Starting phenix.real_space_refine on Wed Mar 4 13:55:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fig_31596/03_2026/7fig_31596_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fig_31596/03_2026/7fig_31596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7fig_31596/03_2026/7fig_31596_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fig_31596/03_2026/7fig_31596_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fig_31596/03_2026/7fig_31596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fig_31596/03_2026/7fig_31596.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1474 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 8122 2.51 5 N 2214 2.21 5 O 2404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12839 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2932 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 350} Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 4334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4334 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 527} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "X" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 678 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain: "Y" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 97} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.88, per 1000 atoms: 0.22 Number of scatterers: 12839 At special positions: 0 Unit cell: (93.005, 97.185, 182.875, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 2404 8.00 N 2214 7.00 C 8122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.06 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 156 " distance=2.03 Simple disulfide: pdb=" SG CYS R 279 " - pdb=" SG CYS R 343 " distance=2.03 Simple disulfide: pdb=" SG CYS R 280 " - pdb=" SG CYS R 353 " distance=2.02 Simple disulfide: pdb=" SG CYS R 439 " - pdb=" SG CYS R 514 " distance=2.02 Simple disulfide: pdb=" SG CYS X 7 " - pdb=" SG CYS X 31 " distance=2.03 Simple disulfide: pdb=" SG CYS X 10 " - pdb=" SG CYS X 60 " distance=2.03 Simple disulfide: pdb=" SG CYS X 28 " - pdb=" SG CYS X 82 " distance=2.03 Simple disulfide: pdb=" SG CYS X 32 " - pdb=" SG CYS X 84 " distance=2.03 Simple disulfide: pdb=" SG CYS X 59 " - pdb=" SG CYS X 87 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 9 " - pdb=" SG CYS Y 57 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 72 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 26 " - pdb=" SG CYS Y 110 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 34 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 38 " - pdb=" SG CYS Y 90 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 93 " - pdb=" SG CYS Y 100 " distance=2.04 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 R2000 " - " ASN R 174 " " NAG R2001 " - " ASN R 195 " " NAG X 101 " - " ASN X 52 " " NAG X 102 " - " ASN X 78 " " NAG Y1000 " - " ASN Y 13 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 620.9 milliseconds 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3082 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 21 sheets defined 36.0% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.514A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 62 through 91 Processing helix chain 'A' and resid 99 through 113 removed outlier: 4.087A pdb=" N ASP A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.826A pdb=" N ALA A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.691A pdb=" N GLN A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.613A pdb=" N TYR A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ARG A 161 " --> pdb=" O ASN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 179 removed outlier: 3.690A pdb=" N VAL A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 removed outlier: 4.471A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 298 through 319 removed outlier: 4.115A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 removed outlier: 4.152A pdb=" N ARG A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 357 " --> pdb=" O MET A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.575A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 25 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 141 through 145 removed outlier: 3.589A pdb=" N PHE R 145 " --> pdb=" O THR R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 219 Processing helix chain 'R' and resid 241 through 245 Processing helix chain 'R' and resid 261 through 266 removed outlier: 3.747A pdb=" N VAL R 266 " --> pdb=" O GLU R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 277 No H-bonds generated for 'chain 'R' and resid 275 through 277' Processing helix chain 'R' and resid 278 through 283 removed outlier: 3.882A pdb=" N PHE R 282 " --> pdb=" O HIS R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 337 removed outlier: 3.918A pdb=" N LEU R 337 " --> pdb=" O GLY R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 359 through 387 removed outlier: 3.595A pdb=" N TRP R 367 " --> pdb=" O ARG R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 423 Processing helix chain 'R' and resid 425 through 436 removed outlier: 3.815A pdb=" N HIS R 429 " --> pdb=" O GLN R 425 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE R 431 " --> pdb=" O TYR R 427 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ASP R 432 " --> pdb=" O ASN R 428 " (cutoff:3.500A) Processing helix chain 'R' and resid 436 through 470 Processing helix chain 'R' and resid 479 through 500 Processing helix chain 'R' and resid 507 through 511 removed outlier: 3.953A pdb=" N VAL R 511 " --> pdb=" O TYR R 508 " (cutoff:3.500A) Processing helix chain 'R' and resid 521 through 554 Processing helix chain 'R' and resid 560 through 594 removed outlier: 3.988A pdb=" N ALA R 568 " --> pdb=" O ASP R 564 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE R 573 " --> pdb=" O LYS R 569 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU R 574 " --> pdb=" O LYS R 570 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP R 578 " --> pdb=" O LEU R 574 " (cutoff:3.500A) Proline residue: R 584 - end of helix removed outlier: 3.590A pdb=" N SER R 591 " --> pdb=" O PHE R 587 " (cutoff:3.500A) Processing helix chain 'R' and resid 603 through 623 removed outlier: 3.777A pdb=" N LEU R 607 " --> pdb=" O ASN R 603 " (cutoff:3.500A) Proline residue: R 613 - end of helix removed outlier: 4.600A pdb=" N SER R 616 " --> pdb=" O TYR R 612 " (cutoff:3.500A) Proline residue: R 620 - end of helix Processing helix chain 'R' and resid 627 through 641 removed outlier: 3.749A pdb=" N ASP R 633 " --> pdb=" O THR R 629 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 45 Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.956A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 191 Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 50 removed outlier: 3.566A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.781A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.826A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 153 removed outlier: 6.405A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.911A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.660A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.803A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.745A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 53 through 56 removed outlier: 6.002A pdb=" N LEU R 54 " --> pdb=" O GLU R 79 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE R 103 " --> pdb=" O SER R 129 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N CYS R 131 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE R 105 " --> pdb=" O CYS R 131 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR R 133 " --> pdb=" O ILE R 105 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASN R 107 " --> pdb=" O THR R 133 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU R 128 " --> pdb=" O GLU R 154 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N CYS R 156 " --> pdb=" O LEU R 128 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE R 130 " --> pdb=" O CYS R 156 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE R 151 " --> pdb=" O THR R 178 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LYS R 180 " --> pdb=" O PHE R 151 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU R 153 " --> pdb=" O LYS R 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL R 177 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER R 201 " --> pdb=" O VAL R 177 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN R 195 " --> pdb=" O GLY R 220 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR R 222 " --> pdb=" O ASN R 195 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N THR R 197 " --> pdb=" O THR R 222 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 53 through 56 removed outlier: 6.002A pdb=" N LEU R 54 " --> pdb=" O GLU R 79 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE R 103 " --> pdb=" O SER R 129 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N CYS R 131 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE R 105 " --> pdb=" O CYS R 131 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR R 133 " --> pdb=" O ILE R 105 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASN R 107 " --> pdb=" O THR R 133 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU R 128 " --> pdb=" O GLU R 154 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N CYS R 156 " --> pdb=" O LEU R 128 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE R 130 " --> pdb=" O CYS R 156 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE R 151 " --> pdb=" O THR R 178 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LYS R 180 " --> pdb=" O PHE R 151 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU R 153 " --> pdb=" O LYS R 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL R 177 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER R 201 " --> pdb=" O VAL R 177 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N THR R 226 " --> pdb=" O THR R 198 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR R 200 " --> pdb=" O THR R 226 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASP R 228 " --> pdb=" O THR R 200 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU R 202 " --> pdb=" O ASP R 228 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU R 227 " --> pdb=" O ILE R 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 63 through 64 Processing sheet with id=AB6, first strand: chain 'R' and resid 94 through 95 removed outlier: 6.348A pdb=" N PHE R 94 " --> pdb=" O ILE R 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'R' and resid 163 through 164 removed outlier: 3.502A pdb=" N VAL R 189 " --> pdb=" O LYS R 212 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'X' and resid 11 through 14 removed outlier: 10.790A pdb=" N THR Y 32 " --> pdb=" O PRO X 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'X' and resid 11 through 14 Processing sheet with id=AC1, first strand: chain 'X' and resid 59 through 69 removed outlier: 5.956A pdb=" N CYS X 60 " --> pdb=" O CYS X 84 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N CYS X 84 " --> pdb=" O CYS X 60 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA X 62 " --> pdb=" O CYS X 82 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N CYS X 82 " --> pdb=" O ALA X 62 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N SER X 64 " --> pdb=" O THR X 80 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'X' and resid 91 through 92 Processing sheet with id=AC3, first strand: chain 'Y' and resid 56 through 68 removed outlier: 