Starting phenix.real_space_refine on Sat Jul 4 16:34:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u1q_26303/07_2026/7u1q_26303.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u1q_26303/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7u1q_26303/07_2026/7u1q_26303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u1q_26303/07_2026/7u1q_26303.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u1q_26303/07_2026/7u1q_26303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u1q_26303/07_2026/7u1q_26303.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7u1q_26303/07_2026/7u1q_26303.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u1q_26303/07_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): 0.21s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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: 1.84 Conformation dependent library (CDL) restraints added in 982.0 milliseconds 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: 0.83 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: 4.58 Time building geometry restraints manager: 2.47 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: 28867 1.98 - 3.96: 278 3.96 - 5.94: 53 5.94 - 7.92: 19 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 - 32.56: 12280 32.56 - 65.12: 221 65.12 - 97.67: 20 97.67 - 130.23: 3 130.23 - 162.79: 7 Dihedral angle restraints: 12531 sinusoidal: 4425 harmonic: 8106 Sorted by residual: dihedral pdb=" C41 P5S A 403 " pdb=" C42 P5S A 403 " pdb=" C43 P5S A 403 " pdb=" C44 P5S A 403 " ideal model delta sinusoidal sigma weight residual 181.47 18.68 162.79 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" O BJX E1603 " pdb=" C16 BJX E1603 " pdb=" C17 BJX E1603 " pdb=" C18 BJX E1603 " ideal model delta sinusoidal sigma weight residual 10.31 -151.43 161.74 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C53 P5S E1610 " pdb=" C54 P5S E1610 " pdb=" C55 P5S E1610 " pdb=" C56 P5S E1610 " ideal model delta sinusoidal sigma weight residual 180.05 23.74 156.31 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 12528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2896 0.053 - 0.107: 516 0.107 - 0.160: 82 0.160 - 0.214: 2 0.214 - 0.267: 1 Chirality restraints: 3497 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN E 10 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5 BJX E1603 " pdb=" C7 BJX E1603 " pdb=" C8 BJX E1603 " pdb=" N1 BJX E1603 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" C4 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" C5 NAG F 1 " pdb=" O4 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.37 -0.16 2.00e-01 2.50e+01 6.58e-01 ... (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: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 20.170 Find NCS groups from input model: 0.360 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: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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= 0.135 Angle : 0.545 9.895 29238 Z= 0.263 Chirality : 0.041 0.267 3497 Planarity : 0.004 0.059 3591 Dihedral : 13.667 162.788 7244 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/Z covalent geometry : bond 0.00275 / 0.14 (21443) covalent geometry : angle 0.54312 / 0.26 (29222) SS BOND : bond 0.00109 / 0.06 ( 5) SS BOND : angle 0.85904 / 0.45 ( 10) hydrogen bonds : bond 0.16158 / 11.06 ( 1161) hydrogen bonds : angle 6.43000 / 4.58 ( 3402) link_BETA1-4 : bond 0.00750 / 0.39 ( 1) link_BETA1-4 : angle 3.83400 / 2.02 ( 3) link_NAG-ASN : bond 0.00118 / 0.06 ( 1) link_NAG-ASN : angle 2.39561 / 1.21 ( 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 : 0.726 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: 0.1357 time to fit residues: 159.2277 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 : 0.724 ------------------------------------------------------------------------------- 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... 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 = 0.3945 r_free = 0.3945 target = 0.183242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.155069 restraints weight = 28262.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.158762 restraints weight = 15330.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.161256 restraints weight = 10065.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.162981 restraints weight = 7512.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.164033 restraints weight = 6091.209| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21450 Z= 0.189 Angle : 0.654 11.360 29238 Z= 0.332 Chirality : 0.047 0.412 3497 Planarity : 0.005 0.053 3591 Dihedral : 13.176 171.856 3378 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 5.11 % Allowed : 14.58 % Favored : 80.32 % 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: -0.56 (0.16), residues: 2773 helix: 1.29 (0.14), residues: 1357 sheet: -2.53 (0.32), residues: 220 loop : -1.98 (0.17), residues: 1196 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 0.014 0.001 TRP A 83 HIS 0.007 0.001 HIS E 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 (21443) covalent geometry : angle 0.65095 / 0.33 (29222) SS BOND : bond 0.00601 / 0.31 ( 5) SS BOND : angle 2.28116 / 1.24 ( 10) hydrogen bonds : bond 0.05266 / 3.64 ( 1161) hydrogen bonds : angle 4.89739 / 3.50 ( 3402) link_BETA1-4 : bond 0.01594 / 0.84 ( 1) link_BETA1-4 : angle 3.47702 / 1.61 ( 3) link_NAG-ASN : bond 0.00385 / 0.20 ( 1) link_NAG-ASN : angle 2.58464 / 1.34 ( 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: 97 poor density : 616 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8495 (m110) cc_final: 0.8195 (m110) REVERT: A 93 ILE cc_start: 0.9189 (tt) cc_final: 0.8926 (mp) REVERT: A 200 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8884 (tt) REVERT: A 314 ARG cc_start: 0.7393 (ptp-170) cc_final: 0.7076 (ptm-80) REVERT: B 77 MET cc_start: 0.6763 (mmm) cc_final: 0.5952 (tmm) REVERT: B 88 MET cc_start: 0.7231 (tpp) cc_final: 0.7004 (tpp) REVERT: B 177 ARG cc_start: 0.8399 (tpt170) cc_final: 0.8196 (tpt170) REVERT: B 311 TRP cc_start: 0.9091 (t-100) cc_final: 0.8632 (t-100) REVERT: B 313 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.8070 (mt0) REVERT: B 325 ARG cc_start: 0.8424 (mtp85) cc_final: 0.7786 (mtp180) REVERT: C 77 MET cc_start: 0.6774 (mmm) cc_final: 0.5555 (tmm) REVERT: D 58 ASP cc_start: 0.7557 (t0) cc_final: 0.7241 (t0) REVERT: D 67 LYS cc_start: 0.8077 (mppt) cc_final: 0.7474 (mtmt) REVERT: D 158 MET cc_start: 0.8110 (mmm) cc_final: 0.7905 (tpp) REVERT: D 304 TYR cc_start: 0.8545 (m-80) cc_final: 0.8115 (m-10) REVERT: E 38 PHE cc_start: 0.7575 (t80) cc_final: 0.7332 (t80) REVERT: E 39 LEU cc_start: 0.8970 (tt) cc_final: 0.8605 (tp) REVERT: E 130 SER cc_start: 0.7787 (OUTLIER) cc_final: 0.7515 (p) REVERT: E 134 LYS cc_start: 0.8814 (mttt) cc_final: 0.8321 (tttp) REVERT: E 158 TYR cc_start: 0.6530 (t80) cc_final: 0.5958 (t80) REVERT: E 176 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8172 (t) REVERT: E 230 TYR cc_start: 0.8616 (m-80) cc_final: 0.7661 (m-80) REVERT: E 247 LEU cc_start: 0.8973 (mt) cc_final: 0.8699 (mt) REVERT: E 252 LYS cc_start: 0.8358 (ttmt) cc_final: 0.8024 (pttp) REVERT: E 264 GLN