Starting phenix.real_space_refine on Sat Jul 4 15:36:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u24_26307/07_2026/7u24_26307.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u24_26307/07_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_26307/07_2026/7u24_26307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u24_26307/07_2026/7u24_26307.map" model { file = "/net/cci-nas-00/data/ceres_data/7u24_26307/07_2026/7u24_26307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u24_26307/07_2026/7u24_26307.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7u24_26307/07_2026/7u24_26307.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u24_26307/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 72 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.27, per 1000 atoms: 0.21 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: 1.99 Conformation dependent library (CDL) restraints added in 763.5 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: 0.78 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: 4.17 Time building geometry restraints manager: 2.37 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: 28412 1.86 - 3.72: 230 3.72 - 5.58: 63 5.58 - 7.43: 19 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 - 35.79: 12048 35.79 - 71.59: 167 71.59 - 107.38: 32 107.38 - 143.17: 30 143.17 - 178.97: 14 Dihedral angle restraints: 12291 sinusoidal: 4238 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=" C21 P5S D 401 " pdb=" C17 P5S D 401 " pdb=" C20 P5S D 401 " pdb=" O18 P5S D 401 " ideal model delta sinusoidal sigma weight residual 9.80 -169.17 178.97 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C21 P5S B 404 " pdb=" C17 P5S B 404 " pdb=" C20 P5S B 404 " pdb=" O18 P5S B 404 " ideal model delta sinusoidal sigma weight residual 9.80 -173.32 -176.88 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2389 0.037 - 0.074: 684 0.074 - 0.111: 272 0.111 - 0.149: 40 0.149 - 0.186: 1 Chirality restraints: 3386 Sorted by residual: chirality pdb=" CG LEU E 218 " pdb=" CB LEU E 218 " pdb=" CD1 LEU E 218 " pdb=" CD2 LEU E 218 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CA ILE A 189 " pdb=" N ILE A 189 " pdb=" C ILE A 189 " pdb=" CB ILE A 189 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA VAL A 316 " pdb=" N VAL A 316 " pdb=" C VAL A 316 " pdb=" CB VAL A 316 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (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: 0.060 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 19.100 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:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.002 0.111 21089 Z= 0.111 Angle : 0.496 9.292 28739 Z= 0.236 Chirality : 0.041 0.186 3386 Planarity : 0.004 0.049 3559 Dihedral : 17.034 178.967 7038 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/Z covalent geometry : bond 0.00226 / 0.11 (21083) covalent geometry : angle 0.49619 / 0.24 (28726) SS BOND : bond 0.00167 / 0.10 ( 5) SS BOND : angle 0.58087 / 0.34 ( 10) hydrogen bonds : bond 0.18339 / 12.66 ( 1162) hydrogen bonds : angle 6.37240 / 4.56 ( 3390) link_NAG-ASN : bond 0.00309 / 0.16 ( 1) link_NAG-ASN : angle 0.85630 / 0.44 ( 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 : 0.526 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: 0.1221 time to fit residues: 110.6450 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 : 0.651 ------------------------------------------------------------------------------- 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: 7.9990 overall best weight: 3.5754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 313 GLN C 43 ASN D 48 ASN E 105 HIS E 125 HIS E 491 HIS E 498 GLN ** E1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.165362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.138211 restraints weight = 24166.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.137105 restraints weight = 22173.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.138949 restraints weight = 17691.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.139758 restraints weight = 13647.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.140111 restraints weight = 11391.035| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21089 Z= 0.168 Angle : 0.576 9.592 28739 Z= 0.293 Chirality : 0.045 0.158 3386 Planarity : 0.004 0.051 3559 Dihedral : 17.713 173.045 3446 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.38 % Allowed : 11.61 % Favored : 85.01 % 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: 1.54 (0.15), residues: 1331 sheet: -1.94 (0.30), residues: 277 loop : -1.58 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 C 68 HIS 0.005 0.001 HIS E 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (21083) covalent geometry : angle 0.57572 / 0.29 (28726) SS BOND : bond 0.00309 / 0.15 ( 5) SS BOND : angle 1.66072 / 1.01 ( 10) hydrogen bonds : bond 0.05128 / 3.58 ( 1162) hydrogen bonds : angle 4.47730 / 3.18 ( 3390) link_NAG-ASN : bond 0.00106 / 0.06 ( 1) link_NAG-ASN : angle 0.70558 / 0.38 ( 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 541 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 482 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 SER cc_start: 0.9078 (t) cc_final: 0.8860 (t) REVERT: A 50 ARG cc_start: 0.8422 (ttm170) cc_final: 0.7694 (mtm110) REVERT: A 158 MET cc_start: 0.8019 (mmm) cc_final: 0.7739 (tpp) REVERT: A 223 THR cc_start: 0.9467 (m) cc_final: 0.9209 (p) REVERT: A 269 ASP cc_start: 0.8320 (m-30) cc_final: 0.8093 (m-30) REVERT: A 276 HIS cc_start: 0.8672 (p-80) cc_final: 0.8257 (p90) REVERT: B 47 LYS cc_start: 0.8622 (mttt) cc_final: 0.8282 (mtpp) REVERT: B 88 MET cc_start: 0.8023 (tpp) cc_final: 0.7711 (tpp) REVERT: B 114 ILE cc_start: 0.8960 (mm) cc_final: 0.8506 (mt) REVERT: B 125 ILE cc_start: 0.8665 (mm) cc_final: 0.8316 (mt) REVERT: B 137 MET cc_start: 0.7739 (mtm) cc_final: 0.6921 (mtm) REVERT: C 58 ASP cc_start: 0.8012 (p0) cc_final: 0.7662 (p0) REVERT: C 113 SER cc_start: 0.9048 (m) cc_final: 0.8621 (t) REVERT: C 210 ILE cc_start: 0.9237 (mt) cc_final: 0.9000 (tt) REVERT: C 212 SER cc_start: 0.9198 (m) cc_final: 0.8484 (t) REVERT: C 314 ARG cc_start: 0.8139 (ptp-170) cc_final: 0.7877 (mtp180) REVERT: C 327 SER cc_start: 0.9056 (t) cc_final: 0.8582 (p) REVERT: C 335 ASN cc_start: 0.8551 (m110) cc_final: 0.8260 (m-40) REVERT: D 47 LYS cc_start: 0.8657 (mmtt) cc_final: 0.8342 (mttm) REVERT: D 158 MET cc_start: 