6.544A pdb=" N SER Y 87 " --> pdb=" O ARG Y 60 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL Y 62 " --> pdb=" O ALA Y 85 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ALA Y 85 " --> pdb=" O VAL Y 62 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE Y 64 " --> pdb=" O ALA Y 83 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA Y 83 " --> pdb=" O PHE Y 64 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER Y 66 " --> pdb=" O SER Y 81 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N SER Y 81 " --> pdb=" O SER Y 66 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG Y 68 " --> pdb=" O VAL Y 79 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL Y 79 " --> pdb=" O ARG Y 68 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1599 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: 2.26 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2509 1.33 - 1.45: 3171 1.45 - 1.57: 7282 1.57 - 1.70: 0 1.70 - 1.82: 134 Bond restraints: 13096 Sorted by residual: bond pdb=" CZ ARG A 205 " pdb=" NH2 ARG A 205 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.30e-02 5.92e+03 1.36e+01 bond pdb=" CZ ARG A 90 " pdb=" NH2 ARG A 90 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.30e-02 5.92e+03 1.36e+01 bond pdb=" CZ ARG A 144 " pdb=" NH2 ARG A 144 " ideal model delta sigma weight residual 1.330 1.285 0.045 1.30e-02 5.92e+03 1.18e+01 bond pdb=" CZ ARG A 142 " pdb=" NH2 ARG A 142 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.16e+01 bond pdb=" CZ ARG N 98 " pdb=" NH2 ARG N 98 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.10e+01 ... (remaining 13091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 15965 1.74 - 3.48: 1423 3.48 - 5.23: 312 5.23 - 6.97: 44 6.97 - 8.71: 7 Bond angle restraints: 17751 Sorted by residual: angle pdb=" CA ASP N 50 " pdb=" CB ASP N 50 " pdb=" CG ASP N 50 " ideal model delta sigma weight residual 112.60 119.49 -6.89 1.00e+00 1.00e+00 4.74e+01 angle pdb=" C ARG N 105 " pdb=" N ASP N 106 " pdb=" CA ASP N 106 " ideal model delta sigma weight residual 120.65 129.03 -8.38 1.32e+00 5.74e-01 4.03e+01 angle pdb=" CA PHE N 68 " pdb=" CB PHE N 68 " pdb=" CG PHE N 68 " ideal model delta sigma weight residual 113.80 119.65 -5.85 1.00e+00 1.00e+00 3.42e+01 angle pdb=" CA ASP N 106 " pdb=" CB ASP N 106 " pdb=" CG ASP N 106 " ideal model delta sigma weight residual 112.60 118.39 -5.79 1.00e+00 1.00e+00 3.36e+01 angle pdb=" C GLN B 176 " pdb=" N THR B 177 " pdb=" CA THR B 177 " ideal model delta sigma weight residual 120.63 129.34 -8.71 1.61e+00 3.86e-01 2.93e+01 ... (remaining 17746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 7327 17.46 - 34.93: 556 34.93 - 52.39: 76 52.39 - 69.85: 28 69.85 - 87.31: 16 Dihedral angle restraints: 8003 sinusoidal: 3238 harmonic: 4765 Sorted by residual: dihedral pdb=" CA CYS B 204 " pdb=" C CYS B 204 " pdb=" N ASP B 205 " pdb=" CA ASP B 205 " ideal model delta harmonic sigma weight residual 180.00 150.53 29.47 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 151.15 28.85 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 8000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1723 0.076 - 0.152: 250 0.152 - 0.228: 51 0.228 - 0.305: 10 0.305 - 0.381: 4 Chirality restraints: 2038 Sorted by residual: chirality pdb=" CA TYR A 69 " pdb=" N TYR A 69 " pdb=" C TYR A 69 " pdb=" CB TYR A 69 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA THR N 114 " pdb=" N THR N 114 " pdb=" C THR N 114 " pdb=" CB THR N 114 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA CYS N 107 " pdb=" N CYS N 107 " pdb=" C CYS N 107 " pdb=" CB CYS N 107 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 2035 not shown) Planarity restraints: 2275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 95 " 0.146 2.00e-02 2.50e+03 8.22e-02 1.35e+02 pdb=" CG TYR N 95 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR N 95 " -0.062 2.00e-02 2.50e+03 pdb=" CD2 TYR N 95 " -0.068 2.00e-02 2.50e+03 pdb=" CE1 TYR N 95 " -0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR N 95 " -0.048 2.00e-02 2.50e+03 pdb=" CZ TYR N 95 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR N 95 " 0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 167 " 0.116 2.00e-02 2.50e+03 6.53e-02 8.52e+01 pdb=" CG TYR A 167 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 167 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR A 167 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR A 167 " -0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR A 167 " -0.034 2.00e-02 2.50e+03 pdb=" CZ TYR A 167 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 167 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 154 " -0.121 2.00e-02 2.50e+03 6.31e-02 7.96e+01 pdb=" CG TYR A 154 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR A 154 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR A 154 " 0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR A 154 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR A 154 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR A 154 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 154 " -0.085 2.00e-02 2.50e+03 ... (remaining 2272 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 116 2.59 - 3.17: 11968 3.17 - 3.74: 20140 3.74 - 4.32: 28900 4.32 - 4.90: 47044 Nonbonded interactions: 108168 Sorted by model distance: nonbonded pdb=" O CYS B 204 " pdb=" OD1 ASP B 228 " model vdw 2.011 3.040 nonbonded pdb=" NZ LYS B 57 " pdb=" OE1 GLN B 75 " model vdw 2.028 3.120 nonbonded pdb=" O3 NAG Y1000 " pdb=" O7 NAG Y1000 " model vdw 2.166 3.040 nonbonded pdb=" NE2 GLN R 170 " pdb=" O6 NAG R2001 " model vdw 2.266 3.120 nonbonded pdb=" NH1 ARG B 48 " pdb=" OD1 ASN B 340 " model vdw 2.267 3.120 ... (remaining 108163 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.220 