cc_start: 0.8124 (mm110) cc_final: 0.7750 (tp-100) REVERT: E 429 MET cc_start: 0.8623 (ttp) cc_final: 0.8300 (ttt) REVERT: E 441 MET cc_start: 0.7835 (mtt) cc_final: 0.7467 (mtm) REVERT: E 604 LEU cc_start: 0.8753 (mt) cc_final: 0.8492 (mt) REVERT: E 1073 SER cc_start: 0.8373 (m) cc_final: 0.8100 (p) REVERT: E 1154 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8053 (mm) REVERT: E 1209 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7511 (mm-30) REVERT: E 1223 PHE cc_start: 0.7313 (m-80) cc_final: 0.7113 (m-80) REVERT: E 1269 SER cc_start: 0.8934 (t) cc_final: 0.8663 (m) outliers start: 97 outliers final: 57 residues processed: 657 average time/residue: 0.1249 time to fit residues: 130.4139 Evaluate side-chains 637 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 575 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 519 CYS 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 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 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: 2.9990 chunk 221 optimal weight: 20.0000 chunk 240 optimal weight: 7.9990 chunk 198 optimal weight: 20.0000 chunk 212 optimal weight: 7.9990 chunk 148 optimal weight: 0.4980 chunk 133 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 145 optimal weight: 8.9990 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.180704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.152554 restraints weight = 28396.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.156147 restraints weight = 15556.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.158627 restraints weight = 10251.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.160281 restraints weight = 7629.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.161308 restraints weight = 6202.860| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21450 Z= 0.214 Angle : 0.660 10.423 29238 Z= 0.336 Chirality : 0.047 0.386 3497 Planarity : 0.005 0.053 3591 Dihedral : 12.700 172.739 3378 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.95 % Allowed : 16.89 % Favored : 77.16 % 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: -0.41 (0.16), residues: 2773 helix: 1.43 (0.14), residues: 1344 sheet: -2.55 (0.32), residues: 228 loop : -1.84 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 191 TYR 0.018 0.002 TYR C 258 PHE 0.025 0.002 PHE C 95 TRP 0.015 0.002 TRP E1088 HIS 0.007 0.001 HIS E 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (21443) covalent geometry : angle 0.65795 / 0.33 (29222) SS BOND : bond 0.00975 / 0.55 ( 5) SS BOND : angle 1.73642 / 0.94 ( 10) hydrogen bonds : bond 0.04921 / 3.41 ( 1161) hydrogen bonds : angle 4.67715 / 3.34 ( 3402) link_BETA1-4 : bond 0.01441 / 0.76 ( 1) link_BETA1-4 : angle 3.49084 / 1.64 ( 3) link_NAG-ASN : bond 0.00447 / 0.24 ( 1) link_NAG-ASN : angle 2.39452 / 1.25 ( 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 692 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 579 time to evaluate : 0.681 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: 0.8543 (m110) cc_final: 0.8214 (m110) REVERT: A 93 ILE cc_start: 0.9169 (tt) cc_final: 0.8872 (mp) REVERT: A 149 LEU cc_start: 0.9259 (tp) cc_final: 0.8917 (tt) REVERT: A 200 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8979 (tt) REVERT: B 39 LYS cc_start: 0.8621 (mttp) cc_final: 0.8416 (mmmt) REVERT: B 58 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6827 (t0) REVERT: B 77 MET cc_start: 0.6825 (mmm) cc_final: 0.6022 (tmm) REVERT: B 88 MET cc_start: 0.7257 (tpp) cc_final: 0.7052 (tpp) REVERT: B 177 ARG cc_start: 0.8397 (tpt170) cc_final: 0.7895 (tpt170) REVERT: B 180 THR cc_start: 0.8679 (p) cc_final: 0.8325 (p) REVERT: B 235 GLN cc_start: 0.8720 (mt0) cc_final: 0.8479 (mt0) REVERT: B 278 HIS cc_start: 0.7267 (m90) cc_final: 0.6973 (m90) REVERT: B 304 TYR cc_start: 0.8538 (m-80) cc_final: 0.8319 (m-10) REVERT: B 313 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7987 (mt0) REVERT: B 325 ARG cc_start: 0.8453 (mtp85) cc_final: 0.7773 (mtp180) REVERT: C 77 MET cc_start: 0.6802 (mmm) cc_final: 0.5692 (tmm) REVERT: D 58 ASP cc_start: 0.7639 (t0) cc_final: 0.7261 (t0) REVERT: D 67 LYS cc_start: 0.8087 (mppt) cc_final: 0.7497 (mtmt) REVERT: D 90 TRP cc_start: 0.8530 (m100) cc_final: 0.8244 (m100) REVERT: D 112 THR cc_start: 0.8910 (p) cc_final: 0.8645 (t) REVERT: D 158 MET cc_start: 0.8149 (mmm) cc_final: 0.7936 (tpp) REVERT: D 173 GLN cc_start: 0.8343 (mm-40) cc_final: 0.7850 (mt0) REVERT: D 177 ARG cc_start: 0.8567 (tpt170) cc_final: 0.8285 (tpt170) REVERT: D 186 HIS cc_start: 0.7393 (p-80) cc_final: 0.7073 (p90) REVERT: D 212 SER cc_start: 0.8979 (m) cc_final: 0.8702 (t) REVERT: D 276 HIS cc_start: 0.7594 (p-80) cc_final: 0.7272 (p-80) REVERT: D 304 TYR cc_start: 0.8526 (m-80) cc_final: 0.8182 (m-80) REVERT: D 305 LEU cc_start: 0.8214 (mm) cc_final: 0.7924 (mt) REVERT: E 39 LEU cc_start: 0.9029 (tt) cc_final: 0.8647 (tp) REVERT: E 81 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7407 (pp) REVERT: E 134 LYS cc_start: 0.8819 (mttt) cc_final: 0.8601 (mttm) REVERT: E 176 VAL cc_start: 0.8506 (OUTLIER) cc_final: 0.8264 (t) REVERT: E 230 TYR cc_start: 0.8615 (m-80) cc_final: 0.7709 (m-80) REVERT: E 247 LEU cc_start: 0.9025 (mt) cc_final: 0.8798 (mt) REVERT: E 252 LYS cc_start: 0.8346 (ttmt) cc_final: 0.8109 (pttp) REVERT: E 264 GLN cc_start: 0.8043 (mm110) cc_final: 0.7708 (tp-100) REVERT: E 358 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8640 (mt) REVERT: E 506 MET cc_start: 0.7085 (tpt) cc_final: 0.6862 (tpt) REVERT: E 604 LEU cc_start: 0.8723 (mt) cc_final: 0.8462 (mt) REVERT: E 883 THR cc_start: 0.6131 (m) cc_final: 0.5731 (p) REVERT: E 1073 SER cc_start: 0.8371 (m) cc_final: 0.8126 (p) REVERT: E 1104 ARG cc_start: 0.7420 (tpp80) cc_final: 0.7205 (tpt-90) REVERT: E 1154 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8054 (mm) REVERT: E 1269 SER cc_start: 0.8976 (t) cc_final: 0.8717 (m) outliers start: 113 outliers final: 79 residues processed: 628 average time/residue: 0.1406 time to fit residues: 139.5764 Evaluate side-chains 638 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 552 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 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 291 VAL Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 58 ASP 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 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 78 SER 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 259 HIS 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 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 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 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 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 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 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: 4.9990 chunk 255 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 148 optimal weight: 0.0870 chunk 97 optimal weight: 4.9990 chunk 266 optimal weight: 30.0000 chunk 264 optimal weight: 30.0000 chunk 112 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 173 GLN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 HIS ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.184385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.155863 restraints weight = 28166.