Starting phenix.real_space_refine on Thu Mar 5 11:07:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u24_26307/03_2026/7u24_26307.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u24_26307/03_2026/7u24_26307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u24_26307/03_2026/7u24_26307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u24_26307/03_2026/7u24_26307.map" model { file = "/net/cci-nas-00/data/ceres_data/7u24_26307/03_2026/7u24_26307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u24_26307/03_2026/7u24_26307.cif" } resolution = 3.58 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 P 33 5.49 5 S 101 5.16 5 Cl 1 4.86 5 C 13356 2.51 5 N 3504 2.21 5 O 3656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20651 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2672 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 16, 'TRANS': 342} Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 9, 'TYR:plan': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 108 Chain: "B" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2513 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 13, 'TRANS': 314} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 7, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2537 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 13, 'TRANS': 314} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2508 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 13, 'TRANS': 314} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 8, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "E" Number of atoms: 9429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1427, 9429 Classifications: {'peptide': 1427} Incomplete info: {'truncation_to_alanine': 577} Link IDs: {'PTRANS': 48, 'TRANS': 1378} Chain breaks: 5 Unresolved non-hydrogen bonds: 1877 Unresolved non-hydrogen angles: 2372 Unresolved non-hydrogen dihedrals: 1461 Unresolved non-hydrogen chiralities: 237 Planarities with less than four sites: {'GLU:plan': 48, 'ASP:plan': 45, 'ASN:plan1': 22, 'HIS:plan': 9, 'ARG:plan': 36, 'GLN:plan1': 34, 'PHE:plan': 17, 'TYR:plan': 2, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 897 Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 207 Unusual residues: {'ATP': 1, 'POV': 1, 'PTY': 1} Classifications: {'peptide': 2, 'undetermined': 3} Link IDs: {'TRANS': 1, None: 3} Not linked: pdbres="ATP A 401 " pdbres="PTY A 402 " Not linked: pdbres="PTY A 402 " pdbres="POV A 403 " Not linked: pdbres="POV A 403 " pdbres="P5S A 404 " Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 175 Unusual residues: {'ATP': 1, 'POV': 1} Classifications: {'peptide': 2, 'undetermined': 2} Link IDs: {'TRANS': 1, None: 2} Not linked: pdbres="ATP B 401 " pdbres="POV B 402 " Not linked: pdbres="POV B 402 " pdbres="P5S B 403 " Chain breaks: 1 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: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 229 Unusual residues: {'ATP': 1, 'POV': 1} Classifications: {'peptide': 3, 'undetermined': 2} Link IDs: {'TRANS': 1, None: 3} Not linked: pdbres="P5S D 401 " pdbres="ATP D 402 " Not linked: pdbres="ATP D 402 " pdbres="POV D 403 " Not linked: pdbres="POV D 403 " pdbres="P5S D 404 " Chain breaks: 1 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: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 260 Unusual residues: {'ATP': 1, 'GBM': 1, 'NAG': 1, 'PTY': 4} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.99, per 1000 atoms: 0.24 Number of scatterers: 20651 At special positions: 0 Unit cell: (166.481, 109.122, 141.299, 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) Cl 1 17.00 S 101 16.00 P 33 15.00 O 3656 8.00 N 3504 7.00 C 13356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 26 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG E2003 " - " ASN E 10 " Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 867.2 milliseconds 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5238 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 37 sheets defined 53.4% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 removed outlier: 3.625A pdb=" N ARG A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 removed outlier: 3.880A pdb=" N ASP A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 67 through 98 Processing helix chain 'A' and resid 116 through 130 Processing helix chain 'A' and resid 142 through 172 removed outlier: 4.040A pdb=" N ILE A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 4.472A pdb=" N ASP A 269 " --> pdb=" O PRO A 266 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 270 " --> pdb=" O LEU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.681A pdb=" N LEU A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' 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 346 through 359 Processing helix chain 'B' and resid 53 through 58 removed outlier: 3.828A pdb=" N ASP B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 66 Processing helix chain 'B' and resid 67 through 97 Processing helix chain 'B' and resid 116 through 129 Processing helix chain 'B' and resid 142 through 172 removed outlier: 3.940A pdb=" N ILE B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 179 removed outlier: 3.539A pdb=" N ALA B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 179 " --> pdb=" O HIS B 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 174 through 179' Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.521A pdb=" N LEU B 275 " --> pdb=" O PRO B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 346 through 358 removed outlier: 3.526A pdb=" N GLU B 351 " --> pdb=" O ARG B 347 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU B 356 " --> pdb=" O ASP B 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 58 removed outlier: 4.017A pdb=" N ASP C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 66 Processing helix chain 'C' and resid 67 through 97 Processing helix chain 'C' and resid 116 through 130 Processing helix chain 'C' and resid 142 through 172 removed outlier: 3.901A pdb=" N ILE C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 179 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 358 Processing helix chain 'D' and resid 53 through 58 removed outlier: 4.026A pdb=" N ASP D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 66 removed outlier: 3.544A pdb=" N THR D 62 " --> pdb=" O ASP D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 98 Processing helix chain 'D' and resid 116 through 130 Processing helix chain 'D' and resid 142 through 171 removed outlier: 3.954A pdb=" N ILE D 146 " --> pdb=" O CYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 179 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 358 Processing helix chain 'E' and resid 12 through 16 Processing helix chain 'E' and resid 24 through 57 removed outlier: 4.146A pdb=" N ASP E 29 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Proline residue: E 35 - end of helix Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 71 through 96 Processing helix chain 'E' and resid 97 through 99 No H-bonds generated for 'chain 'E' and resid 97 through 99' Processing helix chain 'E' and resid 107 through 130 removed outlier: 3.531A pdb=" N TYR E 124 " --> pdb=" O SER E 120 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER E 130 " --> pdb=" O ASN E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 135 removed outlier: 3.845A pdb=" N LEU E 135 " --> pdb=" O PHE E 132 " (cutoff:3.500A) No H-bonds generated for '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: 3.683A pdb=" N CYS E 170 " --> pdb=" O GLN E 166 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL E 185 " --> pdb=" O MET E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 212 Processing helix chain 'E' and resid 223 through 229 Processing helix chain 'E' and resid 232 through 243 removed outlier: 4.298A pdb=" N PHE E 236 " --> pdb=" O TRP E 232 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS E 241 " --> pdb=" O ILE E 237 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS E 242 " --> pdb=" O LYS E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 257 Processing helix chain 'E' and resid 258 through 277 Processing helix chain 'E' and resid 283 through 314 removed outlier: 5.471A pdb=" N ARG E 297 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU E 301 " --> pdb=" O ARG E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 327 Processing helix chain 'E' and resid 328 through 332 removed outlier: 3.655A pdb=" N ASN E 331 " --> pdb=" O GLY E 328 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS E 332 " --> pdb=" O LYS E 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 328 through 332' Processing helix chain 'E' and resid 347 through 352 Processing helix chain 'E' and resid 354 through 400 removed outlier: 3.620A pdb=" N LEU E 358 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR E 371 " --> pdb=" O LEU E 367 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN E 374 " --> pdb=" O ARG E 370 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET E 400 " --> pdb=" O TYR E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 