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 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 : 0.007 0.048 13118 Z= 0.415 Angle : 1.111 8.711 17800 Z= 0.721 Chirality : 0.061 0.381 2038 Planarity : 0.012 0.172 2270 Dihedral : 13.423 87.313 4870 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.06 (0.19), residues: 1616 helix: -1.57 (0.18), residues: 513 sheet: -1.25 (0.28), residues: 327 loop : -1.12 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.003 ARG X 67 TYR 0.146 0.013 TYR N 95 PHE 0.076 0.006 PHE N 27 TRP 0.103 0.013 TRP N 47 HIS 0.010 0.003 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00698 (13096) covalent geometry : angle 1.10647 (17751) SS BOND : bond 0.00802 ( 17) SS BOND : angle 1.87328 ( 34) hydrogen bonds : bond 0.19436 ( 566) hydrogen bonds : angle 8.53522 ( 1599) link_NAG-ASN : bond 0.00068 ( 5) link_NAG-ASN : angle 2.60344 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TRP cc_start: 0.6015 (t-100) cc_final: 0.5464 (t-100) REVERT: A 206 ASP cc_start: 0.7431 (t0) cc_final: 0.7020 (t0) REVERT: A 207 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7949 (mt-10) REVERT: A 258 LEU cc_start: 0.8830 (mp) cc_final: 0.8576 (mp) REVERT: A 267 LYS cc_start: 0.8914 (mttt) cc_final: 0.8640 (mtmm) REVERT: A 359 GLU cc_start: 0.8085 (tp30) cc_final: 0.7762 (tp30) REVERT: B 6 GLN cc_start: 0.8246 (pp30) cc_final: 0.7800 (pp30) REVERT: B 7 LEU cc_start: 0.9286 (mt) cc_final: 0.8706 (mt) REVERT: B 78 LYS cc_start: 0.9048 (mmtt) cc_final: 0.8766 (mmmt) REVERT: B 93 ILE cc_start: 0.9363 (mt) cc_final: 0.8948 (mm) REVERT: B 99 TRP cc_start: 0.8333 (m100) cc_final: 0.7849 (m100) REVERT: B 111 TYR cc_start: 0.8582 (m-80) cc_final: 0.7728 (m-80) REVERT: B 118 ASP cc_start: 0.8319 (t0) cc_final: 0.7942 (p0) REVERT: B 120 ILE cc_start: 0.9012 (mt) cc_final: 0.8778 (mt) REVERT: B 191 SER cc_start: 0.8722 (t) cc_final: 0.8486 (p) REVERT: B 243 THR cc_start: 0.8658 (p) cc_final: 0.8433 (p) REVERT: B 250 CYS cc_start: 0.9088 (t) cc_final: 0.8760 (t) REVERT: B 280 LYS cc_start: 0.9049 (ttpp) cc_final: 0.8692 (ttpt) REVERT: B 292 PHE cc_start: 0.8600 (m-10) cc_final: 0.8113 (m-10) REVERT: B 308 LEU cc_start: 0.8794 (mt) cc_final: 0.8446 (mp) REVERT: B 316 SER cc_start: 0.8545 (t) cc_final: 0.8245 (t) REVERT: B 339 TRP cc_start: 0.8094 (m100) cc_final: 0.7490 (m100) REVERT: G 17 GLU cc_start: 0.8887 (tp30) cc_final: 0.7566 (tp30) REVERT: G 19 LEU cc_start: 0.9328 (mt) cc_final: 0.9062 (mp) REVERT: G 40 TYR cc_start: 0.9248 (t80) cc_final: 0.8910 (t80) REVERT: G 55 PRO cc_start: 0.8736 (Cg_exo) cc_final: 0.8177 (Cg_endo) REVERT: N 29 PHE cc_start: 0.8246 (t80) cc_final: 0.7721 (t80) REVERT: N 34 MET cc_start: 0.8522 (mmm) cc_final: 0.8189 (mmm) REVERT: N 36 TRP cc_start: 0.8519 (m100) cc_final: 0.8101 (m100) REVERT: N 46 GLU cc_start: 0.8287 (tt0) cc_final: 0.7901 (tt0) REVERT: N 47 TRP cc_start: 0.8323 (t60) cc_final: 0.7906 (t60) REVERT: N 50 ASP cc_start: 0.8479 (p0) cc_final: 0.8002 (p0) REVERT: N 95 TYR cc_start: 0.8202 (m-80) cc_final: 0.7979 (m-80) REVERT: N 111 THR cc_start: 0.9278 (p) cc_final: 0.9015 (m) REVERT: N 112 SER cc_start: 0.8608 (m) cc_final: 0.7882 (p) REVERT: R 54 LEU cc_start: 0.9295 (mt) cc_final: 0.8866 (mm) REVERT: R 56 LEU cc_start: 0.9556 (mt) cc_final: 0.9334 (mt) REVERT: R 79 GLU cc_start: 0.8479 (pt0) cc_final: 0.8169 (pm20) REVERT: R 104 LEU cc_start: 0.8786 (tp) cc_final: 0.8551 (tt) REVERT: R 154 GLU cc_start: 0.8137 (tt0) cc_final: 0.7816 (tt0) REVERT: R 186 PHE cc_start: 0.8961 (m-80) cc_final: 0.8683 (m-80) REVERT: R 200 THR cc_start: 0.8939 (m) cc_final: 0.8738 (p) REVERT: R 377 ASN cc_start: 0.8031 (m-40) cc_final: 0.7737 (m-40) REVERT: R 399 CYS cc_start: 0.8963 (m) cc_final: 0.8455 (t) REVERT: R 402 SER cc_start: 0.8756 (m) cc_final: 0.8468 (t) REVERT: R 405 ASP cc_start: 0.8360 (m-30) cc_final: 0.8117 (m-30) REVERT: R 574 LEU cc_start: 0.8881 (mt) cc_final: 0.8487 (mp) REVERT: R 578 ASP cc_start: 0.8760 (t0) cc_final: 0.8536 (t70) REVERT: X 15 ASN cc_start: 0.9369 (t0) cc_final: 0.9161 (t0) REVERT: X 18 PHE cc_start: 0.8497 (m-80) cc_final: 0.7851 (m-80) REVERT: X 27 GLN cc_start: 0.8720 (tt0) cc_final: 0.7966 (tm-30) REVERT: X 29 MET cc_start: 0.7800 (ptm) cc_final: 0.6917 (ptp) REVERT: X 51 LYS cc_start: 0.9327 (mmtt) cc_final: 0.8887 (mmtp) REVERT: Y 10 ARG cc_start: 0.8045 (pmt170) cc_final: 0.7826 (pmt170) REVERT: Y 41 MET cc_start: 0.8332 (ptm) cc_final: 0.7692 (pmm) REVERT: Y 42 THR cc_start: 0.9305 (t) cc_final: 0.9008 (t) REVERT: Y 43 ARG cc_start: 0.9278 (ttm110) cc_final: 0.9040 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.1113 time to fit residues: 79.0552 Evaluate side-chains 326 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 77 ASN R 160 HIS X 5 GLN Y 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.129642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.093821 restraints weight = 26873.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.097038 restraints weight = 13379.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.099478 restraints weight = 8145.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.099801 restraints weight = 6634.