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.159589 restraints weight = 15331.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.162208 restraints weight = 10009.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.163855 restraints weight = 7419.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.165030 restraints weight = 6033.552| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21450 Z= 0.135 Angle : 0.599 10.213 29238 Z= 0.298 Chirality : 0.044 0.342 3497 Planarity : 0.004 0.045 3591 Dihedral : 11.724 158.880 3378 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 5.05 % Allowed : 18.89 % Favored : 76.05 % 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: -0.05 (0.16), residues: 2773 helix: 1.81 (0.14), residues: 1331 sheet: -2.14 (0.33), residues: 225 loop : -1.79 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 168 TYR 0.020 0.001 TYR E 475 PHE 0.018 0.001 PHE C 95 TRP 0.011 0.001 TRP D 83 HIS 0.010 0.001 HIS E 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (21443) covalent geometry : angle 0.59727 / 0.30 (29222) SS BOND : bond 0.00960 / 0.55 ( 5) SS BOND : angle 1.42690 / 0.65 ( 10) hydrogen bonds : bond 0.04411 / 3.06 ( 1161) hydrogen bonds : angle 4.35291 / 3.09 ( 3402) link_BETA1-4 : bond 0.01234 / 0.65 ( 1) link_BETA1-4 : angle 3.52363 / 1.71 ( 3) link_NAG-ASN : bond 0.00232 / 0.12 ( 1) link_NAG-ASN : angle 1.87946 / 0.96 ( 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 679 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 583 time to evaluate : 0.803 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 34 ARG cc_start: 0.7193 (mtt-85) cc_final: 0.6958 (mtt-85) REVERT: A 48 ASN cc_start: 0.8533 (m110) cc_final: 0.8166 (m110) REVERT: A 93 ILE cc_start: 0.9125 (tt) cc_final: 0.8838 (mp) REVERT: A 200 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8862 (tt) REVERT: A 292 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6302 (pp20) REVERT: B 39 LYS cc_start: 0.8615 (mttp) cc_final: 0.8363 (mmmt) REVERT: B 88 MET cc_start: 0.7185 (tpp) cc_final: 0.6980 (tpp) REVERT: B 169 MET cc_start: 0.7929 (mtm) cc_final: 0.7589 (mtp) REVERT: B 177 ARG cc_start: 0.8365 (tpt170) cc_final: 0.7912 (tpt170) REVERT: B 180 THR cc_start: 0.8658 (p) cc_final: 0.8319 (p) REVERT: B 278 HIS cc_start: 0.7135 (m90) cc_final: 0.6848 (m90) REVERT: B 304 TYR cc_start: 0.8476 (m-80) cc_final: 0.8237 (m-10) REVERT: B 313 GLN cc_start: 0.8152 (mt0) cc_final: 0.7872 (mt0) REVERT: B 325 ARG cc_start: 0.8400 (mtp85) cc_final: 0.7776 (mtp180) REVERT: B 338 LYS cc_start: 0.8007 (mmtm) cc_final: 0.7717 (mptt) REVERT: C 77 MET cc_start: 0.6752 (mmm) cc_final: 0.5916 (tmm) REVERT: D 58 ASP cc_start: 0.7713 (t0) cc_final: 0.7223 (t0) REVERT: D 67 LYS cc_start: 0.8063 (mppt) cc_final: 0.7530 (mtmt) REVERT: D 112 THR cc_start: 0.8826 (p) cc_final: 0.8567 (t) REVERT: D 152 GLN cc_start: 0.9165 (tp40) cc_final: 0.8482 (tp40) REVERT: D 158 MET cc_start: 0.8038 (mmm) cc_final: 0.7638 (tpp) REVERT: D 173 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7665 (mt0) REVERT: D 177 ARG cc_start: 0.8550 (tpt170) cc_final: 0.8306 (tpt170) REVERT: D 304 TYR cc_start: 0.8438 (m-80) cc_final: 0.8126 (m-10) REVERT: E 39 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8728 (tp) REVERT: E 134 LYS cc_start: 0.8768 (mttt) cc_final: 0.8523 (mttm) REVERT: E 176 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8222 (t) REVERT: E 230 TYR cc_start: 0.8530 (m-80) cc_final: 0.7618 (m-80) REVERT: E 252 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7849 (pttp) REVERT: E 264 GLN cc_start: 0.8023 (mm110) cc_final: 0.7749 (tp-100) REVERT: E 289 ARG cc_start: 0.7494 (ttm170) cc_final: 0.7222 (ttp-170) REVERT: E 429 MET cc_start: 0.8455 (ttp) cc_final: 0.8109 (ttt) REVERT: E 506 MET cc_start: 0.7143 (tpt) cc_final: 0.6931 (tpt) REVERT: E 604 LEU cc_start: 0.8706 (mt) cc_final: 0.8455 (mt) REVERT: E 775 GLN cc_start: 0.8409 (tp40) cc_final: 0.8124 (tp40) REVERT: E 1073 SER cc_start: 0.8312 (m) cc_final: 0.8071 (p) REVERT: E 1095 LYS cc_start: 0.7461 (tttt) cc_final: 0.7179 (tttp) REVERT: E 1209 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7674 (mm-30) REVERT: E 1269 SER cc_start: 0.8972 (t) cc_final: 0.8703 (m) outliers start: 96 outliers final: 69 residues processed: 623 average time/residue: 0.1344 time to fit residues: 132.9373 Evaluate side-chains 632 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 559 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 92 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 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 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 299 GLN 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 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 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 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 299 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 459 SER 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 1207 THR Chi-restraints excluded: chain E residue 1252 MET Chi-restraints excluded: chain E residue 1259 VAL 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: 7.9990 chunk 129 optimal weight: 9.9990 chunk 184 optimal weight: 30.0000 chunk 29 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 190 optimal weight: 5.9990 chunk 151 optimal weight: 20.0000 chunk 220 optimal weight: 50.0000 chunk 245 optimal weight: 1.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 235 GLN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN E1191 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.185605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.158033 restraints weight = 27950.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.161625 restraints weight = 15376.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.164039 restraints weight = 10119.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.165603 restraints weight = 7543.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.166752 restraints weight = 6135.953| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21450 Z= 0.172 Angle : 0.630 9.624 29238 Z= 0.312 Chirality : 0.045 0.365 3497 Planarity : 0.004 0.051 3591 Dihedral : 11.329 155.823 3378 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.84 % Allowed : 19.63 % Favored : 74.53 % 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: -0.04 (0.16), residues: 2773 helix: 1.79 (0.14), residues: 1335 sheet: -2.16 (0.33), residues: 237 loop : -1.75 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 191 TYR 0.025 0.001 TYR E 772 PHE 0.019 0.002 PHE C 75 TRP 0.014 0.001 TRP D 83 HIS 0.006 0.001 HIS E1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (21443) covalent geometry : angle 0.62851 / 0.31 (29222) SS BOND : bond 0.00458 / 0.26 ( 5) SS BOND : angle 1.71437 / 0.68 ( 10) hydrogen bonds : bond 0.04406 / 3.04 ( 1161) hydrogen bonds : angle 4.35235 / 3.10 ( 3402) link_BETA1-4 : bond 0.01065 / 0.56 ( 1) link_BETA1-4 : angle 3.50894 / 1.69 ( 3) link_NAG-ASN : bond 0.00423 / 0.22 ( 1) link_NAG-ASN : angle 2.03686 / 1.06 ( 