restraints weight = 7181.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.164856 restraints weight = 5795.652| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21450 Z= 0.127 Angle : 0.642 12.505 29238 Z= 0.309 Chirality : 0.045 0.358 3497 Planarity : 0.004 0.048 3591 Dihedral : 15.721 178.579 3783 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.05 % Allowed : 24.47 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.17), residues: 2773 helix: 2.00 (0.14), residues: 1346 sheet: -1.95 (0.31), residues: 271 loop : -1.58 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 16 TYR 0.022 0.001 TYR E 123 PHE 0.016 0.001 PHE C 75 TRP 0.031 0.001 TRP D 83 HIS 0.006 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00271 (21443) covalent geometry : angle 0.63927 (29222) SS BOND : bond 0.00400 ( 5) SS BOND : angle 1.15617 ( 10) hydrogen bonds : bond 0.04043 ( 1161) hydrogen bonds : angle 4.15478 ( 3402) link_BETA1-4 : bond 0.02320 ( 1) link_BETA1-4 : angle 4.75086 ( 3) link_NAG-ASN : bond 0.00377 ( 1) link_NAG-ASN : angle 1.93002 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 573 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8384 (m110) cc_final: 0.7925 (m110) REVERT: A 75 PHE cc_start: 0.8196 (t80) cc_final: 0.7810 (t80) REVERT: A 93 ILE cc_start: 0.8987 (tt) cc_final: 0.8719 (mp) REVERT: A 200 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8902 (tt) REVERT: A 209 MET cc_start: 0.8216 (ttm) cc_final: 0.7853 (mtm) REVERT: A 292 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6229 (pt0) REVERT: A 314 ARG cc_start: 0.7531 (ptp90) cc_final: 0.6646 (ptp90) REVERT: B 77 MET cc_start: 0.6453 (mmm) cc_final: 0.5456 (mtp) REVERT: B 125 ILE cc_start: 0.9388 (mm) cc_final: 0.9168 (mt) REVERT: B 158 MET cc_start: 0.7792 (mmm) cc_final: 0.7556 (mmm) REVERT: B 169 MET cc_start: 0.8018 (mtm) cc_final: 0.7674 (mtp) REVERT: B 199 MET cc_start: 0.7963 (mmm) cc_final: 0.7751 (mmm) REVERT: B 297 THR cc_start: 0.9465 (m) cc_final: 0.9208 (p) REVERT: B 311 TRP cc_start: 0.9041 (t-100) cc_final: 0.8480 (t60) REVERT: C 77 MET cc_start: 0.6755 (mmm) cc_final: 0.5892 (tmm) REVERT: C 258 TYR cc_start: 0.9030 (p90) cc_final: 0.8808 (p90) REVERT: D 58 ASP cc_start: 0.7736 (t0) cc_final: 0.7287 (t0) REVERT: D 67 LYS cc_start: 0.8101 (mppt) cc_final: 0.7349 (mtpt) REVERT: D 112 THR cc_start: 0.8994 (p) cc_final: 0.8742 (t) REVERT: D 152 GLN cc_start: 0.9228 (tp40) cc_final: 0.8569 (tp40) REVERT: D 158 MET cc_start: 0.7964 (mmm) cc_final: 0.7519 (tpp) REVERT: D 173 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7593 (mt0) REVERT: D 177 ARG cc_start: 0.8547 (tpt170) cc_final: 0.8282 (tpt170) REVERT: D 247 ASN cc_start: 0.7417 (m-40) cc_final: 0.7167 (p0) REVERT: D 305 LEU cc_start: 0.8003 (mm) cc_final: 0.7761 (mt) REVERT: E 44 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7580 (t80) REVERT: E 48 PHE cc_start: 0.7898 (m-80) cc_final: 0.7514 (m-10) REVERT: E 230 TYR cc_start: 0.8613 (m-80) cc_final: 0.7659 (m-80) REVERT: E 437 ASN cc_start: 0.7910 (m-40) cc_final: 0.7657 (t0) REVERT: E 506 MET cc_start: 0.6884 (tpt) cc_final: 0.6661 (tpt) REVERT: E 604 LEU cc_start: 0.8637 (mt) cc_final: 0.8341 (mt) REVERT: E 714 GLN cc_start: 0.7063 (mm110) cc_final: 0.6108 (tp40) REVERT: E 1073 SER cc_start: 0.8315 (m) cc_final: 0.8052 (p) REVERT: E 1154 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7886 (mm) REVERT: E 1209 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7688 (mm-30) REVERT: E 1219 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.7220 (t80) REVERT: E 1223 PHE cc_start: 0.7447 (m-80) cc_final: 0.7042 (m-80) outliers start: 77 outliers final: 67 residues processed: 604 average time/residue: 0.1319 time to fit residues: 127.1095 Evaluate side-chains 611 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 539 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain E residue 788 ILE Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1207 THR Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1252 MET Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1416 HIS Chi-restraints excluded: chain E residue 1425 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 266 optimal weight: 7.9990 chunk 263 optimal weight: 30.0000 chunk 207 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 202 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN ** E 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.180352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.151493 restraints weight = 28445.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.155197 restraints weight = 15554.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.157742 restraints weight = 10240.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.159239 restraints weight = 7629.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.160478 restraints weight = 6280.199| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 21450 Z= 0.195 Angle : 0.693 12.846 29238 Z= 0.338 Chirality : 0.046 0.377 3497 Planarity : 0.004 0.048 3591 Dihedral : 15.774 178.209 3783 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.53 % Allowed : 24.47 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2773 helix: 1.86 (0.14), residues: 1350 sheet: -1.95 (0.32), residues: 270 loop : -1.63 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E1300 TYR 0.023 0.002 TYR E 772 PHE 0.020 0.002 PHE C 75 TRP 0.036 0.002 TRP D 83 HIS 0.006 0.001 HIS E1098 Details of bonding type rmsd covalent geometry : bond 0.00445 (21443) covalent geometry : angle 0.69045 (29222) SS BOND : bond 0.00449 ( 5) SS BOND : angle 1.08116 ( 10) hydrogen bonds : bond 0.04279 ( 1161) hydrogen bonds : angle 4.30478 ( 3402) link_BETA1-4 : bond 0.01843 ( 1) link_BETA1-4 : angle 4.92960 ( 3) link_NAG-ASN : bond 0.00570 ( 1) link_NAG-ASN : angle 2.21404 ( 3) =============================================================================== Job complete usr+sys time: 3692.09 seconds wall clock time: 64 minutes 14.44 seconds (3854.44 seconds total)