434 Processing helix chain 'E' and resid 434 through 456 removed outlier: 4.096A pdb=" N LEU E 438 " --> pdb=" O LEU E 434 " (cutoff:3.500A) removed outlier: 4.046A 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 469 Processing helix chain 'E' and resid 470 through 505 removed outlier: 4.238A pdb=" N GLU E 494 " --> pdb=" O GLU E 490 " (cutoff:3.500A) removed outlier: 4.152A 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 515 through 564 removed outlier: 4.073A pdb=" N THR E 525 " --> pdb=" O ARG E 521 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER E 543 " --> pdb=" O TYR E 539 " (cutoff:3.500A) Proline residue: E 551 - end of helix Processing helix chain 'E' and resid 572 through 615 removed outlier: 3.677A pdb=" N LEU E 580 " --> pdb=" O ALA E 576 " (cutoff:3.500A) Proline residue: E 589 - end of helix removed outlier: 3.948A pdb=" N LEU E 592 " --> pdb=" O THR E 588 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER E 594 " --> pdb=" O LEU E 590 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER E 595 " --> pdb=" O PHE E 591 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER E 615 " --> pdb=" O SER E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 719 through 728 Processing helix chain 'E' and resid 783 through 790 Processing helix chain 'E' and resid 795 through 806 Processing helix chain 'E' and resid 808 through 814 Processing helix chain 'E' and resid 831 through 846 removed outlier: 3.618A pdb=" N GLN E 846 " --> pdb=" O ARG E 842 " (cutoff:3.500A) Processing helix chain 'E' and resid 855 through 860 removed outlier: 3.952A pdb=" N ALA E 859 " --> pdb=" O ASP E 855 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU E 860 " --> pdb=" O PRO E 856 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 855 through 860' Processing helix chain 'E' and resid 862 through 881 Processing helix chain 'E' and resid 893 through 898 removed outlier: 3.890A pdb=" N ALA E 897 " --> pdb=" O TYR E 893 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP E 898 " --> pdb=" O LEU E 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 893 through 898' Processing helix chain 'E' and resid 915 through 919 Processing helix chain 'E' and resid 987 through 993 removed outlier: 4.211A pdb=" N ARG E 993 " --> pdb=" O VAL E 989 " (cutoff:3.500A) Processing helix chain 'E' and resid 1000 through 1009 Processing helix chain 'E' and resid 1009 through 1043 removed outlier: 4.061A pdb=" N LEU E1015 " --> pdb=" O LEU E1011 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL E1043 " --> pdb=" O ASP E1039 " (cutoff:3.500A) Processing helix chain 'E' and resid 1061 through 1107 removed outlier: 3.792A pdb=" N LEU E1074 " --> pdb=" O LEU E1070 " (cutoff:3.500A) Processing helix chain 'E' and resid 1109 through 1116 removed outlier: 3.652A pdb=" N PHE E1113 " --> pdb=" O PRO E1109 " (cutoff:3.500A) Processing helix chain 'E' and resid 1117 through 1135 removed outlier: 4.263A pdb=" N ASP E1128 " --> pdb=" O ARG E1124 " (cutoff:3.500A) Processing helix chain 'E' and resid 1135 through 1161 Processing helix chain 'E' and resid 1163 through 1210 removed outlier: 3.856A pdb=" N ALA E1167 " --> pdb=" O VAL E1163 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E1169 " --> pdb=" O LEU E1165 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 4.030A 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 1274 removed outlier: 4.049A pdb=" N PHE E1223 " --> pdb=" O TYR E1219 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA E1237 " --> pdb=" O SER E1233 " (cutoff:3.500A) Processing helix chain 'E' and resid 1278 through 1290 removed outlier: 3.965A pdb=" N GLY E1282 " --> pdb=" O ALA E1278 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR E1287 " --> pdb=" O LEU E1283 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET E1290 " --> pdb=" O THR E1286 " (cutoff:3.500A) Processing helix chain 'E' and resid 1291 through 1320 removed outlier: 4.062A pdb=" N ASN E1296 " --> pdb=" O SER E1292 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TRP E1297 " --> pdb=" O ASN E1293 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA E1311 " --> pdb=" O ILE E1307 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE E1315 " --> pdb=" O ALA E1311 " (cutoff:3.500A) Processing helix chain 'E' and resid 1385 through 1392 removed outlier: 4.313A pdb=" N SER E1389 " --> pdb=" O LYS E1385 " (cutoff:3.500A) 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 removed outlier: 3.537A pdb=" N ARG E1419 " --> pdb=" O LEU E1415 " (cutoff:3.500A) Processing helix chain 'E' and resid 1436 through 1441 Processing helix chain 'E' and resid 1450 through 1459 Processing helix chain 'E' and resid 1460 through 1467 Processing helix chain 'E' and resid 1476 through 1479 Processing helix chain 'E' and resid 1484 through 1498 removed outlier: 3.969A pdb=" N GLN E1488 " --> pdb=" O GLN E1484 " (cutoff:3.500A) Processing helix chain 'E' and resid 1512 through 1531 Processing helix chain 'E' and resid 1539 through 1543 Processing helix chain 'E' and resid 1563 through 1570 removed outlier: 4.013A pdb=" N LEU E1567 " --> pdb=" O PRO E1563 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS E1570 " --> pdb=" O LEU E1566 " (cutoff:3.500A) Processing helix chain 'E' and resid 1571 through 1578 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 47 removed outlier: 3.606A pdb=" N SER B 327 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 259 through 260 removed outlier: 6.714A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 210 through 211 removed outlier: 3.603A pdb=" N VAL A 236 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 315 Processing sheet with id=AA7, first strand: chain 'A' and resid 319 through 320 removed outlier: 6.112A pdb=" N TYR A 326 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LYS D 47 " --> pdb=" O TYR A 326 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL A 328 " --> pdb=" O LYS D 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 36 through 37 removed outlier: 5.085A pdb=" N ASN B 41 " --> pdb=" O SER B 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 44 through 47 Processing sheet with id=AB1, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB2, first strand: chain 'B' and resid 259 through 260 removed outlier: 6.165A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 210 through 211 Processing sheet with id=AB4, first strand: chain 'B' and resid 230 through 237 removed outlier: 5.257A pdb=" N THR B 223 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG B 221 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 236 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 313 through 315 Processing sheet with id=AB6, first strand: chain 'C' and resid 36 through 37 removed outlier: 3.508A pdb=" N SER C 37 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ASN C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 44 through 47 removed outlier: 6.697A pdb=" N ALA C 45 " --> pdb=" O VAL D 328 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB9, first strand: chain 'C' and resid 259 through 260 removed outlier: 6.624A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 210 through 211 removed outlier: 5.329A pdb=" N THR C 223 " --> pdb=" O PRO C 232 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 210 through 211 removed outlier: 3.616A pdb=" N GLY C 289 " --> pdb=" O THR C 298 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 313 through 315 Processing sheet with id=AC4, first strand: chain 'D' and resid 36 through 37 removed outlier: 3.567A pdb=" N SER D 37 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ASN D 41 " --> pdb=" O SER D 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.565A pdb=" N VAL D 202 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 259 through 260 removed outlier: 6.719A pdb=" N ALA D 187 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 210 through 211 removed outlier: 5.222A pdb=" N THR D 223 " --> pdb=" O PRO D 232 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 210 through 211 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 339 through 340 Processing sheet with id=AD2, first strand: chain 'E' and resid 679 through 680 Processing sheet with id=AD3, first strand: chain 'E' and resid 685 through 686 Processing sheet with id=AD4, first strand: chain 'E' and resid 708 through 711 Processing sheet with id=AD5, first strand: chain 'E' and resid 901 through 904 removed outlier: 6.918A pdb=" N ALA E 902 " --> pdb=" O GLN E 909 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 1347 through 1348 removed outlier: 3.911A pdb=" N GLN E1348 " --> pdb=" O ARG E1402 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 1352 through 1353 Processing sheet with id=AD8, first strand: chain 'E' and resid 1423 through 1424 removed outlier: 7.252A pdb=" N SER E1423 " --> pdb=" O ILE E1504 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE E1503 " --> pdb=" O VAL E1534 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'E' and resid 1434 through 1435 removed outlier: 3.516A pdb=" N GLY E1434 " --> pdb=" O ILE E1475 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 1549 through 1552 removed outlier: 3.984A pdb=" N GLU E1559 " --> pdb=" O VAL E1551 " (cutoff:3.500A) 1168 hydrogen bonds defined for protein. 