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 682 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 571 time to evaluate : 0.783 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: 0.8578 (m110) cc_final: 0.8239 (m110) REVERT: A 84 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8545 (tt) REVERT: A 93 ILE cc_start: 0.9149 (tt) cc_final: 0.8892 (mt) REVERT: A 200 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8949 (tt) REVERT: A 292 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6252 (pp20) REVERT: B 39 LYS cc_start: 0.8700 (mttp) cc_final: 0.8445 (mmmt) REVERT: B 88 MET cc_start: 0.7279 (tpp) cc_final: 0.7078 (tpp) REVERT: B 125 ILE cc_start: 0.9467 (mm) cc_final: 0.9127 (mt) REVERT: B 169 MET cc_start: 0.7999 (mtm) cc_final: 0.7690 (mtp) REVERT: B 177 ARG cc_start: 0.8349 (tpt170) cc_final: 0.7896 (tpt170) REVERT: B 180 THR cc_start: 0.8695 (p) cc_final: 0.8323 (p) REVERT: B 278 HIS cc_start: 0.7211 (m90) cc_final: 0.6998 (m90) REVERT: B 304 TYR cc_start: 0.8500 (m-80) cc_final: 0.8260 (m-10) REVERT: B 325 ARG cc_start: 0.8429 (mtp85) cc_final: 0.7964 (mtp180) REVERT: B 338 LYS cc_start: 0.8064 (mmtm) cc_final: 0.7814 (mptt) REVERT: C 67 LYS cc_start: 0.8537 (mttt) cc_final: 0.8332 (mtpt) REVERT: C 77 MET cc_start: 0.6813 (mmm) cc_final: 0.5847 (tmm) REVERT: C 91 TRP cc_start: 0.8463 (t60) cc_final: 0.8227 (t60) REVERT: C 137 MET cc_start: 0.7744 (mmm) cc_final: 0.7529 (tpp) REVERT: D 37 SER cc_start: 0.9200 (OUTLIER) cc_final: 0.8921 (m) REVERT: D 58 ASP cc_start: 0.7758 (t0) cc_final: 0.7246 (t0) REVERT: D 67 LYS cc_start: 0.8163 (mppt) cc_final: 0.7605 (mtmt) REVERT: D 112 THR cc_start: 0.8894 (p) cc_final: 0.8630 (t) REVERT: D 152 GLN cc_start: 0.9302 (tp40) cc_final: 0.8684 (tp40) REVERT: D 158 MET cc_start: 0.8019 (mmm) cc_final: 0.7815 (tpp) REVERT: D 173 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7696 (mt0) REVERT: D 177 ARG cc_start: 0.8500 (tpt170) cc_final: 0.8247 (tpt170) REVERT: D 186 HIS cc_start: 0.7375 (p-80) cc_final: 0.6977 (p90) REVERT: D 205 LEU cc_start: 0.8663 (mp) cc_final: 0.8313 (mt) REVERT: D 304 TYR cc_start: 0.8449 (m-80) cc_final: 0.8139 (m-10) REVERT: E 39 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8770 (tp) REVERT: E 40 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8376 (mt) REVERT: E 81 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7344 (pp) REVERT: E 134 LYS cc_start: 0.8840 (mttt) cc_final: 0.8369 (mtpt) REVERT: E 174 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8111 (tt) REVERT: E 230 TYR cc_start: 0.8618 (m-80) cc_final: 0.7711 (m-80) REVERT: E 252 LYS cc_start: 0.8262 (ttmt) cc_final: 0.7857 (pttp) REVERT: E 264 GLN cc_start: 0.7988 (mm110) cc_final: 0.7701 (tp-100) REVERT: E 273 GLN cc_start: 0.6776 (OUTLIER) cc_final: 0.6394 (tp40) REVERT: E 289 ARG cc_start: 0.7465 (ttm170) cc_final: 0.6413 (ttm110) REVERT: E 437 ASN cc_start: 0.7971 (m-40) cc_final: 0.7674 (t0) REVERT: E 506 MET cc_start: 0.7086 (tpt) cc_final: 0.6853 (tpt) REVERT: E 547 ASN cc_start: 0.8916 (t0) cc_final: 0.8629 (t0) REVERT: E 604 LEU cc_start: 0.8663 (mt) cc_final: 0.8394 (mt) REVERT: E 775 GLN cc_start: 0.8376 (tp40) cc_final: 0.8096 (tp40) REVERT: E 1073 SER cc_start: 0.8361 (m) cc_final: 0.8091 (p) REVERT: E 1154 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8006 (mm) REVERT: E 1209 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7736 (mm-30) REVERT: E 1269 SER cc_start: 0.8997 (t) cc_final: 0.8710 (m) outliers start: 111 outliers final: 81 residues processed: 621 average time/residue: 0.1330 time to fit residues: 132.6542 Evaluate side-chains 636 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 545 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 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 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 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 C residue 338 LYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 76 THR 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 259 HIS Chi-restraints excluded: chain D residue 269 ASP 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 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 174 LEU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 184 LEU 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 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 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 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 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: 5.9990 chunk 239 optimal weight: 8.9990 chunk 232 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 258 optimal weight: 50.0000 chunk 16 optimal weight: 4.9990 chunk 153 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN A 335 ASN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.193682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.167500 restraints weight = 27202.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.171064 restraints weight = 15579.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.172652 restraints weight = 10491.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.175130 restraints weight = 7682.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.175248 restraints weight = 5922.724| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 21450 Z= 0.202 Angle : 0.662 12.060 29238 Z= 0.328 Chirality : 0.046 0.362 3497 Planarity : 0.004 0.051 3591 Dihedral : 11.253 154.761 3378 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 6.00 % Allowed : 21.05 % Favored : 72.95 % 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: -0.12 (0.16), residues: 2773 helix: 1.73 (0.14), residues: 1333 sheet: -2.20 (0.33), residues: 237 loop : -1.79 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 325 TYR 0.024 0.002 TYR E 772 PHE 0.022 0.002 PHE C 75 TRP 0.017 0.001 TRP D 83 HIS 0.006 0.001 HIS E1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (21443) covalent geometry : angle 0.66004 / 0.33 (29222) SS BOND : bond 0.00458 / 0.25 ( 5) SS BOND : angle 1.47955 / 0.65 ( 10) hydrogen bonds : bond 0.04477 / 3.09 ( 1161) hydrogen bonds : angle 4.40959 / 3.14 ( 3402) link_BETA1-4 : bond 0.01123 / 0.59 ( 1) link_BETA1-4 : angle 3.57730 / 1.72 ( 3) link_NAG-ASN : bond 0.00425 / 0.22 ( 1) link_NAG-ASN : angle 2.11411 / 1.11 ( 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 672 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 558 time to evaluate : 0.695 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: 0.8596 (m110) cc_final: 0.8256 (m110) REVERT: A 84 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8580 (tt) REVERT: A 93 ILE cc_start: 0.9148 (tt) cc_final: 0.8877 (mt) REVERT: A 200 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8965 (tt) REVERT: A 292 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6309 (pp20) REVERT: A 325 ARG cc_start: 0.7790 (ptm-80) cc_final: 0.7494 (ptm-80) REVERT: B 39 LYS cc_start: 0.8713 (mttp) cc_final: 0.8473 (mmmt) REVERT: B 77 MET cc_start: 0.6678 (mmm) cc_final: 0.5662 (mtp) REVERT: B 88 MET cc_start: 0.7295 (tpp) cc_final: 0.7093 (tpp) REVERT: B 125 ILE cc_start: 0.9478 (mm) cc_final: 0.9147 (mt) REVERT: B 169 MET cc_start: 