0.7647 (mmm) cc_final: 0.7251 (mmm) REVERT: D 170 LYS cc_start: 0.9063 (mtpp) cc_final: 0.8652 (tptp) REVERT: D 261 ILE cc_start: 0.9188 (mt) cc_final: 0.8985 (mt) REVERT: D 290 VAL cc_start: 0.9595 (OUTLIER) cc_final: 0.9222 (m) REVERT: E 51 TRP cc_start: 0.7652 (t60) cc_final: 0.7357 (t60) REVERT: E 84 VAL cc_start: 0.9331 (m) cc_final: 0.9051 (t) REVERT: E 178 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8563 (mm) REVERT: E 218 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8132 (pp) REVERT: E 299 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8511 (mp) REVERT: E 326 HIS cc_start: 0.8536 (t-90) cc_final: 0.8133 (t70) REVERT: E 327 LEU cc_start: 0.7889 (tp) cc_final: 0.7568 (tp) REVERT: E 361 LEU cc_start: 0.8506 (tp) cc_final: 0.8240 (mp) REVERT: E 370 ARG cc_start: 0.7849 (mmt180) cc_final: 0.7598 (mmt180) REVERT: E 377 TYR cc_start: 0.9125 (m-10) cc_final: 0.8837 (m-10) REVERT: E 397 ASN cc_start: 0.8835 (t0) cc_final: 0.8577 (t0) REVERT: E 483 GLN cc_start: 0.7881 (tt0) cc_final: 0.7344 (tm-30) REVERT: E 491 HIS cc_start: 0.7099 (OUTLIER) cc_final: 0.6415 (m170) REVERT: E 530 MET cc_start: 0.7401 (tpp) cc_final: 0.7090 (tpp) REVERT: E 602 LYS cc_start: 0.8147 (mmmm) cc_final: 0.7682 (mtmt) REVERT: E 817 HIS cc_start: 0.7332 (m-70) cc_final: 0.7040 (m-70) REVERT: E 1219 TYR cc_start: 0.6207 (t80) cc_final: 0.5769 (t80) outliers start: 59 outliers final: 35 residues processed: 512 average time/residue: 0.1226 time to fit residues: 99.6823 Evaluate side-chains 484 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 444 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 223 THR 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 178 LEU Chi-restraints excluded: chain E residue 203 GLU 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 479 THR 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: 20.0000 chunk 103 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 199 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 chunk 120 optimal weight: 20.0000 chunk 164 optimal weight: 6.9990 chunk 243 optimal weight: 7.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 313 GLN D 48 ASN ** 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 = 0.3659 r_free = 0.3659 target = 0.162409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.135152 restraints weight = 24334.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.134276 restraints weight = 21300.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.136091 restraints weight = 17357.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.136691 restraints weight = 13167.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.137005 restraints weight = 11397.664| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21089 Z= 0.190 Angle : 0.577 12.702 28739 Z= 0.293 Chirality : 0.045 0.155 3386 Planarity : 0.004 0.048 3559 Dihedral : 16.637 156.727 3446 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.69 % Allowed : 14.02 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.02 (0.16), residues: 2750 helix: 1.67 (0.14), residues: 1345 sheet: -1.86 (0.28), residues: 308 loop : -1.62 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 192 TYR 0.014 0.002 TYR E 230 PHE 0.027 0.002 PHE A 75 TRP 0.007 0.001 TRP C 68 HIS 0.019 0.001 HIS E 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (21083) covalent geometry : angle 0.57464 / 0.29 (28726) SS BOND : bond 0.01030 / 0.72 ( 5) SS BOND : angle 2.60254 / 1.70 ( 10) hydrogen bonds : bond 0.04876 / 3.39 ( 1162) hydrogen bonds : angle 4.25663 / 3.03 ( 3390) link_NAG-ASN : bond 0.00258 / 0.14 ( 1) link_NAG-ASN : angle 0.72730 / 0.38 ( 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 529 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 447 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8444 (ttm170) cc_final: 0.7769 (mtm110) REVERT: A 158 MET cc_start: 0.8007 (mmm) cc_final: 0.7657 (mmm) REVERT: B 47 LYS cc_start: 0.8630 (mttt) cc_final: 0.8250 (mtpp) REVERT: B 114 ILE cc_start: 0.9108 (mm) cc_final: 0.8714 (mt) REVERT: B 125 ILE cc_start: 0.8715 (mm) cc_final: 0.8395 (mt) REVERT: B 137 MET cc_start: 0.7746 (mtm) cc_final: 0.7010 (mtm) REVERT: C 76 THR cc_start: 0.9103 (m) cc_final: 0.8875 (m) REVERT: C 113 SER cc_start: 0.9029 (m) cc_final: 0.8617 (t) REVERT: C 210 ILE cc_start: 0.9249 (mt) cc_final: 0.8798 (tt) REVERT: C 212 SER cc_start: 0.9119 (m) cc_final: 0.8875 (p) REVERT: C 314 ARG cc_start: 0.8312 (ptp-170) cc_final: 0.7852 (mtp180) REVERT: C 327 SER cc_start: 0.9107 (t) cc_final: 0.8702 (p) REVERT: D 41 ASN cc_start: 0.8699 (t0) cc_final: 0.8313 (t0) REVERT: D 47 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8329 (mttm) REVERT: D 158 MET cc_start: 0.7639 (mmm) cc_final: 0.7413 (mmm) REVERT: D 170 LYS cc_start: 0.9023 (mtpp) cc_final: 0.8617 (tptp) REVERT: D 212 SER cc_start: 0.8953 (m) cc_final: 0.8151 (p) REVERT: D 261 ILE cc_start: 0.9162 (mt) cc_final: 0.8946 (mt) REVERT: D 290 VAL cc_start: 0.9625 (OUTLIER) cc_final: 0.9345 (m) REVERT: E 51 TRP cc_start: 0.7678 (t60) cc_final: 0.7399 (t60) REVERT: E 84 VAL cc_start: 0.9324 (m) cc_final: 0.9097 (t) REVERT: E 139 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8837 (mp) REVERT: E 159 ASP cc_start: 0.7179 (t0) cc_final: 0.6920 (t0) REVERT: E 164 PHE cc_start: 0.7788 (m-80) cc_final: 0.7342 (m-80) REVERT: E 218 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8283 (pp) REVERT: E 299 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8555 (mp) REVERT: E 361 LEU cc_start: 0.8521 (tp) cc_final: 0.8230 (mp) REVERT: E 370 ARG cc_start: 0.7933 (mmt180) cc_final: 0.7708 (mmt180) REVERT: E 377 TYR cc_start: 0.9102 (m-10) cc_final: 0.8763 (m-10) REVERT: E 433 PHE cc_start: 0.8889 (m-10) cc_final: 0.8662 (m-10) REVERT: E 491 HIS cc_start: 0.7547 (t-170) cc_final: 0.6390 (m170) REVERT: E 817 HIS cc_start: 0.7385 (m-70) cc_final: 0.7063 (m-70) outliers start: 82 outliers final: 62 residues processed: 488 average time/residue: 0.1178 time to fit residues: 92.8550 Evaluate side-chains 498 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 432 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET 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 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 184 SER 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 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 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 59 VAL Chi-restraints excluded: chain D residue 84 LEU 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 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 139 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 175 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 403 SER 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 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 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: 0.6980 chunk 217 optimal weight: 50.0000 chunk 220 optimal weight: 10.0000 chunk 211 optimal weight: 50.0000 chunk 127 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 168 optimal weight: 3.9990 chunk 204 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN B 57 GLN B 279 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 = 0.3629 r_free = 0.3629 target = 0.159610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.132656 restraints weight = 24426.