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.099615 restraints weight = 6215.217| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13118 Z= 0.167 Angle : 0.752 8.196 17800 Z= 0.392 Chirality : 0.046 0.197 2038 Planarity : 0.005 0.038 2270 Dihedral : 6.914 56.910 1884 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.78 % Allowed : 14.61 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.75 (0.20), residues: 1616 helix: 0.14 (0.22), residues: 511 sheet: -1.33 (0.28), residues: 330 loop : -0.39 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 13 TYR 0.026 0.002 TYR N 32 PHE 0.030 0.002 PHE B 241 TRP 0.025 0.002 TRP B 82 HIS 0.006 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00364 (13096) covalent geometry : angle 0.74384 (17751) SS BOND : bond 0.00674 ( 17) SS BOND : angle 2.15199 ( 34) hydrogen bonds : bond 0.05053 ( 566) hydrogen bonds : angle 5.86272 ( 1599) link_NAG-ASN : bond 0.00220 ( 5) link_NAG-ASN : angle 2.25577 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 394 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4178 (ptt) cc_final: 0.2451 (mtt) REVERT: A 206 ASP cc_start: 0.7896 (t0) cc_final: 0.7528 (t0) REVERT: A 258 LEU cc_start: 0.8706 (mp) cc_final: 0.8488 (mp) REVERT: B 57 LYS cc_start: 0.8463 (pttm) cc_final: 0.8241 (pttp) REVERT: B 75 GLN cc_start: 0.8481 (mt0) cc_final: 0.8263 (mt0) REVERT: B 111 TYR cc_start: 0.8358 (m-80) cc_final: 0.7900 (m-80) REVERT: B 118 ASP cc_start: 0.8293 (t0) cc_final: 0.8028 (p0) REVERT: B 145 TYR cc_start: 0.9205 (p90) cc_final: 0.8880 (p90) REVERT: B 243 THR cc_start: 0.9094 (p) cc_final: 0.8687 (p) REVERT: B 246 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8098 (t70) REVERT: B 280 LYS cc_start: 0.8958 (ttpp) cc_final: 0.8464 (ttpt) REVERT: B 292 PHE cc_start: 0.8621 (m-10) cc_final: 0.8202 (m-10) REVERT: B 297 TRP cc_start: 0.9145 (m100) cc_final: 0.8919 (m100) REVERT: B 308 LEU cc_start: 0.9112 (mt) cc_final: 0.8273 (mp) REVERT: B 339 TRP cc_start: 0.8159 (m100) cc_final: 0.7551 (m100) REVERT: G 11 GLN cc_start: 0.9447 (tp40) cc_final: 0.9176 (tm-30) REVERT: G 17 GLU cc_start: 0.8884 (tp30) cc_final: 0.8544 (tp30) REVERT: G 28 ILE cc_start: 0.9230 (mm) cc_final: 0.8853 (tt) REVERT: G 40 TYR cc_start: 0.8909 (t80) cc_final: 0.8437 (t80) REVERT: G 48 ASP cc_start: 0.8416 (t0) cc_final: 0.8056 (t0) REVERT: G 51 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8764 (mp) REVERT: N 35 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.8289 (m110) REVERT: N 36 TRP cc_start: 0.8696 (m100) cc_final: 0.7381 (m100) REVERT: N 38 ARG cc_start: 0.7364 (ptm-80) cc_final: 0.5690 (ptm-80) REVERT: N 46 GLU cc_start: 0.8146 (tt0) cc_final: 0.7913 (mp0) REVERT: N 47 TRP cc_start: 0.8083 (t60) cc_final: 0.7731 (t60) REVERT: N 81 LEU cc_start: 0.8422 (tp) cc_final: 0.7649 (tp) REVERT: N 85 SER cc_start: 0.8486 (m) cc_final: 0.7922 (p) REVERT: N 87 LYS cc_start: 0.9281 (ptpt) cc_final: 0.8812 (ptpp) REVERT: N 95 TYR cc_start: 0.8251 (m-80) cc_final: 0.7037 (m-80) REVERT: N 106 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7354 (m-30) REVERT: N 109 ASP cc_start: 0.6397 (m-30) cc_final: 0.5973 (m-30) REVERT: N 112 SER cc_start: 0.8344 (m) cc_final: 0.7885 (p) REVERT: R 102 GLU cc_start: 0.8043 (mp0) cc_final: 0.7732 (mp0) REVERT: R 230 SER cc_start: 0.9293 (m) cc_final: 0.9066 (t) REVERT: R 233 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8840 (ttpt) REVERT: R 240 TYR cc_start: 0.8594 (t80) cc_final: 0.8330 (t80) REVERT: R 269 LEU cc_start: 0.9301 (mm) cc_final: 0.9082 (mm) REVERT: R 377 ASN cc_start: 0.8094 (m-40) cc_final: 0.7841 (m-40) REVERT: R 384 LEU cc_start: 0.9221 (mt) cc_final: 0.8953 (mt) REVERT: R 399 CYS cc_start: 0.8659 (m) cc_final: 0.8266 (t) REVERT: R 433 TRP cc_start: 0.8214 (t-100) cc_final: 0.7028 (t-100) REVERT: R 529 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9017 (tp) REVERT: R 562 ASN cc_start: 0.8594 (p0) cc_final: 0.7922 (p0) REVERT: R 574 LEU cc_start: 0.9078 (mt) cc_final: 0.8819 (mp) REVERT: X 18 PHE cc_start: 0.8551 (m-80) cc_final: 0.8028 (m-80) REVERT: X 20 GLN cc_start: 0.7651 (tp40) cc_final: 0.7293 (tp40) REVERT: X 27 GLN cc_start: 0.8136 (tt0) cc_final: 0.7648 (tm-30) REVERT: X 29 MET cc_start: 0.7551 (ptm) cc_final: 0.6984 (ptt) REVERT: X 37 TYR cc_start: 0.8703 (p90) cc_final: 0.7990 (p90) REVERT: X 42 ARG cc_start: 0.8597 (mmp-170) cc_final: 0.7928 (mmm160) REVERT: X 45 LYS cc_start: 0.9316 (mtmm) cc_final: 0.8643 (mtmm) REVERT: X 51 LYS cc_start: 0.9546 (mmtt) cc_final: 0.9327 (mttm) REVERT: Y 41 MET cc_start: 0.8353 (ptm) cc_final: 0.7801 (pmm) REVERT: Y 42 THR cc_start: 0.9335 (t) cc_final: 0.9042 (t) REVERT: Y 43 ARG cc_start: 0.9292 (ttm110) cc_final: 0.8951 (ttp-110) REVERT: Y 95 ARG cc_start: 0.8396 (tmm160) cc_final: 0.8087 (tmm160) REVERT: Y 98 THR cc_start: 0.9368 (m) cc_final: 0.9025 (p) outliers start: 53 outliers final: 28 residues processed: 418 average time/residue: 0.1080 time to fit residues: 65.6217 Evaluate side-chains 347 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 313 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 233 LYS Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 431 ILE Chi-restraints excluded: chain R residue 458 THR Chi-restraints excluded: chain R residue 529 LEU Chi-restraints excluded: chain R residue 536 VAL Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 547 ILE Chi-restraints excluded: chain R residue 553 VAL Chi-restraints excluded: chain R residue 602 THR Chi-restraints excluded: chain R residue 605 LYS Chi-restraints excluded: chain R residue 606 VAL Chi-restraints excluded: chain R residue 637 LEU Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 97 THR Chi-restraints excluded: chain Y residue 105 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 144 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 141 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 91 HIS R 619 ASN X 83 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.129025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.093202 restraints weight = 26963.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.095994 restraints weight = 13622.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.098783 restraints weight = 8555.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.098639 restraints weight = 7177.