3390 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: 4.66 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3164 1.31 - 1.44: 5618 1.44 - 1.56: 12080 1.56 - 1.69: 61 1.69 - 1.82: 160 Bond restraints: 21083 Sorted by residual: bond pdb=" C17 GBM E2001 " pdb=" N8 GBM E2001 " ideal model delta sigma weight residual 1.340 1.451 -0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C26 GBM E2001 " pdb=" N10 GBM E2001 " ideal model delta sigma weight residual 1.342 1.452 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C28 GBM E2001 " pdb=" O7 GBM E2001 " ideal model delta sigma weight residual 1.339 1.400 -0.061 2.00e-02 2.50e+03 9.16e+00 bond pdb=" C1 NAG E2003 " pdb=" O5 NAG E2003 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 9.14e+00 bond pdb=" C17 GBM E2001 " pdb=" N9 GBM E2001 " ideal model delta sigma weight residual 1.394 1.453 -0.059 2.00e-02 2.50e+03 8.70e+00 ... (remaining 21078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 28293 1.86 - 3.72: 322 3.72 - 5.58: 89 5.58 - 7.43: 20 7.43 - 9.29: 2 Bond angle restraints: 28726 Sorted by residual: angle pdb=" C LEU E 104 " pdb=" N HIS E 105 " pdb=" CA HIS E 105 " ideal model delta sigma weight residual 122.65 115.70 6.95 1.60e+00 3.91e-01 1.88e+01 angle pdb=" N VAL D 244 " pdb=" CA VAL D 244 " pdb=" C VAL D 244 " ideal model delta sigma weight residual 113.20 109.52 3.68 9.60e-01 1.09e+00 1.47e+01 angle pdb=" C VAL E 33 " pdb=" N VAL E 34 " pdb=" CA VAL E 34 " ideal model delta sigma weight residual 120.33 122.96 -2.63 8.00e-01 1.56e+00 1.08e+01 angle pdb=" C ASN E 223 " pdb=" N LEU E 224 " pdb=" CA LEU E 224 " ideal model delta sigma weight residual 120.38 124.15 -3.77 1.37e+00 5.33e-01 7.57e+00 angle pdb=" CA LEU A 275 " pdb=" CB LEU A 275 " pdb=" CG LEU A 275 " ideal model delta sigma weight residual 116.30 125.59 -9.29 3.50e+00 8.16e-02 7.05e+00 ... (remaining 28721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 12257 35.17 - 70.35: 350 70.35 - 105.52: 68 105.52 - 140.70: 43 140.70 - 175.87: 18 Dihedral angle restraints: 12736 sinusoidal: 4683 harmonic: 8053 Sorted by residual: dihedral pdb=" CA ALA E 251 " pdb=" C ALA E 251 " pdb=" N LYS E 252 " pdb=" CA LYS E 252 " ideal model delta harmonic sigma weight residual 180.00 155.44 24.56 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" C38 P5S D 404 " pdb=" C39 P5S D 404 " pdb=" C40 P5S D 404 " pdb=" C41 P5S D 404 " ideal model delta sinusoidal sigma weight residual 64.51 -119.62 -175.87 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 PTY E2006 " pdb=" O11 PTY E2006 " pdb=" P1 PTY E2006 " pdb=" O12 PTY E2006 " ideal model delta sinusoidal sigma weight residual 300.23 124.86 175.37 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3040 0.071 - 0.141: 336 0.141 - 0.212: 1 0.212 - 0.282: 3 0.282 - 0.353: 6 Chirality restraints: 3386 Sorted by residual: chirality pdb=" C2 P5S A 404 " pdb=" C1 P5S A 404 " pdb=" C3 P5S A 404 " pdb=" O37 P5S A 404 " both_signs ideal model delta sigma weight residual False 2.59 2.24 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C2 P5S B 403 " pdb=" C1 P5S B 403 " pdb=" C3 P5S B 403 " pdb=" O37 P5S B 403 " both_signs ideal model delta sigma weight residual False 2.59 2.25 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" C2 P5S B 404 " pdb=" C1 P5S B 404 " pdb=" C3 P5S B 404 " pdb=" O37 P5S B 404 " both_signs ideal model delta sigma weight residual False 2.59 2.26 0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 3383 not shown) Planarity restraints: 3560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 219 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO E 220 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 220 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 220 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C17 P5S B 403 " -0.032 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C20 P5S B 403 " 0.009 2.00e-02 2.50e+03 pdb=" O18 P5S B 403 " 0.012 2.00e-02 2.50e+03 pdb=" O19 P5S B 403 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 253 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO C 254 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 254 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 254 " 0.023 5.00e-02 4.00e+02 ... (remaining 3557 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4318 2.78 - 3.31: 19543 3.31 - 3.84: 32983 3.84 - 4.37: 36196 4.37 - 4.90: 64508 Nonbonded interactions: 157548 Sorted by model distance: nonbonded pdb=" OH TYR B 268 " pdb=" OD2 ASP B 350 " model vdw 2.254 3.040 nonbonded pdb=" NH1 ARG A 177 " pdb=" OG SER A 208 " model vdw 2.277 3.120 nonbonded pdb=" O GLN E 992 " pdb=" NH1 ARG E1187 " model vdw 2.305 3.120 nonbonded pdb=" O TRP E 75 " pdb=" OG1 THR E 78 " model vdw 2.305 3.040 nonbonded pdb=" NH1 ARG D 32 " pdb=" O GLN D 279 " model vdw 2.307 3.120 ... (remaining 157543 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 31 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 through 178 or (resid 179 and (name N or n \ ame CA or name C or name O or name CB )) or resid 180 through 272 or (resid 273 \ through 274 and (name N or name CA or name C or name O or name CB )) or resid 27 \ 5 through 306 or (resid 307 through 308 and (name N or name CA or name C or name \ O or name CB )) or resid 309 through 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 350 or (resid \ 351 through 358 and (name N or name CA or name C or name O or name CB )) or resi \ d 405)) selection = (chain 'B' and ((resid 31 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 64 or (resid 65 and (name N or na \ me CA or name C or name O or name CB )) or resid 66 through 272 or (resid 273 th \ rough 274 and (name N or name CA or name C or name O or name CB )) or resid 275 \ through 306 or (resid 307 through 308 and (name N or name CA or name C or name O \ or name CB )) or resid 309 through 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 353 or (resid 35 \ 4 through 358 and (name N or name CA or name C or name O or name CB )) or resid \ 404)) selection = (chain 'C' and ((resid 31 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 41 or (resid 42 and (name N or na \ me CA or name C or name O or name CB )) or resid 43 through 64 or (resid 65 and \ (name N or name CA or name C or name O or name CB )) or resid 66 through 206 or \ (resid 207 and (name N or name CA or name C or name O or name CB )) or resid 208 \ through 272 or (resid 273 through 274 and (name N or name CA or name C or name \ O or name CB )) or resid 275 through 306 or (resid 307 through 308 and (name N o \ r name CA or name C or name O or name CB )) or resid 309 through 320 or (resid 3 \ 21 through 323 and (name N or name CA or name C or name O or name CB )) or resid \ 324 through 350 or (resid 351 through 358 and (name N or name CA or name C or n \ ame O or name CB )) or resid 403)) selection = (chain 'D' and ((resid 31 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 41 or (resid 42 and (name N or na \ me CA or name C or name O or name CB )) or resid 43 through 64 or (resid 65 and \ (name N or name CA or name C or name O or name CB )) or resid 66 through 273 or \ (resid 274 and (name N or name CA or name C or name O or name CB )) or resid 275 \ through 322 or (resid 323 and (name N or name CA or name C or name O or name CB \ )) or resid 324 through 358 or resid 405)) } 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: 0.050 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.260 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 0.111 21089 Z= 0.130 Angle : 0.544 9.292 28739 Z= 0.248 Chirality : 0.044 0.353 3386 Planarity : 0.004 0.049 3559 Dihedral : 20.195 175.870 7483 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.11 % Allowed : 3.66 % Favored : 96.22 % 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: -0.81 (0.16), residues: 2750 helix: 0.90 (0.14), residues: 1343 sheet: -2.52 (0.30), residues: 262 loop : -1.80 (0.17), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1187 TYR 0.012 0.001 TYR E1219 PHE 0.010 0.001 PHE A 333 TRP 0.006 0.001 TRP E1037 HIS 0.004 0.000 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00264 (21083) covalent geometry : angle 0.54426 (28726) SS BOND : bond 0.00167 ( 5) SS BOND : angle 0.58087 ( 10) hydrogen bonds : bond 0.18339 ( 1162) hydrogen bonds : angle 6.37240 ( 3390) link_NAG-ASN : bond 0.00309 ( 1) link_NAG-ASN : angle 0.85630 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 574 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 SER cc_start: 0.8956 (t) cc_final: 0.8737 (t) REVERT: A 158 MET cc_start: 0.7921 (mmm) cc_final: 0.7716 (tpp) REVERT: A 210 ILE cc_start: 0.9159 (mt) cc_final: 0.8905 (tt) REVERT: A 223 THR cc_start: 0.9388 (m) cc_final: 0.9170 (p) REVERT: A 269 ASP cc_start: 0.8237 (m-30) cc_final: 0.8003 (m-30) REVERT: A 276 HIS cc_start: 0.8601 (p-80) cc_final: 0.8315 (p-80) REVERT: A 302 THR cc_start: 