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.130988 restraints weight = 21588.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.133384 restraints weight = 17335.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.134049 restraints weight = 13232.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.134496 restraints weight = 10840.217| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2323 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= 0.220 Angle : 0.609 10.458 28739 Z= 0.308 Chirality : 0.047 0.168 3386 Planarity : 0.005 0.051 3559 Dihedral : 16.003 159.238 3446 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.61 % Allowed : 14.93 % Favored : 79.46 % 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: -0.01 (0.16), residues: 2750 helix: 1.72 (0.14), residues: 1337 sheet: -1.82 (0.29), residues: 308 loop : -1.66 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 34 TYR 0.015 0.002 TYR E 107 PHE 0.026 0.002 PHE A 75 TRP 0.008 0.001 TRP E1037 HIS 0.006 0.001 HIS E 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 (21083) covalent geometry : angle 0.60686 / 0.31 (28726) SS BOND : bond 0.01543 / 1.07 ( 5) SS BOND : angle 2.71957 / 1.63 ( 10) hydrogen bonds : bond 0.04675 / 3.25 ( 1162) hydrogen bonds : angle 4.18705 / 2.98 ( 3390) link_NAG-ASN : bond 0.00232 / 0.12 ( 1) link_NAG-ASN : angle 0.79740 / 0.42 ( 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 534 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 436 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8479 (ttm170) cc_final: 0.7829 (mtm110) REVERT: B 47 LYS cc_start: 0.8736 (mttt) cc_final: 0.8267 (mtpp) REVERT: B 114 ILE cc_start: 0.9135 (mm) cc_final: 0.8760 (mt) REVERT: B 125 ILE cc_start: 0.8878 (mm) cc_final: 0.8541 (mt) REVERT: B 137 MET cc_start: 0.7759 (mtm) cc_final: 0.6988 (mtm) REVERT: C 59 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8714 (m) REVERT: C 76 THR cc_start: 0.9129 (m) cc_final: 0.8920 (m) REVERT: C 113 SER cc_start: 0.9063 (m) cc_final: 0.8664 (t) REVERT: C 210 ILE cc_start: 0.9245 (mt) cc_final: 0.8848 (tt) REVERT: C 212 SER cc_start: 0.9192 (m) cc_final: 0.8883 (p) REVERT: C 259 HIS cc_start: 0.9097 (OUTLIER) cc_final: 0.8528 (t-170) REVERT: C 314 ARG cc_start: 0.8387 (ptp-170) cc_final: 0.7930 (mtp180) REVERT: D 41 ASN cc_start: 0.8708 (t0) cc_final: 0.8398 (t0) REVERT: D 47 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8458 (mttm) REVERT: D 158 MET cc_start: 0.7639 (mmm) cc_final: 0.7437 (mmm) REVERT: D 170 LYS cc_start: 0.9056 (mtpp) cc_final: 0.8668 (tptp) REVERT: D 206 ARG cc_start: 0.8849 (mmm-85) cc_final: 0.8547 (mmm-85) REVERT: D 212 SER cc_start: 0.9015 (m) cc_final: 0.8250 (p) REVERT: D 290 VAL cc_start: 0.9658 (OUTLIER) cc_final: 0.9363 (m) REVERT: E 51 TRP cc_start: 0.7748 (t60) cc_final: 0.7419 (t60) REVERT: E 158 TYR cc_start: 0.7281 (t80) cc_final: 0.6878 (t80) REVERT: E 159 ASP cc_start: 0.7203 (t0) cc_final: 0.6884 (t0) REVERT: E 164 PHE cc_start: 0.7779 (m-80) cc_final: 0.7413 (m-80) REVERT: E 218 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8652 (pp) REVERT: E 299 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8573 (mp) REVERT: E 318 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8311 (tt) REVERT: E 327 LEU cc_start: 0.7868 (tp) cc_final: 0.7663 (tp) REVERT: E 361 LEU cc_start: 0.8564 (tp) cc_final: 0.8291 (mp) REVERT: E 370 ARG cc_start: 0.8058 (mmt180) cc_final: 0.7820 (mmt180) REVERT: E 377 TYR cc_start: 0.9118 (m-10) cc_final: 0.8758 (m-10) REVERT: E 445 ILE cc_start: 0.9115 (mm) cc_final: 0.8746 (mp) REVERT: E 491 HIS cc_start: 0.7493 (OUTLIER) cc_final: 0.7237 (m170) REVERT: E 590 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8041 (mm) REVERT: E 602 LYS cc_start: 0.8091 (mmmm) cc_final: 0.7608 (mtmt) REVERT: E 1272 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7281 (mp) outliers start: 98 outliers final: 75 residues processed: 481 average time/residue: 0.1163 time to fit residues: 91.0864 Evaluate side-chains 517 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 433 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 215 ILE 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 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 314 ARG 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 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 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 C residue 352 ASP 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 210 ILE 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 D residue 305 LEU 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 140 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 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 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 491 HIS Chi-restraints excluded: chain E residue 582 LEU 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 1219 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 14 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 200 optimal weight: 6.9990 chunk 137 optimal weight: 0.0050 chunk 193 optimal weight: 50.0000 chunk 148 optimal weight: 1.9990 chunk 267 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 178 optimal weight: 0.7980 chunk 218 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 HIS ** E1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.163824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.136577 restraints weight = 24141.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.135733 restraints weight = 22277.