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.098620 restraints weight = 6557.622| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13118 Z= 0.162 Angle : 0.704 9.325 17800 Z= 0.364 Chirality : 0.045 0.169 2038 Planarity : 0.004 0.048 2270 Dihedral : 6.317 55.471 1884 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.27 % Allowed : 16.04 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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 (0.21), residues: 1616 helix: 0.42 (0.22), residues: 516 sheet: -1.29 (0.27), residues: 333 loop : -0.21 (0.24), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 176 TYR 0.026 0.002 TYR A 69 PHE 0.043 0.002 PHE R 186 TRP 0.023 0.002 TRP B 82 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00362 (13096) covalent geometry : angle 0.69940 (17751) SS BOND : bond 0.00529 ( 17) SS BOND : angle 1.46997 ( 34) hydrogen bonds : bond 0.04366 ( 566) hydrogen bonds : angle 5.59651 ( 1599) link_NAG-ASN : bond 0.00169 ( 5) link_NAG-ASN : angle 1.98928 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 328 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4206 (ptt) cc_final: 0.2661 (mtt) REVERT: A 172 GLN cc_start: 0.8406 (pm20) cc_final: 0.8029 (pp30) REVERT: A 206 ASP cc_start: 0.7892 (t0) cc_final: 0.7548 (t0) REVERT: A 244 TRP cc_start: 0.9365 (t-100) cc_final: 0.8778 (t-100) REVERT: A 258 LEU cc_start: 0.8670 (mp) cc_final: 0.8449 (mp) REVERT: A 359 GLU cc_start: 0.8158 (mp0) cc_final: 0.7915 (tp30) REVERT: B 12 GLU cc_start: 0.9197 (tp30) cc_final: 0.8100 (tp30) REVERT: B 15 LYS cc_start: 0.9228 (ttpt) cc_final: 0.8977 (tmmt) REVERT: B 99 TRP cc_start: 0.8522 (m100) cc_final: 0.7886 (m100) REVERT: B 111 TYR cc_start: 0.8281 (m-80) cc_final: 0.7961 (m-80) REVERT: B 118 ASP cc_start: 0.8297 (t0) cc_final: 0.8088 (p0) REVERT: B 130 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8091 (pm20) REVERT: B 243 THR cc_start: 0.9164 (p) cc_final: 0.8770 (p) REVERT: B 246 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8135 (t70) REVERT: B 280 LYS cc_start: 0.8890 (ttpp) cc_final: 0.8569 (ttpt) REVERT: B 292 PHE cc_start: 0.8590 (m-10) cc_final: 0.8207 (m-10) REVERT: B 308 LEU cc_start: 0.9105 (mt) cc_final: 0.8268 (mp) REVERT: B 325 MET cc_start: 0.8885 (mmt) cc_final: 0.8611 (mmm) REVERT: B 339 TRP cc_start: 0.8164 (m100) cc_final: 0.7601 (m100) REVERT: G 11 GLN cc_start: 0.9414 (tp40) cc_final: 0.9021 (tm-30) REVERT: G 17 GLU cc_start: 0.8954 (tp30) cc_final: 0.8491 (tp30) REVERT: G 21 MET cc_start: 0.8519 (mmm) cc_final: 0.8273 (mmm) REVERT: G 28 ILE cc_start: 0.9181 (mm) cc_final: 0.8771 (tt) REVERT: G 40 TYR cc_start: 0.8757 (t80) cc_final: 0.8548 (t80) REVERT: N 32 TYR cc_start: 0.7690 (m-10) cc_final: 0.7265 (m-10) REVERT: N 34 MET cc_start: 0.8718 (mmm) cc_final: 0.8014 (mmm) REVERT: N 35 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8141 (m-40) REVERT: N 36 TRP cc_start: 0.8598 (m100) cc_final: 0.7533 (m100) REVERT: N 38 ARG cc_start: 0.7550 (ptm-80) cc_final: 0.6055 (ptm-80) REVERT: N 46 GLU cc_start: 0.8213 (tt0) cc_final: 0.7977 (mp0) REVERT: N 47 TRP cc_start: 0.7865 (t60) cc_final: 0.7576 (t60) REVERT: N 81 LEU cc_start: 0.8534 (tp) cc_final: 0.8200 (tp) REVERT: N 95 TYR cc_start: 0.8253 (m-80) cc_final: 0.6850 (m-80) REVERT: N 106 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7117 (m-30) REVERT: N 108 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.7050 (m-80) REVERT: N 109 ASP cc_start: 0.6425 (m-30) cc_final: 0.6197 (m-30) REVERT: N 112 SER cc_start: 0.8398 (m) cc_final: 0.8002 (p) REVERT: N 117 TYR cc_start: 0.7856 (m-10) cc_final: 0.7619 (m-80) REVERT: R 108 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8410 (p) REVERT: R 154 GLU cc_start: 0.8197 (tt0) cc_final: 0.7785 (tt0) REVERT: R 200 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8586 (t) REVERT: R 203 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7482 (mt-10) REVERT: R 230 SER cc_start: 0.9306 (m) cc_final: 0.8963 (t) REVERT: R 240 TYR cc_start: 0.8530 (t80) cc_final: 0.8237 (t80) REVERT: R 374 ILE cc_start: 0.8971 (mm) cc_final: 0.8679 (mm) REVERT: R 384 LEU cc_start: 0.9261 (mt) cc_final: 0.8895 (mt) REVERT: R 399 CYS cc_start: 0.8616 (m) cc_final: 0.8231 (t) REVERT: R 433 TRP cc_start: 0.8229 (t-100) cc_final: 0.7166 (t-100) REVERT: R 529 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8941 (tp) REVERT: X 15 ASN cc_start: 0.8973 (OUTLIER) cc_final: 0.8666 (p0) REVERT: X 18 PHE cc_start: 0.8459 (m-80) cc_final: 0.7930 (m-80) REVERT: X 20 GLN cc_start: 0.7648 (tp40) cc_final: 0.7403 (tp40) REVERT: X 27 GLN cc_start: 0.8182 (tt0) cc_final: 0.7447 (tm-30) REVERT: X 29 MET cc_start: 0.7593 (ptm) cc_final: 0.7110 (ptt) REVERT: X 42 ARG cc_start: 0.8543 (mmp-170) cc_final: 0.7909 (mmm160) REVERT: X 45 LYS cc_start: 0.9319 (mtmm) cc_final: 0.8775 (mtmm) REVERT: Y 41 MET cc_start: 0.8437 (ptm) cc_final: 0.7802 (pmm) REVERT: Y 42 THR cc_start: 0.9415 (t) cc_final: 0.9192 (t) REVERT: Y 95 ARG cc_start: 0.8368 (tmm160) cc_final: 0.8121 (tmm160) REVERT: Y 98 THR cc_start: 0.9346 (m) cc_final: 0.9134 (p) outliers start: 74 outliers final: 47 residues processed: 369 average time/residue: 0.1053 time to fit residues: 57.0160 Evaluate side-chains 343 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 288 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 431 ILE Chi-restraints excluded: chain R residue 458 THR Chi-restraints excluded: chain R residue 502 LEU Chi-restraints excluded: chain R residue 529 LEU Chi-restraints excluded: chain R residue 530 THR Chi-restraints excluded: chain R residue 536 VAL Chi-restraints excluded: chain R residue 547 ILE Chi-restraints excluded: chain R residue 549 ILE Chi-restraints excluded: chain R residue 606 VAL Chi-restraints excluded: chain R residue 616 SER Chi-restraints excluded: chain R residue 637 LEU Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain Y residue 38 CYS Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 56 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 134 optimal weight: 0.5980 chunk 118 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 207 ASN ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 425 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.125777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.090265 restraints weight = 27070.