0.9347 (t) cc_final: 0.9069 (m) REVERT: B 47 LYS cc_start: 0.8527 (mttt) cc_final: 0.8149 (mttm) REVERT: B 113 SER cc_start: 0.9294 (m) cc_final: 0.8676 (t) REVERT: B 114 ILE cc_start: 0.8818 (mm) cc_final: 0.8387 (mt) REVERT: B 125 ILE cc_start: 0.8766 (mm) cc_final: 0.8419 (mt) REVERT: C 58 ASP cc_start: 0.7948 (p0) cc_final: 0.7666 (p0) REVERT: C 113 SER cc_start: 0.8998 (m) cc_final: 0.8686 (t) REVERT: C 158 MET cc_start: 0.7654 (mmm) cc_final: 0.7440 (mmm) REVERT: C 171 THR cc_start: 0.9269 (p) cc_final: 0.9032 (p) REVERT: C 210 ILE cc_start: 0.9222 (mt) cc_final: 0.8771 (tt) REVERT: C 248 SER cc_start: 0.9288 (p) cc_final: 0.9059 (m) REVERT: C 290 VAL cc_start: 0.9582 (p) cc_final: 0.9315 (m) REVERT: C 335 ASN cc_start: 0.8472 (m110) cc_final: 0.8216 (m-40) REVERT: D 43 ASN cc_start: 0.8199 (t0) cc_final: 0.7793 (t0) REVERT: D 47 LYS cc_start: 0.8572 (mmtt) cc_final: 0.8326 (mttm) REVERT: D 107 ASN cc_start: 0.8158 (t0) cc_final: 0.7863 (t0) REVERT: D 158 MET cc_start: 0.7632 (mmm) cc_final: 0.7401 (mmm) REVERT: D 212 SER cc_start: 0.8769 (m) cc_final: 0.8283 (p) REVERT: D 261 ILE cc_start: 0.9091 (mt) cc_final: 0.8854 (mt) REVERT: D 290 VAL cc_start: 0.9678 (p) cc_final: 0.9329 (m) REVERT: E 40 LEU cc_start: 0.8936 (mp) cc_final: 0.8300 (mt) REVERT: E 51 TRP cc_start: 0.7725 (t60) cc_final: 0.7413 (t60) REVERT: E 158 TYR cc_start: 0.6684 (t80) cc_final: 0.6217 (t80) REVERT: E 224 LEU cc_start: 0.9359 (tp) cc_final: 0.9147 (tp) REVERT: E 326 HIS cc_start: 0.8381 (t-90) cc_final: 0.8060 (t70) REVERT: E 361 LEU cc_start: 0.8653 (tp) cc_final: 0.8386 (mp) REVERT: E 483 GLN cc_start: 0.7786 (tt0) cc_final: 0.7236 (tm-30) REVERT: E 530 MET cc_start: 0.7524 (tpp) cc_final: 0.7173 (tpp) REVERT: E 817 HIS cc_start: 0.7516 (m-70) cc_final: 0.7143 (m-70) REVERT: E 1103 ASN cc_start: 0.8210 (m-40) cc_final: 0.7963 (m110) REVERT: E 1171 LEU cc_start: 0.8053 (tp) cc_final: 0.7682 (tt) REVERT: E 1189 LEU cc_start: 0.9166 (mt) cc_final: 0.8963 (mt) REVERT: E 1197 GLN cc_start: 0.8562 (pp30) cc_final: 0.8095 (pp30) REVERT: E 1219 TYR cc_start: 0.6299 (t80) cc_final: 0.5985 (t80) outliers start: 2 outliers final: 2 residues processed: 575 average time/residue: 0.1373 time to fit residues: 124.2496 Evaluate side-chains 480 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 478 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 1283 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 197 optimal weight: 40.0000 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 0.0040 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 0.0770 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 overall best weight: 3.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 GLN C 43 ASN D 48 ASN E 491 HIS E 498 GLN ** E1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.165840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.136506 restraints weight = 24159.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.137602 restraints weight = 18832.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.139339 restraints weight = 13731.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.139995 restraints weight = 10226.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.140195 restraints weight = 9500.221| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21089 Z= 0.165 Angle : 0.575 9.640 28739 Z= 0.293 Chirality : 0.045 0.174 3386 Planarity : 0.004 0.048 3559 Dihedral : 22.228 178.516 3891 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.03 % Allowed : 12.19 % Favored : 84.78 % 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: 2750 helix: 1.56 (0.15), residues: 1336 sheet: -1.99 (0.29), residues: 295 loop : -1.63 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 192 TYR 0.018 0.002 TYR E 772 PHE 0.026 0.002 PHE A 75 TRP 0.007 0.001 TRP E1037 HIS 0.006 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00371 (21083) covalent geometry : angle 0.57464 (28726) SS BOND : bond 0.00607 ( 5) SS BOND : angle 1.56982 ( 10) hydrogen bonds : bond 0.05280 ( 1162) hydrogen bonds : angle 4.53013 ( 3390) link_NAG-ASN : bond 0.00019 ( 1) link_NAG-ASN : angle 0.68670 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 483 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 SER cc_start: 0.9056 (t) cc_final: 0.8833 (t) REVERT: A 158 MET cc_start: 0.8029 (mmm) cc_final: 0.7556 (mmm) REVERT: A 223 THR cc_start: 0.9473 (m) cc_final: 0.9198 (p) REVERT: A 229 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8368 (mm-30) REVERT: A 269 ASP cc_start: 0.8316 (m-30) cc_final: 0.8062 (m-30) REVERT: A 276 HIS cc_start: 0.8674 (p-80) cc_final: 0.8260 (p90) REVERT: A 325 ARG cc_start: 0.7590 (mtm180) cc_final: 0.7215 (mtp85) REVERT: B 47 LYS cc_start: 0.8602 (mttt) cc_final: 0.8288 (mtpp) REVERT: B 66 LEU cc_start: 0.8330 (mt) cc_final: 0.8111 (mt) REVERT: B 88 MET cc_start: 0.7990 (tpp) cc_final: 0.7651 (tpp) REVERT: B 114 ILE cc_start: 0.8931 (mm) cc_final: 0.8441 (mt) REVERT: B 125 ILE cc_start: 0.8861 (mm) cc_final: 0.8473 (mt) REVERT: B 137 MET cc_start: 0.7705 (mtm) cc_final: 0.6930 (mtm) REVERT: C 58 ASP cc_start: 0.8139 (p0) cc_final: 0.7712 (p0) REVERT: C 113 SER cc_start: 0.9044 (m) cc_final: 0.8617 (t) REVERT: C 210 ILE cc_start: 0.9236 (mt) cc_final: 0.8783 (tt) REVERT: C 212 SER cc_start: 0.9181 (m) cc_final: 0.8479 (t) REVERT: C 314 ARG cc_start: 0.8102 (ptp-170) cc_final: 0.7836 (mtp180) REVERT: C 327 SER cc_start: 0.9033 (t) cc_final: 0.8541 (p) REVERT: C 335 ASN cc_start: 0.8499 (m110) cc_final: 0.8222 (m-40) REVERT: D 47 LYS cc_start: 0.8640 (mmtt) cc_final: 0.8336 (mttm) REVERT: D 158 MET cc_start: 0.7645 (mmm) cc_final: 0.7257 (mmm) REVERT: D 170 LYS cc_start: 0.9191 (mtpp) cc_final: 0.8601 (tptp) REVERT: D 173 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8133 (mm-40) REVERT: D 261 ILE cc_start: 0.9174 (mt) cc_final: 0.8968 (mt) REVERT: D 290 VAL cc_start: 0.9563 (OUTLIER) cc_final: 0.9225 (m) REVERT: E 51 TRP cc_start: 0.7697 (t60) cc_final: 0.7457 (t60) REVERT: E 218 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8096 (pp) REVERT: E 299 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8488 (mp) REVERT: E 326 HIS cc_start: 0.8527 (t-90) cc_final: 0.8155 (t70) REVERT: E 361 LEU cc_start: 0.8505 (tp) cc_final: 0.8211 (mp) REVERT: E 370 ARG cc_start: 0.7773 (mmt180) cc_final: 0.7487 (mmt180) REVERT: E 377 TYR cc_start: 0.9120 (m-10) cc_final: 0.8838 (m-10) REVERT: E 397 ASN cc_start: 0.8820 (t0) cc_final: 0.8544 (t0) REVERT: E 483 GLN cc_start: 0.7881 (tt0) cc_final: 0.7323 (tm-30) REVERT: E 530 MET cc_start: 0.7414 (tpp) cc_final: 0.7119 (tpp) REVERT: E 587 VAL cc_start: 0.9092 (t) cc_final: 0.8879 (t) REVERT: E 602 LYS cc_start: 0.8136 (mmmm) cc_final: 0.7679 (mtmt) REVERT: E 817 HIS cc_start: 0.7337 (m-70) cc_final: 0.7027 (m-70) REVERT: E 1219 TYR cc_start: 0.6196 (t80) cc_final: 0.5736 (t80) outliers start: 53 outliers final: 33 residues processed: 508 average time/residue: 0.1316 time to fit residues: 106.1000 Evaluate side-chains 488 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 452 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 571 LEU Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1155 THR Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1198 LEU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1286 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 202 optimal weight: 30.0000 chunk 103 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 199 optimal weight: 20.0000 chunk 130 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 chunk 243 optimal weight: 7.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 GLN D 48 ASN D 128 GLN E 105 HIS ** E1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.159890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.131288 restraints weight = 24471.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.130658 restraints weight = 19564.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.132701 restraints weight = 15572.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.133673 restraints weight = 11757.