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.137446 restraints weight = 18281.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.138495 restraints weight = 14268.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.138650 restraints weight = 12015.904| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21089 Z= 0.115 Angle : 0.526 11.644 28739 Z= 0.263 Chirality : 0.044 0.167 3386 Planarity : 0.004 0.051 3559 Dihedral : 15.158 156.966 3444 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.29 % Allowed : 16.82 % 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: 0.40 (0.17), residues: 2750 helix: 2.05 (0.14), residues: 1348 sheet: -1.63 (0.30), residues: 290 loop : -1.50 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 34 TYR 0.013 0.001 TYR E 107 PHE 0.024 0.001 PHE A 75 TRP 0.006 0.001 TRP E 430 HIS 0.021 0.001 HIS E 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (21083) covalent geometry : angle 0.52336 / 0.26 (28726) SS BOND : bond 0.00445 / 0.29 ( 5) SS BOND : angle 2.58786 / 1.46 ( 10) hydrogen bonds : bond 0.04132 / 2.86 ( 1162) hydrogen bonds : angle 3.92917 / 2.79 ( 3390) link_NAG-ASN : bond 0.00415 / 0.22 ( 1) link_NAG-ASN : angle 1.10183 / 0.58 ( 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 519 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 444 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8361 (ttm170) cc_final: 0.7728 (mtm110) REVERT: A 196 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8046 (tp) REVERT: A 199 MET cc_start: 0.8087 (mmm) cc_final: 0.7656 (mmp) REVERT: A 262 ASP cc_start: 0.7106 (t0) cc_final: 0.6801 (t0) REVERT: B 47 LYS cc_start: 0.8822 (mttt) cc_final: 0.8368 (mtpp) REVERT: B 114 ILE cc_start: 0.9058 (mm) cc_final: 0.8671 (mt) REVERT: B 125 ILE cc_start: 0.8656 (mm) cc_final: 0.8381 (mt) REVERT: B 137 MET cc_start: 0.7625 (mtm) cc_final: 0.6920 (mtm) REVERT: C 113 SER cc_start: 0.8980 (m) cc_final: 0.8632 (t) REVERT: C 128 GLN cc_start: 0.8435 (tt0) cc_final: 0.8149 (tt0) REVERT: C 212 SER cc_start: 0.8906 (m) cc_final: 0.8667 (p) REVERT: C 314 ARG cc_start: 0.8208 (ptp-170) cc_final: 0.7779 (mtp-110) REVERT: D 34 ARG cc_start: 0.8625 (mtp85) cc_final: 0.8238 (mtt-85) REVERT: D 41 ASN cc_start: 0.8679 (t0) cc_final: 0.8431 (t0) REVERT: D 47 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8386 (mttm) REVERT: D 107 ASN cc_start: 0.7492 (t0) cc_final: 0.7220 (t0) REVERT: D 170 LYS cc_start: 0.9051 (mtpp) cc_final: 0.8731 (tptp) REVERT: D 290 VAL cc_start: 0.9599 (OUTLIER) cc_final: 0.9339 (m) REVERT: E 51 TRP cc_start: 0.7711 (t60) cc_final: 0.7364 (t60) REVERT: E 158 TYR cc_start: 0.7108 (t80) cc_final: 0.6806 (t80) REVERT: E 159 ASP cc_start: 0.7080 (t0) cc_final: 0.6782 (t0) REVERT: E 164 PHE cc_start: 0.7675 (m-80) cc_final: 0.7312 (m-80) REVERT: E 218 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8664 (pp) REVERT: E 299 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8479 (mp) REVERT: E 327 LEU cc_start: 0.7842 (tp) cc_final: 0.7451 (mp) REVERT: E 361 LEU cc_start: 0.8514 (tp) cc_final: 0.8263 (mp) REVERT: E 370 ARG cc_start: 0.7974 (mmt180) cc_final: 0.7748 (mmt180) REVERT: E 377 TYR cc_start: 0.8961 (m-10) cc_final: 0.8659 (m-10) REVERT: E 397 ASN cc_start: 0.8988 (t0) cc_final: 0.8731 (t0) REVERT: E 445 ILE cc_start: 0.9053 (mm) cc_final: 0.8642 (mp) REVERT: E 530 MET cc_start: 0.7180 (tpp) cc_final: 0.6890 (tpp) REVERT: E 590 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8008 (mm) REVERT: E 1272 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7210 (mp) outliers start: 75 outliers final: 49 residues processed: 481 average time/residue: 0.1203 time to fit residues: 93.2985 Evaluate side-chains 486 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 431 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 196 LEU 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 108 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 259 HIS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 314 ARG 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 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 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 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 140 LEU 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 399 ILE Chi-restraints excluded: chain E residue 403 SER Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 428 LEU 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 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 1197 GLN Chi-restraints excluded: chain E residue 1272 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: 3.9990 chunk 119 optimal weight: 0.2980 chunk 218 optimal weight: 20.0000 chunk 47 optimal weight: 0.8980 chunk 178 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 263 optimal weight: 50.0000 chunk 3 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 167 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3675 r_free = 0.3675 target = 0.163852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.137164 restraints weight = 24023.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.135623 restraints weight = 22376.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.137037 restraints weight = 18704.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.137863 restraints weight = 15261.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.138337 restraints weight = 12687.148| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21089 Z= 0.124 Angle : 0.533 10.988 28739 Z= 0.264 Chirality : 0.044 0.167 3386 Planarity : 0.004 0.070 3559 Dihedral : 14.630 161.154 3444 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.41 % Allowed : 17.91 % Favored : 77.69 % 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: 0.48 (0.17), residues: 2750 helix: 2.19 (0.14), residues: 1346 sheet: -1.63 (0.29), residues: 312 loop : -1.54 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 34 TYR 0.014 0.001 TYR E 195 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/Z covalent geometry : bond 0.00280 / 0.12 (21083) covalent geometry : angle 0.53046 / 0.26 (28726) SS BOND : bond 0.00446 / 0.32 ( 5) SS BOND : angle 2.62189 / 1.46 ( 10) hydrogen bonds : bond 0.04003 / 2.77 ( 1162) hydrogen bonds : angle 3.82460 / 2.72 ( 3390) link_NAG-ASN : bond 0.00380 / 0.20 ( 1) link_NAG-ASN : angle 1.05651 / 0.56 ( 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 495 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 