0.8104 (mtm) cc_final: 0.7801 (mtp) REVERT: B 177 ARG cc_start: 0.8354 (tpt170) cc_final: 0.7921 (tpt170) REVERT: B 180 THR cc_start: 0.8728 (p) cc_final: 0.8331 (p) REVERT: B 325 ARG cc_start: 0.8458 (mtp85) cc_final: 0.7853 (mtp180) REVERT: C 77 MET cc_start: 0.6858 (mmm) cc_final: 0.5867 (tmm) REVERT: C 137 MET cc_start: 0.7845 (mmm) cc_final: 0.7633 (tpp) REVERT: C 258 TYR cc_start: 0.9137 (p90) cc_final: 0.8932 (p90) REVERT: D 37 SER cc_start: 0.9194 (OUTLIER) cc_final: 0.8960 (m) REVERT: D 58 ASP cc_start: 0.7748 (t0) cc_final: 0.7209 (t0) REVERT: D 67 LYS cc_start: 0.8215 (mppt) cc_final: 0.7594 (mtmt) REVERT: D 112 THR cc_start: 0.8922 (p) cc_final: 0.8693 (t) REVERT: D 158 MET cc_start: 0.8082 (mmm) cc_final: 0.7621 (tpp) REVERT: D 173 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7863 (mt0) REVERT: D 186 HIS cc_start: 0.7388 (p-80) cc_final: 0.7012 (p90) REVERT: D 304 TYR cc_start: 0.8439 (m-80) cc_final: 0.8133 (m-10) REVERT: E 39 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8802 (tp) REVERT: E 40 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8433 (mt) REVERT: E 44 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7510 (t80) REVERT: E 81 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7420 (pp) REVERT: E 134 LYS cc_start: 0.8849 (mttt) cc_final: 0.8371 (mtpt) REVERT: E 230 TYR cc_start: 0.8698 (m-80) cc_final: 0.7754 (m-80) REVERT: E 252 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7938 (pttp) REVERT: E 345 PHE cc_start: 0.7224 (m-80) cc_final: 0.7015 (m-80) REVERT: E 437 ASN cc_start: 0.8037 (m-40) cc_final: 0.7734 (t0) REVERT: E 506 MET cc_start: 0.7060 (tpt) cc_final: 0.6731 (tpt) REVERT: E 604 LEU cc_start: 0.8634 (mt) cc_final: 0.8339 (mt) REVERT: E 733 VAL cc_start: 0.4698 (m) cc_final: 0.3950 (t) REVERT: E 1073 SER cc_start: 0.8380 (m) cc_final: 0.8129 (p) REVERT: E 1095 LYS cc_start: 0.7196 (tttp) cc_final: 0.6875 (tttp) REVERT: E 1154 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8036 (mm) REVERT: E 1209 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7791 (mm-30) REVERT: E 1269 SER cc_start: 0.8977 (t) cc_final: 0.8656 (m) outliers start: 114 outliers final: 85 residues processed: 613 average time/residue: 0.1268 time to fit residues: 123.7034 Evaluate side-chains 642 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 548 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 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 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 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 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 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 37 SER Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 76 THR 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 259 HIS 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 37 VAL Chi-restraints excluded: chain E residue 39 LEU 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 130 SER Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 184 LEU 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 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: 5.9990 chunk 151 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 267 optimal weight: 30.0000 chunk 189 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 chunk 264 optimal weight: 30.0000 chunk 70 optimal weight: 20.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 235 GLN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** 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 = 0.4064 r_free = 0.4064 target = 0.194090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.167970 restraints weight = 27084.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.171476 restraints weight = 15463.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.173196 restraints weight = 10458.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.174871 restraints weight = 7699.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.175211 restraints weight = 6326.128| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21450 Z= 0.185 Angle : 0.656 11.440 29238 Z= 0.323 Chirality : 0.046 0.352 3497 Planarity : 0.004 0.050 3591 Dihedral : 11.163 154.089 3378 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 6.00 % Allowed : 21.74 % Favored : 72.26 % 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: -0.08 (0.16), residues: 2773 helix: 1.74 (0.14), residues: 1338 sheet: -2.18 (0.33), residues: 231 loop : -1.76 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 177 TYR 0.025 0.002 TYR E 772 PHE 0.021 0.002 PHE C 75 TRP 0.019 0.001 TRP D 83 HIS 0.006 0.001 HIS E1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (21443) covalent geometry : angle 0.65404 / 0.32 (29222) SS BOND : bond 0.00639 / 0.36 ( 5) SS BOND : angle 1.24455 / 0.60 ( 10) hydrogen bonds : bond 0.04413 / 3.05 ( 1161) hydrogen bonds : angle 4.36837 / 3.12 ( 3402) link_BETA1-4 : bond 0.01109 / 0.58 ( 1) link_BETA1-4 : angle 3.60472 / 1.74 ( 3) link_NAG-ASN : bond 0.00366 / 0.19 ( 1) link_NAG-ASN : angle 2.02799 / 1.06 ( 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 669 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 555 time to evaluate : 0.689 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 34 ARG cc_start: 0.7217 (mtt-85) cc_final: 0.7000 (mtt-85) REVERT: A 48 ASN cc_start: 0.8585 (m110) cc_final: 0.8237 (m110) REVERT: A 84 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8589 (tt) REVERT: A 93 ILE cc_start: 0.9139 (tt) cc_final: 0.8876 (mt) REVERT: A 200 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8972 (tt) REVERT: A 292 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6338 (pp20) REVERT: B 39 LYS cc_start: 0.8737 (mttp) cc_final: 0.8528 (mmmt) REVERT: B 77 MET cc_start: 0.6621 (mmm) cc_final: 0.5586 (mtp) REVERT: B 125 ILE cc_start: 0.9470 (mm) cc_final: 0.9183 (mt) REVERT: B 169 MET cc_start: 0.8091 (mtm) cc_final: 0.7777 (mtp) REVERT: B 177 ARG cc_start: 0.8342 (tpt170) cc_final: 0.7927 (tpt170) REVERT: B 180 THR cc_start: 0.8718 (p) cc_final: 0.8288 (p) REVERT: B 311 TRP cc_start: 0.9098 (t-100) cc_final: 0.8564 (t60) REVERT: B 325 ARG cc_start: 0.8433 (mtp85) cc_final: 0.7972 (mtp180) REVERT: C 77 MET cc_start: 0.6843 (mmm) cc_final: 0.5856 (tmm) REVERT: C 169 MET cc_start: 0.7116 (mtp) cc_final: 0.6738 (ptm) REVERT: C 258 TYR cc_start: 0.9125 (p90) cc_final: 0.8915 (p90) REVERT: D 37 SER cc_start: 0.9189 (OUTLIER) cc_final: 0.8983 (m) REVERT: D 58 ASP cc_start: 0.7743 (t0) cc_final: 0.7260 (t0) REVERT: D 67 LYS cc_start: 0.8218 (mppt) cc_final: 0.7597 (mtmt) REVERT: D 72 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8771 (mm) REVERT: D 112 THR cc_start: 0.8987 (p) cc_final: 0.8732 (t) REVERT: D 152 GLN cc_start: 0.9316 (tp40) cc_final: 0.8606 (tp40) REVERT: D 158 MET cc_start: 0.8068 (mmm) cc_final: 0.7579 (tpp) REVERT: D 173 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7863 (mt0) REVERT: D 177 ARG cc_start: 0.8336 (tpt170) cc_final: 0.7854 (tpt170) REVERT: D 251 LEU cc_start: 0.8253 (tp) cc_final: 0.7965 (tp) REVERT: D 304 TYR cc_start: 0.8436 (m-80) cc_final: 0.8157 (m-10) REVERT: E 39 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8790 (tp) REVERT: E 40 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8398 (mt) REVERT: E 81 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7399 (pp) REVERT: E 112 MET cc_start: 0.7689 (mtt) cc_final: 0.7444 (mtm) REVERT: E 134 LYS cc_start: 0.8827 (mttt) cc_final: 0.8353 (mtpt) REVERT: E 230 TYR cc_start: 0.8697 (m-80) cc_final: 0.7742 (m-80) REVERT: E 252 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7911 (pttp) REVERT: E 345 PHE cc_start: 0.7203 (m-80) cc_final: 0.6986 (m-80) REVERT: E 437 ASN cc_start: 0.8021 (m-40) cc_final: 0.7688 (t0) REVERT: E 506 MET cc_start: 0.6997 (tpt) cc_final: 0.6680 (tpt) REVERT: E 604 LEU cc_start: 0.8632 (mt) cc_final: 0.8345 (mt) REVERT: E 1073 SER cc_start: 0.8378 (m) cc_final: 0.8127 (p) REVERT: E 1095 LYS cc_start: 0.7136 (tttp) cc_final: 0.6860 (tttp) REVERT: E 1154 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8064 (mm) REVERT: E 1209 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7791 (mm-30) REVERT: E 1219 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.7328 (t80) outliers start: 114 outliers final: 86 residues processed: 611 average time/residue: 0.1289 time to fit residues: 125.3995 Evaluate side-chains 639 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 543 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 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 92 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 184 SER 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 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 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 37 SER Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 76 THR 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 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 184 LEU 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 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 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 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 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: 0.9980 chunk 250 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 224 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 258 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 HIS C 235 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN E 498 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.183141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.154833 restraints weight = 28015.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.158598 restraints weight = 15203.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.161121 restraints weight = 9921.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.162742 restraints weight = 7350.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.163918 restraints weight = 5958.413| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21450 Z= 0.139 Angle : 0.621 11.166 29238 Z= 0.304 Chirality : 0.044 0.338 3497 Planarity : 0.004 0.049 3591 Dihedral : 10.883 153.915 3378 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 5.16 % Allowed : 22.89 % Favored : 71.95 % 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: 0.14 (0.16), residues: 2773 helix: 1.92 (0.14), residues: 1346 sheet: -2.11 (0.33), residues: 234 loop : -1.66 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 16 TYR 0.022 0.001 TYR E 772 PHE 0.018 0.001 PHE C 75 TRP 0.021 0.001 TRP D 83 HIS 0.006 0.001 HIS E1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (21443) covalent geometry : angle 0.61935 / 0.30 (29222) SS BOND : bond 0.00292 / 0.17 ( 5) SS BOND : angle 1.19928 / 0.58 ( 10) hydrogen bonds : bond 0.04187 / 2.90 ( 1161) hydrogen bonds : angle 4.23757 / 3.03 ( 3402) link_BETA1-4 : bond 0.01100 / 0.58 ( 1) link_BETA1-4 : angle 3.56118 / 1.74 ( 3) link_NAG-ASN : bond 0.00236 / 0.12 ( 1) link_NAG-ASN : angle 1.83457 / 0.95 ( 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 665 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 567 time to evaluate : 0.559 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: 0.7168 (mtt-85) cc_final: 0.6961 (mtt-85) REVERT: A 48 ASN cc_start: 0.8563 (m110) cc_final: 0.8203 (m110) REVERT: A 84 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8513 (tt) REVERT: A 93 ILE cc_start: 0.9106 (tt) cc_final: 0.8797 (mp) REVERT: A 200 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8928 (tt) REVERT: A 251 LEU cc_start: 0.8932 (tp) cc_final: 0.8671 (tp) REVERT: A 292 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6133 (pp20) REVERT: A 314 ARG cc_start: 0.7588 (ptp90) cc_final: 0.6651 (ptp90) REVERT: A 325 ARG cc_start: 0.7717 (ptm-80) cc_final: 0.7502 (ptm-80) REVERT: B 39 LYS cc_start: 0.8728 (mttp) cc_final: 0.8499 (mmmt) REVERT: B 77 MET cc_start: 0.6540 (mmm) cc_final: 0.5529 (mtp) REVERT: B 125 ILE cc_start: 0.9427 (mm) cc_final: 0.9180 (mt) REVERT: B 169 MET cc_start: 0.8033 (mtm) cc_final: 0.7673 (mtp) REVERT: B 177 ARG cc_start: 0.8312 (tpt170) cc_final: 0.7956 (tpt170) REVERT: B 180 THR cc_start: 0.8801 (p) cc_final: 0.8392 (p) REVERT: B 311 TRP cc_start: 0.9123 (t-100) cc_final: 0.8565 (t60) REVERT: B 325 ARG cc_start: 0.8448 (mtp85) cc_final: 0.7946 (mtp180) REVERT: C 77 MET cc_start: 0.6744 (mmm) cc_final: 0.5837 (tmm) REVERT: D 37 SER cc_start: 0.9182 (OUTLIER) cc_final: 0.8962 (m) REVERT: D 58 ASP cc_start: 0.7684 (t0) cc_final: 0.7216 (t0) REVERT: D 67 LYS cc_start: 0.8202 (mppt) cc_final: 0.7572 (mtmt) REVERT: D 72 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8756 (mm) REVERT: D 112 THR cc_start: 0.8939 (p) cc_final: 0.8687 (t) REVERT: D 152 GLN cc_start: 0.9264 (tp40) cc_final: 0.8584 (tp40) REVERT: D 158 MET cc_start: 0.7996 (mmm) cc_final: 0.7486 (tpp) REVERT: D 173 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7846 (mt0) REVERT: D 177 ARG cc_start: 0.8406 (tpt170) cc_final: 0.8050 (tpt170) REVERT: D 247 ASN cc_start: 0.7724 (m-40) cc_final: 0.7142 (p0) REVERT: D 251 LEU cc_start: 0.8214 (tp) cc_final: 0.7940 (tt) REVERT: D 304 TYR cc_start: 0.8429 (m-80) cc_final: 0.8156 (m-10) REVERT: E 39 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8722 (tp) REVERT: E 134 LYS cc_start: 0.8790 (mttt) cc_final: 0.8324 (mtpt) REVERT: E 230 TYR cc_start: 0.8638 (m-80) cc_final: 0.7694 (m-80) REVERT: E 252 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7867 (pttp) REVERT: E 437 ASN cc_start: 0.7977 (m-40) cc_final: 0.7725 (t0) REVERT: E 604 LEU cc_start: 0.8635 (mt) cc_final: 0.8338 (mt) REVERT: E 714 GLN cc_start: 0.7249 (mm110) cc_final: 0.6218 (tp40) REVERT: E 1073 SER cc_start: 0.8330 (m) cc_final: 0.8078 (p) REVERT: E 1154 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7928 (mm) REVERT: E 1183 ARG cc_start: 0.7816 (mtm110) cc_final: 0.7201 (mtm-85) REVERT: E 1209 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7717 (mm-30) REVERT: E 1219 TYR cc_start: 0.7750 (OUTLIER) cc_final: 0.7272 (t80) outliers start: 98 outliers final: 74 residues processed: 610 average time/residue: 0.1277 time to fit residues: 123.9881 Evaluate side-chains 633 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 551 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 46 HIS 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 92 