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.134068 restraints weight = 9561.963| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 21089 Z= 0.254 Angle : 0.648 13.072 28739 Z= 0.328 Chirality : 0.048 0.164 3386 Planarity : 0.005 0.051 3559 Dihedral : 20.951 177.916 3891 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.03 % Allowed : 13.79 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.16), residues: 2750 helix: 1.47 (0.14), residues: 1344 sheet: -1.92 (0.28), residues: 308 loop : -1.69 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 314 TYR 0.017 0.002 TYR E1064 PHE 0.028 0.002 PHE A 75 TRP 0.009 0.001 TRP C 68 HIS 0.024 0.002 HIS E 491 Details of bonding type rmsd covalent geometry : bond 0.00596 (21083) covalent geometry : angle 0.64672 (28726) SS BOND : bond 0.00370 ( 5) SS BOND : angle 2.56411 ( 10) hydrogen bonds : bond 0.05164 ( 1162) hydrogen bonds : angle 4.40066 ( 3390) link_NAG-ASN : bond 0.00202 ( 1) link_NAG-ASN : angle 0.76086 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 466 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8440 (ttm170) cc_final: 0.7768 (mtm110) REVERT: A 92 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8604 (tp) REVERT: B 47 LYS cc_start: 0.8644 (mttt) cc_final: 0.8241 (mtpp) REVERT: B 84 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8427 (tt) REVERT: B 114 ILE cc_start: 0.9132 (mm) cc_final: 0.8740 (mt) REVERT: B 125 ILE cc_start: 0.8881 (mm) cc_final: 0.8541 (mt) REVERT: B 137 MET cc_start: 0.7790 (mtm) cc_final: 0.7024 (mtm) REVERT: B 274 ASP cc_start: 0.6145 (t70) cc_final: 0.5895 (t0) REVERT: C 58 ASP cc_start: 0.8200 (p0) cc_final: 0.7856 (p0) REVERT: C 76 THR cc_start: 0.9127 (m) cc_final: 0.8886 (m) REVERT: C 113 SER cc_start: 0.9071 (m) cc_final: 0.8652 (t) REVERT: C 210 ILE cc_start: 0.9272 (mt) cc_final: 0.8830 (tt) REVERT: C 212 SER cc_start: 0.9222 (m) cc_final: 0.8941 (p) REVERT: C 314 ARG cc_start: 0.8383 (ptp-170) cc_final: 0.7945 (mtp180) REVERT: C 327 SER cc_start: 0.9124 (t) cc_final: 0.8732 (p) REVERT: D 41 ASN cc_start: 0.8753 (t0) cc_final: 0.8396 (t0) REVERT: D 47 LYS cc_start: 0.8756 (mmtt) cc_final: 0.8460 (mttm) REVERT: D 212 SER cc_start: 0.9069 (m) cc_final: 0.8374 (p) REVERT: D 261 ILE cc_start: 0.9215 (mt) cc_final: 0.9007 (mt) REVERT: D 290 VAL cc_start: 0.9624 (OUTLIER) cc_final: 0.9344 (m) REVERT: E 31 LEU cc_start: 0.8987 (mt) cc_final: 0.8759 (mt) REVERT: E 51 TRP cc_start: 0.7783 (t60) cc_final: 0.7499 (t60) REVERT: E 84 VAL cc_start: 0.9335 (m) cc_final: 0.9135 (t) REVERT: E 158 TYR cc_start: 0.7353 (t80) cc_final: 0.6949 (t80) REVERT: E 159 ASP cc_start: 0.7213 (t0) cc_final: 0.6989 (t0) REVERT: E 164 PHE cc_start: 0.7831 (m-80) cc_final: 0.7401 (m-80) REVERT: E 178 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8783 (mm) REVERT: E 218 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8462 (pp) REVERT: E 299 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8593 (mp) REVERT: E 361 LEU cc_start: 0.8576 (tp) cc_final: 0.8257 (mp) REVERT: E 377 TYR cc_start: 0.9154 (m-10) cc_final: 0.8875 (m-10) REVERT: E 602 LYS cc_start: 0.8069 (mmmm) cc_final: 0.7574 (mtmt) REVERT: E 1272 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7387 (mp) outliers start: 88 outliers final: 68 residues processed: 511 average time/residue: 0.1290 time to fit residues: 105.7852 Evaluate side-chains 522 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 447 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 259 HIS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 492 SER Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1146 SER Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1155 THR Chi-restraints excluded: chain E residue 1173 VAL Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1197 GLN Chi-restraints excluded: chain E residue 1198 LEU Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1286 THR Chi-restraints excluded: chain E residue 1318 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 166 optimal weight: 0.9990 chunk 217 optimal weight: 50.0000 chunk 220 optimal weight: 7.9990 chunk 211 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 234 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 204 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN C 173 GLN D 128 GLN E 491 HIS ** E1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.162548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.135779 restraints weight = 24266.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.134416 restraints weight = 21448.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.135975 restraints weight = 17614.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.137411 restraints weight = 13680.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.137611 restraints weight = 11166.584| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21089 Z= 0.145 Angle : 0.555 10.937 28739 Z= 0.280 Chirality : 0.045 0.164 3386 Planarity : 0.004 0.050 3559 Dihedral : 20.042 179.856 3891 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.41 % Allowed : 15.79 % Favored : 79.81 % 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: 0.13 (0.16), residues: 2750 helix: 1.84 (0.14), residues: 1337 sheet: -1.79 (0.29), residues: 298 loop : -1.60 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 192 TYR 0.014 0.001 TYR E 107 PHE 0.027 0.001 PHE A 75 TRP 0.006 0.001 TRP E1037 HIS 0.007 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00327 (21083) covalent geometry : angle 0.55328 (28726) SS BOND : bond 0.00490 ( 5) SS BOND : angle 2.51192 ( 10) hydrogen bonds : bond 0.04460 ( 1162) hydrogen bonds : angle 4.08320 ( 3390) link_NAG-ASN : bond 0.00332 ( 1) link_NAG-ASN : angle 0.94296 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 434 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8442 (ttm170) cc_final: 0.7815 (mtm110) REVERT: A 196 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.7894 (tp) REVERT: A 262 ASP cc_start: 0.7080 (t0) cc_final: 0.6727 (t0) REVERT: B 47 LYS cc_start: 0.8715 (mttt) cc_final: 0.8294 (mtpp) REVERT: B 88 MET cc_start: 0.8158 (tpp) cc_final: 0.7686 (tpp) REVERT: B 114 ILE cc_start: 0.9081 (mm) cc_final: 0.8683 (mt) REVERT: B 125 ILE cc_start: 0.8671 (mm) cc_final: 0.8348 (mt) REVERT: B 137 MET cc_start: 0.7677 (mtm) cc_final: 0.6966 (mtm) REVERT: B 274 ASP cc_start: 0.6113 (t70) cc_final: 0.5829 (t0) REVERT: C 58 ASP cc_start: 0.8087 (p0) cc_final: 0.7832 (p0) REVERT: C 59 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8681 (m) REVERT: C 113 SER cc_start: 0.9017 (m) cc_final: 0.8646 (t) REVERT: C 128 GLN cc_start: 0.8498 (tt0) cc_final: 0.8226 (tt0) REVERT: C 210 ILE cc_start: 0.9226 (mt) cc_final: 0.8840 (tt) REVERT: C 212 SER cc_start: 0.8985 (m) cc_final: 0.8752 (p) REVERT: C 259 HIS cc_start: 0.9077 (OUTLIER) cc_final: 0.8455 (t-170) REVERT: C 314 ARG cc_start: 0.8264 (ptp-170) cc_final: 0.7824 (mtp-110) REVERT: D 41 ASN cc_start: 0.8699 (t0) cc_final: 0.8385 (t0) REVERT: D 47 LYS cc_start: 0.8732 (mmtt) cc_final: 0.8446 (mttm) REVERT: D 170 LYS cc_start: 0.9069 (mtpp) cc_final: 0.8719 (tptp) REVERT: D 212 SER cc_start: 0.8949 (m) cc_final: 0.8134 (p) REVERT: D 261 ILE cc_start: 0.9189 (mt) cc_final: 0.8938 (mt) REVERT: D 290 VAL cc_start: 0.9653 (OUTLIER) cc_final: 0.9358 (m) REVERT: E 31 LEU cc_start: 0.9009 (mt) cc_final: 0.8577 (mt) REVERT: E 34 VAL cc_start: 0.8759 (OUTLIER) cc_final: 0.8527 (t) REVERT: E 51 TRP cc_start: 0.7779 (t60) cc_final: 0.7487 (t60) REVERT: E 158 TYR cc_start: 0.7211 (t80) cc_final: 0.6866 (t80) REVERT: E 159 ASP cc_start: 0.7166 (t0) cc_final: 0.6855 (t0) REVERT: E 164 PHE cc_start: 0.7773 (m-80) cc_final: 0.7373 (m-80) REVERT: E 218 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8466 (pp) REVERT: E 299 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8551 (mp) REVERT: E 318 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8199 (tt) REVERT: E 327 LEU cc_start: 0.7973 (tp) cc_final: 0.7770 (tp) REVERT: E 361 LEU cc_start: 0.8553 (tp) cc_final: 0.8284 (mp) REVERT: E 445 ILE cc_start: 0.9085 (mm) cc_final: 0.8602 (mp) REVERT: E 491 HIS cc_start: 0.7245 (OUTLIER) cc_final: 0.6710 (m170) REVERT: E 590 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8012 (mm) outliers start: 77 outliers final: 52 residues processed: 472 average time/residue: 0.1319 time to fit residues: 100.5934 Evaluate side-chains 487 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 425 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 259 HIS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 259 HIS Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 403 SER Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1197 GLN Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1318 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 14 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 200 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 193 optimal weight: 50.0000 chunk 148 optimal weight: 9.9990 chunk 267 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 218 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN E 491 HIS ** E1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.163034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.136240 restraints weight = 24183.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.134587 restraints weight = 22122.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.136326 restraints weight = 18308.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.136916 restraints weight = 15170.