418 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8416 (ttm170) cc_final: 0.7825 (mtm110) REVERT: A 196 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8046 (tp) REVERT: A 199 MET cc_start: 0.8085 (mmm) cc_final: 0.7850 (mmp) REVERT: A 262 ASP cc_start: 0.7002 (t0) cc_final: 0.6748 (t0) REVERT: B 47 LYS cc_start: 0.8864 (mttt) cc_final: 0.8446 (mtpp) REVERT: B 84 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8122 (tt) REVERT: B 114 ILE cc_start: 0.9008 (mm) cc_final: 0.8613 (mt) REVERT: B 125 ILE cc_start: 0.8715 (mm) cc_final: 0.8391 (mt) REVERT: C 113 SER cc_start: 0.8965 (m) cc_final: 0.8638 (t) REVERT: C 128 GLN cc_start: 0.8448 (tt0) cc_final: 0.8139 (tt0) REVERT: C 314 ARG cc_start: 0.8220 (ptp-170) cc_final: 0.7754 (mtp-110) REVERT: D 41 ASN cc_start: 0.8633 (t0) cc_final: 0.8314 (t0) REVERT: D 47 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8436 (mttm) REVERT: D 170 LYS cc_start: 0.9034 (mtpp) cc_final: 0.8722 (tptp) REVERT: D 206 ARG cc_start: 0.8810 (mmm-85) cc_final: 0.8555 (mmm-85) REVERT: D 212 SER cc_start: 0.8915 (m) cc_final: 0.8058 (p) REVERT: D 290 VAL cc_start: 0.9655 (OUTLIER) cc_final: 0.9393 (m) REVERT: D 332 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8042 (mtmm) REVERT: E 51 TRP cc_start: 0.7799 (t60) cc_final: 0.7417 (t60) REVERT: E 158 TYR cc_start: 0.7057 (t80) cc_final: 0.6817 (t80) REVERT: E 159 ASP cc_start: 0.6987 (t0) cc_final: 0.6691 (t0) REVERT: E 164 PHE cc_start: 0.7673 (m-80) cc_final: 0.7346 (m-80) REVERT: E 318 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8175 (tt) REVERT: E 327 LEU cc_start: 0.7934 (tp) cc_final: 0.7695 (tp) REVERT: E 361 LEU cc_start: 0.8509 (tp) cc_final: 0.8292 (mp) REVERT: E 370 ARG cc_start: 0.7881 (mmt180) cc_final: 0.7623 (mmt180) REVERT: E 377 TYR cc_start: 0.9005 (m-10) cc_final: 0.8792 (m-10) REVERT: E 397 ASN cc_start: 0.9014 (t0) cc_final: 0.8767 (t0) REVERT: E 445 ILE cc_start: 0.8999 (mm) cc_final: 0.8559 (mp) REVERT: E 530 MET cc_start: 0.7053 (tpp) cc_final: 0.6798 (tpp) REVERT: E 590 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8011 (mm) REVERT: E 1088 TRP cc_start: 0.7861 (t60) cc_final: 0.6987 (t60) REVERT: E 1212 THR cc_start: 0.8841 (p) cc_final: 0.8598 (t) REVERT: E 1272 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7228 (mp) outliers start: 77 outliers final: 60 residues processed: 458 average time/residue: 0.1270 time to fit residues: 93.0082 Evaluate side-chains 479 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 413 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 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 84 LEU 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 225 SER Chi-restraints excluded: chain B residue 231 VAL 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 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 263 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 303 SER 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 222 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 318 LEU 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 428 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 582 LEU 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 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 1201 VAL 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 1318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 106 optimal weight: 6.9990 chunk 269 optimal weight: 40.0000 chunk 191 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 267 optimal weight: 30.0000 chunk 139 optimal weight: 2.9990 chunk 201 optimal weight: 50.0000 chunk 219 optimal weight: 50.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 293 HIS ** E1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.158446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.132964 restraints weight = 24418.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.132786 restraints weight = 21734.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.133380 restraints weight = 19074.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.133984 restraints weight = 16484.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.134138 restraints weight = 14244.498| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 21089 Z= 0.255 Angle : 0.648 13.961 28739 Z= 0.323 Chirality : 0.048 0.178 3386 Planarity : 0.005 0.053 3559 Dihedral : 14.904 172.167 3444 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.49 % Allowed : 17.51 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.16), residues: 2750 helix: 1.85 (0.14), residues: 1345 sheet: -1.82 (0.29), residues: 305 loop : -1.62 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 34 TYR 0.015 0.002 TYR E 107 PHE 0.020 0.002 PHE A 75 TRP 0.007 0.002 TRP C 68 HIS 0.011 0.001 HIS E 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.25 (21083) covalent geometry : angle 0.64611 / 0.32 (28726) SS BOND : bond 0.00293 / 0.16 ( 5) SS BOND : angle 2.66580 / 1.50 ( 10) hydrogen bonds : bond 0.04596 / 3.18 ( 1162) hydrogen bonds : angle 4.07091 / 2.90 ( 3390) link_NAG-ASN : bond 0.00261 / 0.14 ( 1) link_NAG-ASN : angle 0.92669 / 0.48 ( 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 530 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 434 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8437 (ttm170) cc_final: 0.7865 (mtm110) REVERT: A 196 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8059 (tp) REVERT: A 229 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8157 (mm-30) REVERT: A 256 ILE cc_start: 0.8999 (mm) cc_final: 0.8776 (mm) REVERT: B 47 LYS cc_start: 0.8822 (mttt) cc_final: 0.8406 (mtpp) REVERT: B 84 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8250 (tt) REVERT: B 114 ILE cc_start: 0.9124 (mm) cc_final: 0.8745 (mt) REVERT: C 76 THR cc_start: 0.9195 (m) cc_final: 0.8963 (m) REVERT: C 113 SER cc_start: 0.9033 (m) cc_final: 0.8687 (t) REVERT: C 210 ILE cc_start: 0.9350 (mt) cc_final: 0.8896 (tt) REVERT: C 259 HIS cc_start: 0.9052 (OUTLIER) cc_final: 0.8454 (t-170) REVERT: C 268 TYR cc_start: 0.8647 (t80) cc_final: 0.8083 (t80) REVERT: C 314 ARG cc_start: 0.8356 (ptp-170) cc_final: 0.7908 (mtp-110) REVERT: D 41 ASN cc_start: 0.8524 (t0) cc_final: 0.8215 (t0) REVERT: D 47 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8499 (mttm) REVERT: D 107 ASN cc_start: 0.7437 (t0) cc_final: 0.7141 (t0) REVERT: D 170 LYS cc_start: 0.9035 (mtpp) cc_final: 