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 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 339 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 100 LEU 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 37 SER Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 72 LEU 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 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 336 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 39 LEU 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 108 MET Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 184 LEU 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 273 GLN Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 400 MET 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 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 1219 TYR Chi-restraints excluded: chain E residue 1252 MET Chi-restraints excluded: chain E residue 1259 VAL 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: 0.9980 chunk 195 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 230 optimal weight: 7.9990 chunk 204 optimal weight: 30.0000 chunk 65 optimal weight: 0.2980 chunk 261 optimal weight: 2.9990 chunk 214 optimal weight: 20.0000 chunk 138 optimal weight: 3.9990 chunk 168 optimal weight: 20.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.185116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.156927 restraints weight = 27929.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.160700 restraints weight = 15094.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.163236 restraints weight = 9808.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.164903 restraints weight = 7264.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.165971 restraints weight = 5882.005| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21450 Z= 0.131 Angle : 0.619 11.745 29238 Z= 0.302 Chirality : 0.044 0.344 3497 Planarity : 0.004 0.048 3591 Dihedral : 10.597 154.129 3378 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.42 % Allowed : 23.74 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.17), residues: 2773 helix: 1.97 (0.14), residues: 1351 sheet: -1.85 (0.33), residues: 243 loop : -1.59 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 289 TYR 0.022 0.001 TYR E 772 PHE 0.020 0.001 PHE A 95 TRP 0.024 0.001 TRP D 83 HIS 0.010 0.001 HIS E 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (21443) covalent geometry : angle 0.61766 / 0.30 (29222) SS BOND : bond 0.01151 / 0.66 ( 5) SS BOND : angle 1.23585 / 0.66 ( 10) hydrogen bonds : bond 0.04083 / 2.83 ( 1161) hydrogen bonds : angle 4.19347 / 2.99 ( 3402) link_BETA1-4 : bond 0.01185 / 0.62 ( 1) link_BETA1-4 : angle 3.53471 / 1.72 ( 3) link_NAG-ASN : bond 0.00218 / 0.11 ( 1) link_NAG-ASN : angle 1.72564 / 0.89 ( 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 637 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 553 time to evaluate : 0.779 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 34 ARG cc_start: 0.7092 (mtt-85) cc_final: 0.6884 (mtt-85) REVERT: A 48 ASN cc_start: 0.8554 (m110) cc_final: 0.8186 (m110) REVERT: A 75 PHE cc_start: 0.8218 (t80) cc_final: 0.7806 (t80) REVERT: A 93 ILE cc_start: 0.9093 (tt) cc_final: 0.8871 (mt) REVERT: A 200 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8917 (tt) REVERT: A 314 ARG cc_start: 0.7555 (ptp90) cc_final: 0.6687 (ptp90) REVERT: A 325 ARG cc_start: 0.7708 (ptm-80) cc_final: 0.7481 (ptm-80) REVERT: B 39 LYS cc_start: 0.8709 (mttp) cc_final: 0.8486 (mmmt) REVERT: B 125 ILE cc_start: 0.9426 (mm) cc_final: 0.9193 (mt) REVERT: B 158 MET cc_start: 0.7847 (mmm) cc_final: 0.7586 (mmm) REVERT: B 169 MET cc_start: 0.8025 (mtm) cc_final: 0.7661 (mtp) REVERT: B 177 ARG cc_start: 0.8286 (tpt170) cc_final: 0.7935 (tpt170) REVERT: B 180 THR cc_start: 0.8761 (p) cc_final: 0.8337 (p) REVERT: B 199 MET cc_start: 0.8026 (mmm) cc_final: 0.7539 (mmm) REVERT: B 297 THR cc_start: 0.9471 (m) cc_final: 0.9214 (p) REVERT: B 311 TRP cc_start: 0.9092 (t-100) cc_final: 0.8511 (t60) REVERT: B 325 ARG cc_start: 0.8430 (mtp85) cc_final: 0.7947 (mtp180) REVERT: C 77 MET cc_start: 0.6752 (mmm) cc_final: 0.5901 (tmm) REVERT: C 258 TYR cc_start: 0.9038 (p90) cc_final: 0.8796 (p90) REVERT: D 58 ASP cc_start: 0.7730 (t0) cc_final: 0.7308 (t0) REVERT: D 67 LYS cc_start: 0.8214 (mppt) cc_final: 0.7587 (mtmt) REVERT: D 72 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8778 (mm) REVERT: D 112 THR cc_start: 0.8933 (p) cc_final: 0.8654 (t) REVERT: D 152 GLN cc_start: 0.9227 (tp40) cc_final: 0.8535 (tp40) REVERT: D 158 MET cc_start: 0.7966 (mmm) cc_final: 0.7509 (tpp) REVERT: D 177 ARG cc_start: 0.8467 (tpt170) cc_final: 0.8079 (tpt170) REVERT: D 247 ASN cc_start: 0.7697 (m-40) cc_final: 0.7238 (p0) REVERT: D 304 TYR cc_start: 0.8414 (m-80) cc_final: 0.8159 (m-10) REVERT: E 39 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8761 (tp) REVERT: E 134 LYS cc_start: 0.8756 (mttt) cc_final: 0.8274 (mtpt) REVERT: E 230 TYR cc_start: 0.8594 (m-80) cc_final: 0.7634 (m-80) REVERT: E 252 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7825 (pttp) REVERT: E 437 ASN cc_start: 0.7961 (m-40) cc_final: 0.7726 (t0) REVERT: E 506 MET cc_start: 0.7050 (tpt) cc_final: 0.6821 (tpt) REVERT: E 604 LEU cc_start: 0.8632 (mt) cc_final: 0.8331 (mt) REVERT: E 1073 SER cc_start: 0.8207 (m) cc_final: 0.7992 (p) REVERT: E 1154 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7943 (mm) REVERT: E 1183 ARG cc_start: 0.7850 (mtm110) cc_final: 0.7280 (ttm170) REVERT: E 1209 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7698 (mm-30) REVERT: E 1219 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.7255 (t80) outliers start: 84 outliers final: 69 residues processed: 586 average time/residue: 0.1281 time to fit residues: 119.2132 Evaluate side-chains 613 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 539 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 46 HIS 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 283 ILE Chi-restraints excluded: chain A residue 286 ILE 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 107 ASN Chi-restraints excluded: chain B residue 182 ILE 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 290 VAL Chi-restraints excluded: chain B residue 313 GLN 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 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 72 LEU 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 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 E residue 37 VAL Chi-restraints excluded: chain E residue 39 LEU 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 108 MET Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 184 LEU 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 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 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 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 1219 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 144 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 255 optimal weight: 20.0000 chunk 143 optimal weight: 0.9990 chunk 109 optimal weight: 0.0470 chunk 182 optimal weight: 3.