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.137618 restraints weight = 12187.436| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21089 Z= 0.139 Angle : 0.548 11.389 28739 Z= 0.273 Chirality : 0.045 0.231 3386 Planarity : 0.004 0.050 3559 Dihedral : 19.343 175.730 3889 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.21 % Allowed : 15.90 % Favored : 78.89 % 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: 0.30 (0.17), residues: 2750 helix: 2.02 (0.14), residues: 1337 sheet: -1.76 (0.29), residues: 313 loop : -1.54 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 32 TYR 0.014 0.001 TYR E 195 PHE 0.023 0.001 PHE A 75 TRP 0.006 0.001 TRP C 91 HIS 0.014 0.001 HIS E 491 Details of bonding type rmsd covalent geometry : bond 0.00316 (21083) covalent geometry : angle 0.54571 (28726) SS BOND : bond 0.00467 ( 5) SS BOND : angle 2.54757 ( 10) hydrogen bonds : bond 0.04263 ( 1162) hydrogen bonds : angle 3.97839 ( 3390) link_NAG-ASN : bond 0.00340 ( 1) link_NAG-ASN : angle 0.97433 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 447 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8398 (ttm170) cc_final: 0.7808 (mtm110) REVERT: A 196 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8029 (tp) REVERT: A 199 MET cc_start: 0.8067 (mmm) cc_final: 0.7649 (mmp) REVERT: A 262 ASP cc_start: 0.7070 (t0) cc_final: 0.6702 (t0) REVERT: B 47 LYS cc_start: 0.8725 (mttt) cc_final: 0.8320 (mtpp) REVERT: B 114 ILE cc_start: 0.9038 (mm) cc_final: 0.8647 (mt) REVERT: B 125 ILE cc_start: 0.8645 (mm) cc_final: 0.8332 (mt) REVERT: B 137 MET cc_start: 0.7690 (mtm) cc_final: 0.6972 (mtm) REVERT: B 274 ASP cc_start: 0.6178 (t70) cc_final: 0.5933 (t0) REVERT: C 113 SER cc_start: 0.9001 (m) cc_final: 0.8654 (t) REVERT: C 128 GLN cc_start: 0.8391 (tt0) cc_final: 0.8128 (tt0) REVERT: C 212 SER cc_start: 0.8932 (m) cc_final: 0.8715 (p) REVERT: C 314 ARG cc_start: 0.8247 (ptp-170) cc_final: 0.7806 (mtp-110) REVERT: D 41 ASN cc_start: 0.8679 (t0) cc_final: 0.8387 (t0) REVERT: D 47 LYS cc_start: 0.8723 (mmtt) cc_final: 0.8400 (mttm) REVERT: D 170 LYS cc_start: 0.9071 (mtpp) cc_final: 0.8725 (tptp) REVERT: D 206 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.8155 (mmm-85) REVERT: D 212 SER cc_start: 0.8925 (m) cc_final: 0.8084 (p) REVERT: D 261 ILE cc_start: 0.9186 (mt) cc_final: 0.8940 (mt) REVERT: D 290 VAL cc_start: 0.9641 (OUTLIER) cc_final: 0.9367 (m) REVERT: E 51 TRP cc_start: 0.7796 (t60) cc_final: 0.7458 (t60) REVERT: E 158 TYR cc_start: 0.7196 (t80) cc_final: 0.6822 (t80) REVERT: E 159 ASP cc_start: 0.7158 (t0) cc_final: 0.6844 (t0) REVERT: E 164 PHE cc_start: 0.7704 (m-80) cc_final: 0.7331 (m-80) REVERT: E 299 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8508 (mp) REVERT: E 318 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8206 (tt) REVERT: E 361 LEU cc_start: 0.8527 (tp) cc_final: 0.8279 (mp) REVERT: E 377 TYR cc_start: 0.9018 (m-10) cc_final: 0.8679 (m-10) REVERT: E 397 ASN cc_start: 0.9009 (t0) cc_final: 0.8709 (t0) REVERT: E 590 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8063 (mm) outliers start: 91 outliers final: 69 residues processed: 493 average time/residue: 0.1260 time to fit residues: 100.4036 Evaluate side-chains 504 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 430 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 259 HIS Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 403 SER Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1197 GLN Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 116 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 218 optimal weight: 30.0000 chunk 47 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 263 optimal weight: 50.0000 chunk 3 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 GLN D 128 GLN ** E1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.158987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.133224 restraints weight = 24221.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.133124 restraints weight = 24420.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.135645 restraints weight = 17959.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.135346 restraints weight = 12594.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.135615 restraints weight = 12369.392| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21089 Z= 0.230 Angle : 0.626 10.378 28739 Z= 0.314 Chirality : 0.047 0.174 3386 Planarity : 0.005 0.048 3559 Dihedral : 19.146 177.546 3889 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.95 % Allowed : 16.59 % Favored : 77.46 % 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: 2750 helix: 1.80 (0.14), residues: 1341 sheet: -1.84 (0.29), residues: 308 loop : -1.58 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 32 TYR 0.015 0.002 TYR E 396 PHE 0.021 0.002 PHE D 75 TRP 0.007 0.001 TRP E1037 HIS 0.009 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00541 (21083) covalent geometry : angle 0.62422 (28726) SS BOND : bond 0.00276 ( 5) SS BOND : angle 2.62893 ( 10) hydrogen bonds : bond 0.04607 ( 1162) hydrogen bonds : angle 4.11850 ( 3390) link_NAG-ASN : bond 0.00263 ( 1) link_NAG-ASN : angle 0.91936 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 429 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8461 (ttm170) cc_final: 0.7904 (mtm110) REVERT: A 108 VAL cc_start: 0.9340 (t) cc_final: 0.8967 (m) REVERT: A 196 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8002 (tp) REVERT: A 262 ASP cc_start: 0.7100 (t0) cc_final: 0.6764 (t0) REVERT: B 47 LYS cc_start: 0.8763 (mttt) cc_final: 0.8319 (mtpp) REVERT: B 114 ILE cc_start: 0.9141 (mm) cc_final: 0.8778 (mt) REVERT: B 125 ILE cc_start: 0.8893 (mm) cc_final: 0.8568 (mt) REVERT: B 137 MET cc_start: 0.7779 (mtm) cc_final: 0.7085 (mtm) REVERT: B 274 ASP cc_start: 0.6324 (t70) cc_final: 0.6039 (t0) REVERT: C 113 SER cc_start: 0.9040 (m) cc_final: 0.8690 (t) REVERT: C 173 GLN cc_start: 0.9094 (mm110) cc_final: 0.8797 (mm110) REVERT: C 210 ILE cc_start: 0.9378 (mt) cc_final: 0.8861 (tt) REVERT: C 212 SER cc_start: 0.9189 (m) cc_final: 0.8850 (p) REVERT: C 259 HIS cc_start: 0.9085 (OUTLIER) cc_final: 0.8441 (t-170) REVERT: C 314 ARG cc_start: 0.8380 (ptp-170) cc_final: 0.8016 (mtp180) REVERT: D 41 ASN cc_start: 0.8589 (t0) cc_final: 0.8279 (t0) REVERT: D 47 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8443 (mttm) REVERT: D 170 LYS cc_start: 0.9043 (mtpp) cc_final: 0.8770 (tptp) REVERT: D 173 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8443 (mm-40) REVERT: D 206 ARG cc_start: 0.8798 (mmm-85) cc_final: 0.8522 (mmm-85) REVERT: D 212 SER cc_start: 0.9093 (m) cc_final: 0.8375 (p) REVERT: D 290 VAL cc_start: 0.9656 (OUTLIER) cc_final: 0.9387 (m) REVERT: E 51 TRP cc_start: 0.7944 (t60) cc_final: 0.7574 (t60) REVERT: E 158 TYR cc_start: 0.7168 (t80) cc_final: 0.6920 (t80) REVERT: E 159 ASP cc_start: 0.7048 (t0) cc_final: 0.6762 (t0) REVERT: E 164 PHE cc_start: 0.7628 (m-80) cc_final: 0.7363 (m-80) REVERT: E 299 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8544 (mp) REVERT: E 361 LEU cc_start: 0.8586 (tp) cc_final: 0.8332 (mp) REVERT: E 397 ASN cc_start: 0.9055 (t0) cc_final: 0.8757 (t0) REVERT: E 530 MET cc_start: 0.7139 (tpp) cc_final: 0.6851 (tpp) REVERT: E 590 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8077 (mm) REVERT: E 1272 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7253 (mp) outliers start: 104 outliers final: 80 residues processed: 482 average time/residue: 0.1264 time to fit residues: 98.6029 Evaluate side-chains 493 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 407 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 259 HIS Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 259 HIS Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 403 SER Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1146 SER Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1155 THR Chi-restraints excluded: chain E residue 1173 VAL Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1197 GLN Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1286 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 106 optimal weight: 9.9990 chunk 269 optimal weight: 50.0000 chunk 191 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 267 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 201 optimal weight: 50.0000 chunk 219 optimal weight: 40.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 GLN D 128 GLN E 293 HIS ** E1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.160995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.134782 restraints weight = 24261.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.133280 restraints weight = 22929.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.134685 restraints weight = 19326.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.135527 restraints weight = 15342.