0.8791 (tptp) REVERT: D 200 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7814 (tt) REVERT: D 206 ARG cc_start: 0.8861 (mmm-85) cc_final: 0.8592 (mmm-85) REVERT: D 212 SER cc_start: 0.9047 (m) cc_final: 0.8297 (p) REVERT: D 290 VAL cc_start: 0.9707 (OUTLIER) cc_final: 0.9429 (m) REVERT: E 51 TRP cc_start: 0.7907 (t60) cc_final: 0.7522 (t60) REVERT: E 158 TYR cc_start: 0.7113 (t80) cc_final: 0.6876 (t80) REVERT: E 159 ASP cc_start: 0.6917 (t0) cc_final: 0.6634 (t0) REVERT: E 164 PHE cc_start: 0.7785 (m-80) cc_final: 0.7530 (m-80) REVERT: E 299 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8501 (mp) REVERT: E 361 LEU cc_start: 0.8531 (tp) cc_final: 0.8317 (mp) REVERT: E 370 ARG cc_start: 0.7925 (mmt180) cc_final: 0.7673 (mmt180) REVERT: E 377 TYR cc_start: 0.9056 (m-10) cc_final: 0.8761 (m-10) REVERT: E 397 ASN cc_start: 0.9077 (t0) cc_final: 0.8809 (t0) REVERT: E 445 ILE cc_start: 0.8997 (mm) cc_final: 0.8668 (mt) REVERT: E 530 MET cc_start: 0.6982 (tpp) cc_final: 0.6748 (tpp) REVERT: E 1272 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7376 (mp) outliers start: 96 outliers final: 74 residues processed: 483 average time/residue: 0.1228 time to fit residues: 95.5848 Evaluate side-chains 507 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 426 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 A residue 316 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 LEU 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 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 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 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 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 215 ILE Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 303 SER 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 104 LEU 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 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 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 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 582 LEU 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 1156 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 1259 VAL Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1272 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 104 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 246 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 38 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3637 r_free = 0.3637 target = 0.160304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.133746 restraints weight = 24271.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.132738 restraints weight = 20051.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.134539 restraints weight = 16973.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.135039 restraints weight = 13296.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.135308 restraints weight = 11647.348| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21089 Z= 0.172 Angle : 0.585 12.176 28739 Z= 0.289 Chirality : 0.045 0.172 3386 Planarity : 0.004 0.052 3559 Dihedral : 14.632 171.155 3442 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.58 % Allowed : 19.22 % Favored : 76.20 % 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: 2.02 (0.14), residues: 1345 sheet: -1.83 (0.29), residues: 305 loop : -1.59 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 192 TYR 0.015 0.001 TYR E 107 PHE 0.022 0.002 PHE B 75 TRP 0.006 0.001 TRP E 430 HIS 0.006 0.001 HIS E1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (21083) covalent geometry : angle 0.58304 / 0.29 (28726) SS BOND : bond 0.00474 / 0.35 ( 5) SS BOND : angle 2.70023 / 1.57 ( 10) hydrogen bonds : bond 0.04240 / 2.94 ( 1162) hydrogen bonds : angle 3.96263 / 2.82 ( 3390) link_NAG-ASN : bond 0.00372 / 0.20 ( 1) link_NAG-ASN : angle 1.04539 / 0.55 ( 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 524 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 444 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8397 (ttm170) cc_final: 0.7804 (mtm110) REVERT: A 196 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8041 (tp) REVERT: A 229 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8341 (mm-30) REVERT: A 262 ASP cc_start: 0.6745 (t0) cc_final: 0.6477 (t0) REVERT: B 47 LYS cc_start: 0.8712 (mttt) cc_final: 0.8193 (mtpp) REVERT: B 84 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8216 (tt) REVERT: B 114 ILE cc_start: 0.9105 (mm) cc_final: 0.8727 (mt) REVERT: B 125 ILE cc_start: 0.8925 (mm) cc_final: 0.8607 (mt) REVERT: C 76 THR cc_start: 0.9144 (m) cc_final: 0.8924 (m) REVERT: C 113 SER cc_start: 0.9010 (m) cc_final: 0.8672 (t) REVERT: C 128 GLN cc_start: 0.8538 (tt0) cc_final: 0.8261 (tt0) REVERT: C 158 MET cc_start: 0.7877 (mmm) cc_final: 0.7552 (tpp) REVERT: C 259 HIS cc_start: 0.9025 (OUTLIER) cc_final: 0.8400 (t-170) REVERT: C 314 ARG cc_start: 0.8246 (ptp-170) cc_final: 0.7778 (mtp-110) REVERT: D 41 ASN cc_start: 0.8599 (t0) cc_final: 0.8276 (t0) REVERT: D 47 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8339 (mttm) REVERT: D 107 ASN cc_start: 0.7519 (t0) cc_final: 0.7205 (t0) REVERT: D 170 LYS cc_start: 0.9001 (mtpp) cc_final: 0.8793 (tptp) REVERT: D 200 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7596 (tt) REVERT: D 206 ARG cc_start: 0.8940 (mmm-85) cc_final: 0.8579 (mmm-85) REVERT: D 212 SER cc_start: 0.9002 (m) cc_final: 0.8222 (p) REVERT: D 249 ILE cc_start: 0.8306 (tp) cc_final: 0.8030 (tp) REVERT: D 290 VAL cc_start: 0.9608 (OUTLIER) cc_final: 0.9379 (m) REVERT: E 51 TRP cc_start: 0.8039 (t60) cc_final: 0.7611 (t60) REVERT: E 158 TYR cc_start: 0.7185 (t80) cc_final: 0.6950 (t80) REVERT: E 159 ASP cc_start: 0.7071 (t0) cc_final: 0.6781 (t0) REVERT: E 164 PHE cc_start: 0.7690 (m-80) cc_final: 0.7415 (m-80) REVERT: E 299 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8534 (mp) REVERT: E 361 LEU cc_start: 0.8526 (tp) cc_final: 0.8283 (mp) REVERT: E 370 ARG cc_start: 0.8092 (mmt180) cc_final: 0.7828 (mmt180) REVERT: E 377 TYR cc_start: 0.9070 (m-10) cc_final: 0.8830 (m-10) REVERT: E 397 ASN cc_start: 0.9066 (t0) cc_final: 0.8809 (t0) REVERT: E 445 ILE cc_start: 0.8969 (mm) cc_final: 0.8603 (mt) REVERT: E 590 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8129 (mm) REVERT: E 1103 ASN cc_start: 0.8255 (m110) cc_final: 0.7985 (m110) REVERT: E 1272 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7211 (mp) outliers