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 173 GLN ** D 235 GLN ** 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 = 0.3946 r_free = 0.3946 target = 0.183216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.154884 restraints weight = 28214.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.158621 restraints weight = 15240.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.161101 restraints weight = 9937.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.162842 restraints weight = 7384.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.163746 restraints weight = 5925.141| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21450 Z= 0.150 Angle : 0.640 12.073 29238 Z= 0.312 Chirality : 0.045 0.345 3497 Planarity : 0.004 0.049 3591 Dihedral : 10.468 154.121 3378 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.11 % Allowed : 24.68 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.17), residues: 2773 helix: 1.93 (0.14), residues: 1350 sheet: -1.87 (0.32), residues: 267 loop : -1.57 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 16 TYR 0.022 0.001 TYR E 772 PHE 0.023 0.001 PHE E 48 TRP 0.029 0.001 TRP D 83 HIS 0.009 0.001 HIS E 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (21443) covalent geometry : angle 0.63809 / 0.31 (29222) SS BOND : bond 0.00311 / 0.18 ( 5) SS BOND : angle 1.11825 / 0.60 ( 10) hydrogen bonds : bond 0.04119 / 2.85 ( 1161) hydrogen bonds : angle 4.19423 / 3.00 ( 3402) link_BETA1-4 : bond 0.01079 / 0.57 ( 1) link_BETA1-4 : angle 3.56404 / 1.73 ( 3) link_NAG-ASN : bond 0.00298 / 0.16 ( 1) link_NAG-ASN : angle 1.83155 / 0.95 ( 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 623 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 545 time to evaluate : 0.754 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 34 ARG cc_start: 0.7075 (mtt-85) cc_final: 0.6859 (mtt-85) REVERT: A 48 ASN cc_start: 0.8564 (m110) cc_final: 0.8201 (m110) REVERT: A 93 ILE cc_start: 0.9098 (tt) cc_final: 0.8896 (mt) REVERT: A 181 LEU cc_start: 0.8435 (mt) cc_final: 0.7934 (mt) REVERT: A 200 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8943 (tt) REVERT: A 314 ARG cc_start: 0.7627 (ptp90) cc_final: 0.6757 (ptp90) REVERT: A 325 ARG cc_start: 0.7640 (ptm-80) cc_final: 0.7400 (ptm-80) REVERT: B 39 LYS cc_start: 0.8746 (mttp) cc_final: 0.8515 (mmmt) REVERT: B 77 MET cc_start: 0.6634 (mmm) cc_final: 0.5597 (mtp) REVERT: B 125 ILE cc_start: 0.9447 (mm) cc_final: 0.9123 (mt) REVERT: B 158 MET cc_start: 0.7829 (mmm) cc_final: 0.7558 (mmm) REVERT: B 169 MET cc_start: 0.8046 (mtm) cc_final: 0.7669 (mtp) REVERT: B 177 ARG cc_start: 0.8304 (tpt170) cc_final: 0.7858 (tpt170) REVERT: B 180 THR cc_start: 0.8752 (p) cc_final: 0.8246 (p) REVERT: B 297 THR cc_start: 0.9470 (m) cc_final: 0.9214 (p) REVERT: B 311 TRP cc_start: 0.9099 (t-100) cc_final: 0.8534 (t60) REVERT: B 325 ARG cc_start: 0.8461 (mtp85) cc_final: 0.7964 (mtp180) REVERT: C 77 MET cc_start: 0.6786 (mmm) cc_final: 0.5878 (tmm) REVERT: C 258 TYR cc_start: 0.8976 (p90) cc_final: 0.8731 (p90) REVERT: D 58 ASP cc_start: 0.7664 (t0) cc_final: 0.7223 (t0) REVERT: D 67 LYS cc_start: 0.8203 (mppt) cc_final: 0.7549 (mtmt) REVERT: D 112 THR cc_start: 0.8904 (p) cc_final: 0.8641 (t) REVERT: D 152 GLN cc_start: 0.9248 (tp40) cc_final: 0.8542 (tp40) REVERT: D 177 ARG cc_start: 0.8511 (tpt170) cc_final: 0.8255 (tpt170) REVERT: D 247 ASN cc_start: 0.7698 (m-40) cc_final: 0.7275 (p0) REVERT: D 304 TYR cc_start: 0.8443 (m-80) cc_final: 0.8169 (m-10) REVERT: E 39 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8713 (tp) REVERT: E 134 LYS cc_start: 0.8756 (mttt) cc_final: 0.8263 (mtpt) REVERT: E 230 TYR cc_start: 0.8639 (m-80) cc_final: 0.7703 (m-80) REVERT: E 252 LYS cc_start: 0.8076 (ttmt) cc_final: 0.7813 (pttp) REVERT: E 437 ASN cc_start: 0.7989 (m-40) cc_final: 0.7741 (t0) REVERT: E 506 MET cc_start: 0.7049 (tpt) cc_final: 0.6838 (tpt) REVERT: E 604 LEU cc_start: 0.8642 (mt) cc_final: 0.8340 (mt) REVERT: E 1073 SER cc_start: 0.8243 (m) cc_final: 0.8021 (p) REVERT: E 1095 LYS cc_start: 0.7020 (tttp) cc_final: 0.6773 (tttp) REVERT: E 1154 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8000 (mm) REVERT: E 1183 ARG cc_start: 0.7850 (mtm110) cc_final: 0.7185 (mtm-85) REVERT: E 1209 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7848 (tp30) REVERT: E 1219 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.7195 (t80) outliers start: 78 outliers final: 67 residues processed: 579 average time/residue: 0.1272 time to fit residues: 117.6585 Evaluate side-chains 610 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 539 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 46 HIS 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 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 210 ILE 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 339 VAL Chi-restraints excluded: chain C residue 42 CYS 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 184 SER 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 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 108 MET Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 184 LEU 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 405 SER Chi-restraints excluded: chain E residue 459 SER 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 266 optimal weight: 30.0000 chunk 263 optimal weight: 40.0000 chunk 207 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 202 optimal weight: 7.9990 chunk 187 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.177306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.148776 restraints weight = 28548.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.152408 restraints weight = 15538.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.154942 restraints weight = 10201.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.156422 restraints weight = 7562.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.157618 restraints weight = 6214.055| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3351 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= 0.240 Angle : 0.730 11.996 29238 Z= 0.361 Chirality : 0.047 0.357 3497 Planarity : 0.005 0.051 3591 Dihedral : 10.723 153.270 3378 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 4.63 % Allowed : 23.95 % Favored : 71.42 % 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 (0.16), residues: 2773 helix: 1.60 (0.14), residues: 1348 sheet: -1.99 (0.31), residues: 267 loop : -1.67 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 16 TYR 0.025 0.002 TYR E 772 PHE 0.024 0.002 PHE C 75 TRP 0.038 0.002 TRP D 83 HIS 0.008 0.001 HIS E 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.24 (21443) covalent geometry : angle 0.72864 / 0.36 (29222) SS BOND : bond 0.00563 / 0.31 ( 5) SS BOND : angle 1.16035 / 0.62 ( 10) hydrogen bonds : bond 0.04523 / 3.12 ( 1161) hydrogen bonds : angle 4.46077 / 3.19 ( 3402) link_BETA1-4 : bond 0.00878 / 0.46 ( 1) link_BETA1-4 : angle 3.67369 / 1.76 ( 3) link_NAG-ASN : bond 0.00551 / 0.29 ( 1) link_NAG-ASN : angle 2.27291 / 1.20 ( 3) =============================================================================== Job complete usr+sys time: 3654.68 seconds wall clock time: 63 minutes 41.40 seconds (3821.40 seconds total)