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.135704 restraints weight = 12516.298| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21089 Z= 0.151 Angle : 0.573 10.936 28739 Z= 0.284 Chirality : 0.045 0.177 3386 Planarity : 0.004 0.049 3559 Dihedral : 18.542 170.448 3889 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 5.49 % Allowed : 17.96 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.17), residues: 2750 helix: 1.98 (0.14), residues: 1341 sheet: -1.79 (0.29), residues: 303 loop : -1.53 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 192 TYR 0.014 0.001 TYR E 107 PHE 0.025 0.002 PHE E 38 TRP 0.007 0.001 TRP E 430 HIS 0.011 0.001 HIS E 293 Details of bonding type rmsd covalent geometry : bond 0.00350 (21083) covalent geometry : angle 0.57122 (28726) SS BOND : bond 0.00420 ( 5) SS BOND : angle 2.66138 ( 10) hydrogen bonds : bond 0.04270 ( 1162) hydrogen bonds : angle 3.97156 ( 3390) link_NAG-ASN : bond 0.00366 ( 1) link_NAG-ASN : angle 1.02983 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 430 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8388 (ttm170) cc_final: 0.7835 (mtm110) REVERT: A 108 VAL cc_start: 0.9283 (t) cc_final: 0.8933 (m) REVERT: A 196 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8015 (tp) REVERT: A 262 ASP cc_start: 0.6942 (t0) cc_final: 0.6657 (t0) REVERT: B 47 LYS cc_start: 0.8837 (mttt) cc_final: 0.8344 (mtpp) REVERT: B 114 ILE cc_start: 0.9047 (mm) cc_final: 0.8635 (mt) REVERT: B 125 ILE cc_start: 0.8877 (mm) cc_final: 0.8559 (mt) REVERT: B 140 GLU cc_start: 0.8058 (pm20) cc_final: 0.7755 (pm20) REVERT: B 274 ASP cc_start: 0.6315 (t70) cc_final: 0.6048 (t0) REVERT: C 113 SER cc_start: 0.8980 (m) cc_final: 0.8684 (t) REVERT: C 128 GLN cc_start: 0.8544 (tt0) cc_final: 0.8269 (tt0) REVERT: C 212 SER cc_start: 0.8936 (m) cc_final: 0.8694 (p) REVERT: C 259 HIS cc_start: 0.8984 (OUTLIER) cc_final: 0.8347 (t-170) REVERT: C 314 ARG cc_start: 0.8326 (ptp-170) cc_final: 0.7862 (mtp-110) REVERT: D 41 ASN cc_start: 0.8474 (t0) cc_final: 0.8185 (t0) REVERT: D 47 LYS cc_start: 0.8690 (mmtt) cc_final: 0.8405 (mttm) REVERT: D 170 LYS cc_start: 0.9039 (mtpp) cc_final: 0.8801 (tptp) REVERT: D 200 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7599 (tt) REVERT: D 206 ARG cc_start: 0.8719 (mmm-85) cc_final: 0.8497 (mmm-85) REVERT: D 212 SER cc_start: 0.8974 (m) cc_final: 0.8158 (p) REVERT: D 290 VAL cc_start: 0.9690 (OUTLIER) cc_final: 0.9424 (m) REVERT: E 51 TRP cc_start: 0.7919 (t60) cc_final: 0.7563 (t60) REVERT: E 107 TYR cc_start: 0.8925 (OUTLIER) cc_final: 0.8697 (p90) REVERT: E 159 ASP cc_start: 0.6884 (t0) cc_final: 0.6591 (t0) REVERT: E 164 PHE cc_start: 0.7451 (m-80) cc_final: 0.7200 (m-80) REVERT: E 299 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8474 (mp) REVERT: E 361 LEU cc_start: 0.8529 (tp) cc_final: 0.8317 (mp) REVERT: E 397 ASN cc_start: 0.9017 (t0) cc_final: 0.8720 (t0) REVERT: E 433 PHE cc_start: 0.9087 (m-10) cc_final: 0.8823 (m-10) REVERT: E 590 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7946 (mm) REVERT: E 1103 ASN cc_start: 0.8105 (m110) cc_final: 0.7872 (m110) outliers start: 96 outliers final: 82 residues processed: 478 average time/residue: 0.1256 time to fit residues: 97.3352 Evaluate side-chains 511 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 422 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 259 HIS Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 259 HIS Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1146 SER Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1155 THR Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1197 GLN Chi-restraints excluded: chain E residue 1198 LEU Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1286 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 104 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 246 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 38 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 264 optimal weight: 30.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1245 ASN ** 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 = 0.3664 r_free = 0.3664 target = 0.162764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.136297 restraints weight = 24144.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.134829 restraints weight = 21829.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.136644 restraints weight = 17894.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.137264 restraints weight = 13691.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.137462 restraints weight = 12453.852| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21089 Z= 0.133 Angle : 0.557 10.507 28739 Z= 0.274 Chirality : 0.045 0.171 3386 Planarity : 0.004 0.048 3559 Dihedral : 17.557 161.022 3889 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.98 % Allowed : 18.25 % Favored : 76.77 % 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: 0.50 (0.17), residues: 2750 helix: 2.19 (0.14), residues: 1340 sheet: -1.71 (0.29), residues: 303 loop : -1.46 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 192 TYR 0.018 0.001 TYR E 845 PHE 0.022 0.001 PHE A 75 TRP 0.006 0.001 TRP E 430 HIS 0.007 0.001 HIS E1024 Details of bonding type rmsd covalent geometry : bond 0.00302 (21083) covalent geometry : angle 0.55462 (28726) SS BOND : bond 0.00406 ( 5) SS BOND : angle 2.69261 ( 10) hydrogen bonds : bond 0.04000 ( 1162) hydrogen bonds : angle 3.86737 ( 3390) link_NAG-ASN : bond 0.00435 ( 1) link_NAG-ASN : angle 1.02934 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 426 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 VAL cc_start: 0.9269 (t) cc_final: 0.8920 (m) REVERT: A 196 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8063 (tp) REVERT: A 262 ASP cc_start: 0.6873 (t0) cc_final: 0.6558 (t0) REVERT: B 47 LYS cc_start: 0.8898 (mttt) cc_final: 0.8413 (mtpp) REVERT: B 114 ILE cc_start: 0.9015 (mm) cc_final: 0.8596 (mt) REVERT: B 137 MET cc_start: 0.7572 (mtm) cc_final: 0.6896 (mtm) REVERT: B 274 ASP cc_start: 0.6132 (t70) cc_final: 0.5866 (t0) REVERT: C 76 THR cc_start: 0.9127 (m) cc_final: 0.8808 (m) REVERT: C 113 SER cc_start: 0.8942 (m) cc_final: 0.8663 (t) REVERT: C 128 GLN cc_start: 0.8518 (tt0) cc_final: 0.8226 (tt0) REVERT: C 210 ILE cc_start: 0.9401 (mt) cc_final: 0.8958 (tt) REVERT: C 212 SER cc_start: 0.8711 (m) cc_final: 0.8504 (p) REVERT: C 259 HIS cc_start: 0.9020 (OUTLIER) cc_final: 0.8374 (t-170) REVERT: C 314 ARG cc_start: 0.8149 (ptp-170) cc_final: 0.7747 (mtp-110) REVERT: D 41 ASN cc_start: 0.8412 (t0) cc_final: 0.8152 (t0) REVERT: D 47 LYS cc_start: 0.8681 (mmtt) cc_final: 0.8399 (mttm) REVERT: D 170 LYS cc_start: 0.9048 (mtpp) cc_final: 0.8817 (tptp) REVERT: D 200 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7471 (tt) REVERT: D 212 SER cc_start: 0.8870 (m) cc_final: 0.8033 (p) REVERT: D 290 VAL cc_start: 0.9680 (OUTLIER) cc_final: 0.9407 (m) REVERT: E 51 TRP cc_start: 0.7924 (t60) cc_final: 0.7535 (t60) REVERT: E 107 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.8643 (p90) REVERT: E 159 ASP cc_start: 0.6916 (t0) cc_final: 0.6639 (t0) REVERT: E 164 PHE cc_start: 0.7534 (m-80) cc_final: 0.7267 (m-80) REVERT: E 218 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8744 (pp) REVERT: E 361 LEU cc_start: 0.8610 (tp) cc_final: 0.8399 (mp) REVERT: E 397 ASN cc_start: 0.9007 (t0) cc_final: 0.8714 (t0) REVERT: E 590 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7916 (mm) REVERT: E 1088 TRP cc_start: 0.7879 (t60) cc_final: 0.7059 (t60) REVERT: E 1103 ASN cc_start: 0.8169 (m110) cc_final: 0.7910 (m110) REVERT: E 1272 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7114 (mp) outliers start: 87 outliers final: 71 residues processed: 471 average time/residue: 0.1276 time to fit residues: 97.2363 Evaluate side-chains 500 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 421 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 259 HIS Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 259 HIS Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1146 SER Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1155 THR Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1197 GLN Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1286 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 167 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 245 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 249 optimal weight: 8.9990 chunk 200 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 204 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN B 216 HIS ** E1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.157932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.131102 restraints weight = 24430.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.130647 restraints weight = 20288.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.131736 restraints weight = 17310.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.132513 restraints weight = 13888.