start: 80 outliers final: 65 residues processed: 483 average time/residue: 0.1246 time to fit residues: 95.9097 Evaluate side-chains 499 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 426 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 A residue 316 VAL Chi-restraints excluded: chain B residue 84 LEU 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 251 LEU 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 238 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 259 HIS 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 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 D residue 303 SER 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 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 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 454 TYR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 582 LEU 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 1156 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 1201 VAL Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1318 LEU 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: 4.9990 chunk 245 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 249 optimal weight: 0.6980 chunk 200 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3659 r_free = 0.3659 target = 0.162204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.136230 restraints weight = 24075.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.136253 restraints weight = 25211.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.137690 restraints weight = 18135.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.137859 restraints weight = 13620.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.138206 restraints weight = 11563.965| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21089 Z= 0.134 Angle : 0.559 11.348 28739 Z= 0.276 Chirality : 0.044 0.167 3386 Planarity : 0.004 0.053 3559 Dihedral : 14.262 172.014 3442 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.52 % Allowed : 19.45 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.48 (0.17), residues: 2750 helix: 2.23 (0.15), residues: 1344 sheet: -1.77 (0.29), residues: 305 loop : -1.54 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 192 TYR 0.017 0.001 TYR E 845 PHE 0.021 0.001 PHE B 75 TRP 0.007 0.001 TRP E 430 HIS 0.006 0.001 HIS E1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (21083) covalent geometry : angle 0.55672 / 0.27 (28726) SS BOND : bond 0.00246 / 0.17 ( 5) SS BOND : angle 2.65162 / 1.55 ( 10) hydrogen bonds : bond 0.03984 / 2.77 ( 1162) hydrogen bonds : angle 3.85496 / 2.75 ( 3390) link_NAG-ASN : bond 0.00416 / 0.22 ( 1) link_NAG-ASN : angle 1.08518 / 0.57 ( 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 502 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 423 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8423 (ttm170) cc_final: 0.7891 (mtm110) REVERT: A 196 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8107 (tp) REVERT: A 262 ASP cc_start: 0.6694 (t0) cc_final: 0.6454 (t0) REVERT: B 32 ARG cc_start: 0.7523 (tpt-90) cc_final: 0.7063 (tpt90) REVERT: B 47 LYS cc_start: 0.8824 (mttt) cc_final: 0.8331 (mtpp) REVERT: B 84 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8170 (tt) REVERT: B 114 ILE cc_start: 0.9038 (mm) cc_final: 0.8622 (mt) REVERT: C 76 THR cc_start: 0.9168 (m) cc_final: 0.8955 (m) REVERT: C 113 SER cc_start: 0.8934 (m) cc_final: 0.8652 (t) REVERT: C 128 GLN cc_start: 0.8517 (tt0) cc_final: 0.8232 (tt0) REVERT: C 314 ARG cc_start: 0.8126 (ptp-170) cc_final: 0.7740 (mtp-110) REVERT: D 41 ASN cc_start: 0.8464 (t0) cc_final: 0.8182 (t0) REVERT: D 47 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8404 (mttm) REVERT: D 170 LYS cc_start: 0.9025 (mtpp) cc_final: 0.8804 (tptp) REVERT: D 200 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7650 (tt) REVERT: D 206 ARG cc_start: 0.8845 (mmm-85) cc_final: 0.8526 (mmm-85) REVERT: D 212 SER cc_start: 0.8890 (m) cc_final: 0.8057 (p) REVERT: D 290 VAL cc_start: 0.9650 (OUTLIER) cc_final: 0.9397 (m) REVERT: D 332 LYS cc_start: 0.8449 (mtpt) cc_final: 0.8046 (mtmm) REVERT: E 51 TRP cc_start: 0.8111 (t60) cc_final: 0.7705 (t60) REVERT: E 159 ASP cc_start: 0.6832 (t0) cc_final: 0.6581 (t0) REVERT: E 164 PHE cc_start: 0.7539 (m-80) cc_final: 0.7290 (m-80) REVERT: E 361 LEU cc_start: 0.8521 (tp) cc_final: 0.8319 (mp) REVERT: E 370 ARG cc_start: 0.7910 (mmt180) cc_final: 0.7676 (mmt180) REVERT: E 397 ASN cc_start: 0.9035 (t0) cc_final: 0.8790 (t0) REVERT: E 445 ILE cc_start: 0.8957 (mm) cc_final: 0.8575 (mp) REVERT: E 590 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8008 (mm) REVERT: E 1088 TRP cc_start: 0.7887 (t60) cc_final: 0.7070 (t60) REVERT: E 1103 ASN cc_start: 0.8138 (m110) cc_final: 0.7888 (m110) REVERT: E 1272 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7167 (mp) outliers start: 79 outliers final: 66 residues processed: 465 average time/residue: 0.1213 time to fit residues: 89.8189 Evaluate side-chains 493 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 421 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 59 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 225 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 186 HIS Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 248 SER 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 C residue 344 CYS 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 263 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 303 SER 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 454 TYR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 582 LEU 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 1154 LEU Chi-restraints excluded: chain E residue 1155 THR Chi-restraints excluded: chain E residue 1156 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 1201 VAL Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 139 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 269 optimal weight: 50.0000 chunk 30 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 ASN B 216 HIS B 313 GLN ** 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 = 0.3629 r_free = 0.3629 target = 0.159517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.132974 restraints weight = 24419.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.132002 restraints weight = 20302.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.133572 restraints weight = 17045.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.134148 restraints weight = 13397.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.134425 restraints weight = 12177.192| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21089 Z= 0.195 Angle : 0.605 11.349 28739 Z= 0.301 Chirality : 0.046 0.173 3386 Planarity : 0.004 0.049 3559 Dihedral : 14.303 177.367 3442 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.52 % Allowed : 19.91 % Favored : 75.57 % 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: 0.32 (0.17), residues: 2750 helix: 2.07 (0.14), residues: 1344 sheet: -1.89 (0.29), residues: 303 loop : -1.58 (0.18), residues: 1103 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 0.023 0.002 PHE B 75 TRP 0.006 0.001 TRP D 68 HIS 0.006 0.001 HIS E1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 (21083) covalent geometry : angle 0.60290 / 0.30 (28726) SS BOND : bond 0.00318 / 0.20 ( 5) SS BOND : angle 2.68260 / 1.60 ( 10) hydrogen bonds : bond 0.04256 / 2.95 ( 1162) hydrogen bonds : angle 3.96745 / 2.84 ( 3390) link_NAG-ASN : bond 0.00410 / 0.22 ( 1) link_NAG-ASN : angle 1.06588 / 0.56 ( 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 500 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 421 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8087 (tp) REVERT: A 262 ASP cc_start: 0.6863 (t0) cc_final: 0.6550 (t0) REVERT: B 32 ARG cc_start: 0.7773 (tpt-90) cc_final: 0.7342 (tpt90) REVERT: B 47 LYS cc_start: 0.8733 (mttt) cc_final: 0.8220 (mtpp) REVERT: B 84 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8246 (tt) REVERT: B 114 ILE cc_start: 0.9108 (mm) cc_final: 0.8730 (mt) REVERT: B 257 ILE cc_start: 0.9301 (mm) cc_final: 0.9006 (mt) REVERT: C 76 THR cc_start: 0.9174 (m) cc_final: 0.8950 (m) REVERT: C 113 SER cc_start: 0.9016 (m) cc_final: 0.8681 (t) REVERT: C 128 GLN cc_start: 0.8539 (tt0) cc_final: 0.8255 (tt0) REVERT: C 259 HIS cc_start: 0.9028 (OUTLIER) cc_final: 0.8370 (t-170) REVERT: C 314 ARG cc_start: 0.8212 (ptp-170) cc_final: 0.7757 (mtp-110) REVERT: D 41 ASN cc_start: 0.8507 (t0) cc_final: 0.8235 (t0) REVERT: D 47 LYS cc_start: 0.8732 (mmtt) cc_final: 0.8352 (mttm) REVERT: D 107 ASN cc_start: 0.7474 (t0) cc_final: 0.7135 (t0) REVERT: D 170 LYS cc_start: 0.9023 (mtpp) cc_final: 0.8771 (tptp) REVERT: D 200 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7696 (tt) REVERT: D 206 ARG cc_start: 0.8904 (mmm-85) cc_final: 0.8554 (mmm-85) REVERT: D 212 SER cc_start: 0.9005 (m) cc_final: 0.8231 (p) REVERT: D 249 ILE cc_start: 0.8338 (tp) cc_final: 0.8074 (tp) REVERT: D 290 VAL cc_start: 0.9647 (OUTLIER) cc_final: 0.9387 (m) REVERT: D 332 LYS cc_start: 0.8596 (mtpt) cc_final: 0.8109 (mtmm) REVERT: E 51 TRP cc_start: 0.8122 (t60) cc_final: 0.7679 (t60) REVERT: E 159 ASP cc_start: 0.7040 (t0) cc_final: 0.6755 (t0) REVERT: E 164 PHE cc_start: 0.7682 (m-80) cc_final: 0.7415 (m-80) REVERT: E 361 LEU cc_start: 0.8567 (tp) cc_final: 0.8298 (mp) REVERT: E 370 ARG cc_start: 0.8107 (mmt180) cc_final: 0.7842 (mmt180) REVERT: E 397 ASN cc_start: 0.9093 (t0) cc_final: 0.8833 (t0) REVERT: E 445 ILE cc_start: 0.8991 (mm) cc_final: 0.8614 (mt) REVERT: E 530 MET cc_start: 0.7082 (tpp) cc_final: 0.6785 (tpp) REVERT: E 590 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8174 (mm) REVERT: E 1064 TYR cc_start: 0.7380 (m-10) cc_final: 0.6722 (m-10) REVERT: E 1088 TRP cc_start: 0.7975 (t60) cc_final: 0.7050 (t60) REVERT: E 1103 ASN cc_start: 0.8236 (m110) cc_final: 0.7956 (m110) REVERT: E 1272 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7186 (mp) outliers start: 79 outliers final: 67 residues processed: 464 average time/residue: 0.1190 time to fit residues: 89.4805 Evaluate side-chains 488 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 414 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 A residue 316 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 181 LEU 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 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 238 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 259 HIS 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 C residue 344 CYS 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 263 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU 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 222 VAL 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 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 1156 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 1259 VAL Chi-restraints excluded: chain E residue 1272 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 255 optimal weight: 50.0000 chunk 23 optimal weight: 0.9980 chunk 220 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 268 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 271 optimal weight: 0.0040 chunk 96 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3660 r_free = 0.3660 target = 0.162385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.133115 restraints weight = 24082.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.133864 restraints weight = 18167.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.135653 restraints weight = 13112.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.137127 restraints weight = 9939.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.137336 restraints weight = 8215.604| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21089 Z= 0.131 Angle : 0.559 10.946 28739 Z= 0.277 Chirality : 0.044 0.171 3386 Planarity : 0.004 0.052 3559 Dihedral : 13.896 178.873 3442 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.06 % Allowed : 20.54 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.52 (0.17), residues: 2750 helix: 2.25 (0.14), residues: 1351 sheet: -1.76 (0.30), residues: 302 loop : -1.54 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 192 TYR 0.019 0.001 TYR E 845 PHE 0.018 0.001 PHE A 75 TRP 0.007 0.001 TRP E 65 HIS 0.006 0.001 HIS E1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (21083) covalent geometry : angle 0.55646 / 0.28 (28726) SS BOND : bond 0.00193 / 0.13 ( 5) SS BOND : angle 2.65511 / 1.55 ( 10) hydrogen bonds : bond 0.03926 / 2.72 ( 1162) hydrogen bonds : angle 3.83731 / 2.74 ( 3390) link_NAG-ASN : bond 0.00459 / 0.24 ( 1) link_NAG-ASN : angle 1.15089 / 0.61 ( 3) =============================================================================== Job complete usr+sys time: 2942.51 seconds wall clock time: 51 minutes 29.17 seconds (3089.17 seconds total)