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.132649 restraints weight = 12301.341| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 21089 Z= 0.253 Angle : 0.659 10.561 28739 Z= 0.329 Chirality : 0.048 0.180 3386 Planarity : 0.005 0.046 3559 Dihedral : 17.633 161.170 3889 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 5.61 % Allowed : 17.85 % Favored : 76.54 % 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: 2750 helix: 1.87 (0.14), residues: 1339 sheet: -1.93 (0.29), residues: 303 loop : -1.60 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 192 TYR 0.016 0.002 TYR E 107 PHE 0.026 0.002 PHE E 38 TRP 0.008 0.001 TRP B 83 HIS 0.010 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00597 (21083) covalent geometry : angle 0.65737 (28726) SS BOND : bond 0.00395 ( 5) SS BOND : angle 2.80205 ( 10) hydrogen bonds : bond 0.04554 ( 1162) hydrogen bonds : angle 4.10384 ( 3390) link_NAG-ASN : bond 0.00367 ( 1) link_NAG-ASN : angle 1.07363 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 425 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 VAL cc_start: 0.9357 (t) cc_final: 0.8981 (m) REVERT: A 185 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8075 (ttmm) REVERT: A 196 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8068 (tp) REVERT: A 229 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8162 (mm-30) REVERT: A 262 ASP cc_start: 0.7062 (t0) cc_final: 0.6671 (t0) REVERT: B 47 LYS cc_start: 0.8746 (mttt) cc_final: 0.8270 (mtpp) REVERT: B 114 ILE cc_start: 0.9159 (mm) cc_final: 0.8797 (mt) REVERT: B 257 ILE cc_start: 0.9357 (mm) cc_final: 0.9030 (mt) REVERT: C 76 THR cc_start: 0.9155 (m) cc_final: 0.8790 (m) REVERT: C 113 SER cc_start: 0.9048 (m) cc_final: 0.8698 (t) REVERT: C 158 MET cc_start: 0.7828 (mmm) cc_final: 0.7481 (tpt) REVERT: C 212 SER cc_start: 0.9210 (m) cc_final: 0.8860 (p) REVERT: C 259 HIS cc_start: 0.9068 (OUTLIER) cc_final: 0.8418 (t-170) REVERT: C 314 ARG cc_start: 0.8310 (ptp-170) cc_final: 0.7817 (mtp-110) REVERT: D 41 ASN cc_start: 0.8512 (t0) cc_final: 0.8239 (t0) REVERT: D 47 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8234 (mttm) REVERT: D 72 LEU cc_start: 0.8866 (mt) cc_final: 0.8514 (mp) REVERT: D 170 LYS cc_start: 0.9059 (mtpp) cc_final: 0.8804 (tptp) REVERT: D 200 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7768 (tt) REVERT: D 212 SER cc_start: 0.9074 (m) cc_final: 0.8319 (p) REVERT: D 290 VAL cc_start: 0.9672 (OUTLIER) cc_final: 0.9393 (m) REVERT: E 51 TRP cc_start: 0.8193 (t60) cc_final: 0.7765 (t60) REVERT: E 159 ASP cc_start: 0.7081 (t0) cc_final: 0.6755 (t0) REVERT: E 164 PHE cc_start: 0.7602 (m-80) cc_final: 0.7352 (m-80) REVERT: E 218 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8867 (pp) REVERT: E 361 LEU cc_start: 0.8589 (tp) cc_final: 0.8295 (mp) REVERT: E 397 ASN cc_start: 0.9098 (t0) cc_final: 0.8796 (t0) REVERT: E 530 MET cc_start: 0.7070 (tpp) cc_final: 0.6787 (tpp) REVERT: E 590 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8065 (mm) REVERT: E 602 LYS cc_start: 0.8385 (mmmm) cc_final: 0.7881 (mtmt) REVERT: E 1103 ASN cc_start: 0.8194 (m110) cc_final: 0.7916 (m110) REVERT: E 1272 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7131 (mp) outliers start: 98 outliers final: 81 residues processed: 473 average time/residue: 0.1407 time to fit residues: 106.4430 Evaluate side-chains 500 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 411 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 259 HIS Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 259 HIS Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1146 SER Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1155 THR Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1197 GLN Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1286 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 0.9990 chunk 199 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 269 optimal weight: 50.0000 chunk 30 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 234 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 847 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.162596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.136788 restraints weight = 23982.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.136111 restraints weight = 22851.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.138277 restraints weight = 20071.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.138272 restraints weight = 14553.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.138520 restraints weight = 12653.926| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21089 Z= 0.129 Angle : 0.567 10.049 28739 Z= 0.279 Chirality : 0.045 0.173 3386 Planarity : 0.004 0.050 3559 Dihedral : 16.820 158.508 3889 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.00 % Allowed : 20.14 % Favored : 75.86 % 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: 0.51 (0.17), residues: 2750 helix: 2.21 (0.14), residues: 1344 sheet: -1.82 (0.29), residues: 306 loop : -1.44 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 192 TYR 0.015 0.001 TYR E 107 PHE 0.023 0.001 PHE A 75 TRP 0.007 0.001 TRP E 65 HIS 0.007 0.001 HIS E1024 Details of bonding type rmsd covalent geometry : bond 0.00294 (21083) covalent geometry : angle 0.56498 (28726) SS BOND : bond 0.00174 ( 5) SS BOND : angle 2.75870 ( 10) hydrogen bonds : bond 0.03996 ( 1162) hydrogen bonds : angle 3.88436 ( 3390) link_NAG-ASN : bond 0.00478 ( 1) link_NAG-ASN : angle 1.13121 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 420 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8402 (ttm170) cc_final: 0.7783 (mtm110) REVERT: A 108 VAL cc_start: 0.9259 (t) cc_final: 0.8898 (m) REVERT: A 185 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8087 (ttmm) REVERT: A 229 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7663 (mm-30) REVERT: A 262 ASP cc_start: 0.6859 (t0) cc_final: 0.6514 (t0) REVERT: B 47 LYS cc_start: 0.8755 (mttt) cc_final: 0.8305 (mtpp) REVERT: B 114 ILE cc_start: 0.9053 (mm) cc_final: 0.8627 (mt) REVERT: B 137 MET cc_start: 0.7599 (mtm) cc_final: 0.6900 (mtm) REVERT: B 257 ILE cc_start: 0.9311 (mm) cc_final: 0.9037 (mt) REVERT: B 274 ASP cc_start: 0.6233 (t70) cc_final: 0.5985 (t0) REVERT: C 76 THR cc_start: 0.9126 (m) cc_final: 0.8762 (m) REVERT: C 113 SER cc_start: 0.8940 (m) cc_final: 0.8657 (t) REVERT: C 128 GLN cc_start: 0.8510 (tt0) cc_final: 0.8254 (tt0) REVERT: C 212 SER cc_start: 0.9010 (m) cc_final: 0.8645 (p) REVERT: C 248 SER cc_start: 0.9095 (OUTLIER) cc_final: 0.8811 (m) REVERT: C 314 ARG cc_start: 0.8150 (ptp-170) cc_final: 0.7745 (mtm110) REVERT: D 41 ASN cc_start: 0.8417 (t0) cc_final: 0.8172 (t0) REVERT: D 47 LYS cc_start: 0.8688 (mmtt) cc_final: 0.8379 (mttm) REVERT: D 200 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7573 (tt) REVERT: D 212 SER cc_start: 0.8930 (m) cc_final: 0.8092 (p) REVERT: D 249 ILE cc_start: 0.8271 (tp) cc_final: 0.8027 (tp) REVERT: D 290 VAL cc_start: 0.9653 (OUTLIER) cc_final: 0.9392 (m) REVERT: E 51 TRP cc_start: 0.8181 (t60) cc_final: 0.7759 (t60) REVERT: E 159 ASP cc_start: 0.6863 (t0) cc_final: 0.6617 (t0) REVERT: E 164 PHE cc_start: 0.7548 (m-80) cc_final: 0.7267 (m-80) REVERT: E 218 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8733 (pp) REVERT: E 361 LEU cc_start: 0.8641 (tp) cc_final: 0.8412 (mp) REVERT: E 397 ASN cc_start: 0.9032 (t0) cc_final: 0.8765 (t0) REVERT: E 445 ILE cc_start: 0.9149 (mm) cc_final: 0.8717 (mp) REVERT: E 530 MET cc_start: 0.6992 (tpp) cc_final: 0.6733 (tpp) REVERT: E 590 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7925 (mm) REVERT: E 1103 ASN cc_start: 0.8151 (m110) cc_final: 0.7935 (m110) REVERT: E 1272 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7007 (mp) outliers start: 70 outliers final: 59 residues processed: 455 average time/residue: 0.1299 time to fit residues: 95.1003 Evaluate side-chains 478 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 412 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 590 LEU Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 1097 LEU Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1155 THR Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1189 LEU Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1283 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 255 optimal weight: 50.0000 chunk 23 optimal weight: 0.8980 chunk 220 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 268 optimal weight: 40.0000 chunk 131 optimal weight: 10.0000 chunk 271 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN B 313 GLN ** E1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.157552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.128895 restraints weight = 24507.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.128651 restraints weight = 18724.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.131128 restraints weight = 15073.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.131829 restraints weight = 10625.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.132216 restraints weight = 9208.507| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 21089 Z= 0.266 Angle : 0.678 10.589 28739 Z= 0.338 Chirality : 0.049 0.184 3386 Planarity : 0.005 0.049 3559 Dihedral : 16.929 159.319 3889 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.58 % Allowed : 19.45 % Favored : 75.97 % 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: 2750 helix: 1.88 (0.14), residues: 1336 sheet: -1.97 (0.29), residues: 288 loop : -1.62 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 192 TYR 0.017 0.002 TYR E 107 PHE 0.026 0.002 PHE B 75 TRP 0.014 0.002 TRP B 90 HIS 0.010 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00629 (21083) covalent geometry : angle 0.67599 (28726) SS BOND : bond 0.00391 ( 5) SS BOND : angle 2.79114 ( 10) hydrogen bonds : bond 0.04591 ( 1162) hydrogen bonds : angle 4.14007 ( 3390) link_NAG-ASN : bond 0.00396 ( 1) link_NAG-ASN : angle 1.13620 ( 3) =============================================================================== Job complete usr+sys time: 3097.38 seconds wall clock time: 54 minutes 4.85 seconds (3244.85 seconds total)