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.094567 restraints weight = 13035.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.095181 restraints weight = 7902.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.095665 restraints weight = 7278.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.095773 restraints weight = 6636.466| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13118 Z= 0.218 Angle : 0.701 8.522 17800 Z= 0.366 Chirality : 0.045 0.186 2038 Planarity : 0.004 0.038 2270 Dihedral : 6.085 53.787 1884 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.99 % Allowed : 17.46 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -0.42 (0.21), residues: 1616 helix: 0.60 (0.23), residues: 504 sheet: -1.21 (0.26), residues: 347 loop : -0.27 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 8 TYR 0.024 0.002 TYR A 69 PHE 0.034 0.002 PHE B 241 TRP 0.022 0.002 TRP B 82 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00479 (13096) covalent geometry : angle 0.69756 (17751) SS BOND : bond 0.00522 ( 17) SS BOND : angle 1.36695 ( 34) hydrogen bonds : bond 0.04366 ( 566) hydrogen bonds : angle 5.51949 ( 1599) link_NAG-ASN : bond 0.00121 ( 5) link_NAG-ASN : angle 1.90044 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 303 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4097 (ptt) cc_final: 0.2586 (mtt) REVERT: A 206 ASP cc_start: 0.7974 (t0) cc_final: 0.7673 (t0) REVERT: A 241 LYS cc_start: 0.9298 (tttt) cc_final: 0.9065 (ttpt) REVERT: A 244 TRP cc_start: 0.9396 (t-100) cc_final: 0.8726 (t-100) REVERT: A 359 GLU cc_start: 0.8194 (mp0) cc_final: 0.7912 (mp0) REVERT: B 10 GLU cc_start: 0.9383 (mt-10) cc_final: 0.9088 (mp0) REVERT: B 99 TRP cc_start: 0.8497 (m100) cc_final: 0.7948 (m100) REVERT: B 111 TYR cc_start: 0.8389 (m-80) cc_final: 0.7990 (m-80) REVERT: B 130 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8060 (pm20) REVERT: B 243 THR cc_start: 0.9113 (p) cc_final: 0.8845 (p) REVERT: B 246 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8109 (t70) REVERT: B 280 LYS cc_start: 0.8873 (ttpp) cc_final: 0.8606 (ttpt) REVERT: B 292 PHE cc_start: 0.8661 (m-10) cc_final: 0.8249 (m-10) REVERT: B 308 LEU cc_start: 0.9159 (mt) cc_final: 0.8013 (mt) REVERT: B 325 MET cc_start: 0.8879 (mmt) cc_final: 0.8571 (mmm) REVERT: B 339 TRP cc_start: 0.8189 (m100) cc_final: 0.7344 (m100) REVERT: G 11 GLN cc_start: 0.9480 (tp40) cc_final: 0.9098 (tm-30) REVERT: G 17 GLU cc_start: 0.9012 (tp30) cc_final: 0.8547 (tp30) REVERT: G 18 GLN cc_start: 0.8339 (tp40) cc_final: 0.8051 (tp-100) REVERT: G 28 ILE cc_start: 0.9212 (mm) cc_final: 0.8773 (tt) REVERT: G 30 VAL cc_start: 0.8752 (m) cc_final: 0.8530 (m) REVERT: G 40 TYR cc_start: 0.8769 (t80) cc_final: 0.8471 (t80) REVERT: G 44 HIS cc_start: 0.8843 (m-70) cc_final: 0.8359 (m90) REVERT: G 51 LEU cc_start: 0.9144 (mt) cc_final: 0.8855 (mp) REVERT: N 32 TYR cc_start: 0.7897 (m-10) cc_final: 0.7075 (m-10) REVERT: N 34 MET cc_start: 0.8765 (mmm) cc_final: 0.8207 (mmm) REVERT: N 36 TRP cc_start: 0.8699 (m100) cc_final: 0.7389 (m100) REVERT: N 38 ARG cc_start: 0.7528 (ptm-80) cc_final: 0.6278 (ptm-80) REVERT: N 47 TRP cc_start: 0.7731 (t60) cc_final: 0.7512 (t60) REVERT: N 85 SER cc_start: 0.8475 (m) cc_final: 0.7868 (p) REVERT: N 87 LYS cc_start: 0.9213 (ptpt) cc_final: 0.9007 (ttmm) REVERT: N 108 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7229 (m-80) REVERT: N 109 ASP cc_start: 0.6508 (m-30) cc_final: 0.6164 (m-30) REVERT: N 117 TYR cc_start: 0.7913 (m-10) cc_final: 0.7655 (m-80) REVERT: R 102 GLU cc_start: 0.8131 (mp0) cc_final: 0.7918 (mp0) REVERT: R 108 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8456 (p) REVERT: R 200 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8491 (t) REVERT: R 230 SER cc_start: 0.9330 (m) cc_final: 0.8977 (t) REVERT: R 240 TYR cc_start: 0.8428 (t80) cc_final: 0.8191 (t80) REVERT: R 377 ASN cc_start: 0.8075 (m-40) cc_final: 0.7649 (t0) REVERT: R 384 LEU cc_start: 0.9303 (mt) cc_final: 0.9065 (mt) REVERT: R 399 CYS cc_start: 0.8572 (m) cc_final: 0.8221 (t) REVERT: R 433 TRP cc_start: 0.8230 (t-100) cc_final: 0.7305 (t-100) REVERT: R 529 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8960 (tp) REVERT: R 571 MET cc_start: 0.8745 (ttp) cc_final: 0.8297 (ttt) REVERT: R 605 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8565 (mttt) REVERT: X 6 ASP cc_start: 0.8744 (m-30) cc_final: 0.8152 (p0) REVERT: X 18 PHE cc_start: 0.8482 (m-80) cc_final: 0.8076 (m-80) REVERT: X 20 GLN cc_start: 0.7614 (tp40) cc_final: 0.7361 (tp40) REVERT: X 27 GLN cc_start: 0.8180 (tt0) cc_final: 0.7461 (tm-30) REVERT: X 29 MET cc_start: 0.7607 (ptm) cc_final: 0.7277 (ptt) REVERT: X 42 ARG cc_start: 0.8511 (mmp-170) cc_final: 0.7914 (mmm160) REVERT: X 45 LYS cc_start: 0.9330 (mtmm) cc_final: 0.8724 (mtmm) REVERT: Y 41 MET cc_start: 0.8449 (ptm) cc_final: 0.7961 (pmm) outliers start: 84 outliers final: 59 residues processed: 350 average time/residue: 0.0985 time to fit residues: 51.0710 Evaluate side-chains 336 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 271 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 458 THR Chi-restraints excluded: chain R residue 502 LEU Chi-restraints excluded: chain R residue 529 LEU Chi-restraints excluded: chain R residue 530 THR Chi-restraints excluded: chain R residue 536 VAL Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 547 ILE Chi-restraints excluded: chain R residue 549 ILE Chi-restraints excluded: chain R residue 575 ILE Chi-restraints excluded: chain R residue 605 LYS Chi-restraints excluded: chain R residue 606 VAL Chi-restraints excluded: chain R residue 610 LEU Chi-restraints excluded: chain R residue 614 ILE Chi-restraints excluded: chain R residue 637 LEU Chi-restraints excluded: chain X residue 51 LYS Chi-restraints excluded: chain X residue 53 VAL Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain Y residue 38 CYS Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 56 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 120 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 ASN ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 400 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 = 0.3954 r_free = 0.3954 target = 0.125808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.090598 restraints weight = 27380.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.094974 restraints weight = 13224.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.095508 restraints weight = 7991.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.096018 restraints weight = 7320.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.096027 restraints weight = 6693.033| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13118 Z= 0.193 Angle : 0.684 9.961 17800 Z= 0.356 Chirality : 0.044 0.200 2038 Planarity : 0.004 0.038 2270 Dihedral : 5.923 53.088 1884 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.84 % Allowed : 18.75 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -0.37 (0.21), residues: 1616 helix: 0.71 (0.23), residues: 504 sheet: -1.27 (0.26), residues: 364 loop : -0.21 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 27 TYR 0.026 0.001 TYR A 69 PHE 0.014 0.002 PHE R 169 TRP 0.025 0.002 TRP B 297 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00421 (13096) covalent geometry : angle 0.67930 (17751) SS BOND : bond 0.00641 ( 17) SS BOND : angle 1.62549 ( 34) hydrogen bonds : bond 0.04215 ( 566) hydrogen bonds : angle 5.41329 ( 1599) link_NAG-ASN : bond 0.00099 ( 5) link_NAG-ASN : angle 1.81864 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 291 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4232 (ptt) cc_final: 0.2639 (mtt) REVERT: A 172 GLN cc_start: 0.8384 (pm20) cc_final: 0.8029 (pp30) REVERT: A 206 ASP cc_start: 0.8136 (t0) cc_final: 0.7729 (t0) REVERT: A 232 ARG cc_start: 0.8925 (tpp80) cc_final: 0.8717 (tpt-90) REVERT: A 241 LYS cc_start: 0.9277 (tttt) cc_final: 0.9038 (ttpt) REVERT: A 244 TRP cc_start: 0.9407 (t-100) cc_final: 0.8825 (t-100) REVERT: A 359 GLU cc_start: 0.8128 (mp0) cc_final: 0.7843 (mp0) REVERT: B 12 GLU cc_start: 0.9282 (tp30) cc_final: 0.8321 (tp30) REVERT: B 111 TYR cc_start: 0.8399 (m-80) cc_final: 0.8004 (m-80) REVERT: B 118 ASP cc_start: 0.8429 (t0) cc_final: 0.8067 (p0) REVERT: B 130 GLU cc_start: 0.8660 (mt-10) cc_final: 0.7981 (pm20) REVERT: B 243 THR cc_start: 0.9125 (p) cc_final: 0.8893 (p) REVERT: B 246 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8131 (t70) REVERT: B 280 LYS cc_start: 0.8848 (ttpp) cc_final: 0.8381 (ttpt) REVERT: B 292 PHE cc_start: 0.8636 (m-10) cc_final: 0.8244 (m-10) REVERT: B 296 VAL cc_start: 0.9378 (OUTLIER) cc_final: 0.9018 (p) REVERT: B 308 LEU cc_start: 0.9104 (mt) cc_final: 0.8011 (mt) REVERT: B 325 MET cc_start: 0.8882 (mmt) cc_final: 0.8569 (mmm) REVERT: B 339 TRP cc_start: 0.8172 (m100) cc_final: 0.7377 (m100) REVERT: G 11 GLN cc_start: 0.9522 (tp40) cc_final: 0.9145 (tm-30) REVERT: G 16 VAL cc_start: 0.9530 (t) cc_final: 0.9137 (p) REVERT: G 17 GLU cc_start: 0.9032 (tp30) cc_final: 0.8522 (tp30) REVERT: G 20 LYS cc_start: 0.9351 (mttt) cc_final: 0.9119 (mttm) REVERT: G 28 ILE cc_start: 0.8939 (mm) cc_final: 0.8722 (mm) REVERT: G 40 TYR cc_start: 0.8756 (t80) cc_final: 0.8485 (t80) REVERT: G 44 HIS cc_start: 0.8852 (m-70) cc_final: 0.8329 (m90) REVERT: G 51 LEU cc_start: 0.9150 (mt) cc_final: 0.8871 (mp) REVERT: N 34 MET cc_start: 0.8794 (mmm) cc_final: 0.8307 (mmm) REVERT: N 36 TRP cc_start: 0.8719 (m100) cc_final: 0.7364 (m100) REVERT: N 38 ARG cc_start: 0.6985 (ptm-80) cc_final: 0.6448 (ptm-80) REVERT: N 85 SER cc_start: 0.8438 (m) cc_final: 0.7874 (p) REVERT: N 109 ASP cc_start: 0.6179 (m-30) cc_final: 0.5898 (m-30) REVERT: N 117 TYR cc_start: 0.7943 (m-10) cc_final: 0.7688 (m-80) REVERT: R 102 GLU cc_start: 0.8043 (mp0) cc_final: 0.7721 (mp0) REVERT: R 108 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8450 (p) REVERT: R 200 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8362 (t) REVERT: R 228 ASP cc_start: 0.8197 (t0) cc_final: 0.7847 (t0) REVERT: R 230 SER cc_start: 0.9286 (m) cc_final: 0.9022 (t) REVERT: R 240 TYR cc_start: 0.8461 (t80) cc_final: 0.8253 (t80) REVERT: R 372 LEU cc_start: 0.9511 (tt) cc_final: 0.9261 (tp) REVERT: R 377 ASN cc_start: 0.7963 (m-40) cc_final: 0.7587 (m-40) REVERT: R 384 LEU cc_start: 0.9310 (mt) cc_final: 0.9004 (mt) REVERT: R 398 MET cc_start: 0.8600 (tpp) cc_final: 0.8389 (tpp) REVERT: R 399 CYS cc_start: 0.8604 (m) cc_final: 0.8137 (t) REVERT: R 405 ASP cc_start: 0.8639 (m-30) cc_final: 0.8340 (t0) REVERT: R 433 TRP cc_start: 0.8212 (t-100) cc_final: 0.7256 (t-100) REVERT: R 529 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8943 (tp) REVERT: R 534 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8493 (mp) REVERT: R 571 MET cc_start: 0.8721 (ttp) cc_final: 0.8334 (ttt) REVERT: X 6 ASP cc_start: 0.8650 (m-30) cc_final: 0.8090 (p0) REVERT: X 18 PHE cc_start: 0.8504 (m-80) cc_final: 0.7970 (m-80) REVERT: X 20 GLN cc_start: 0.7696 (tp40) cc_final: 0.7441 (tp40) REVERT: X 27 GLN cc_start: 0.8091 (tt0) cc_final: 0.7475 (tm-30) REVERT: X 29 MET cc_start: 0.7796 (ptm) cc_final: 0.7370 (ptt) REVERT: X 35 ARG cc_start: 0.8689 (ttt180) cc_final: 0.8258 (ttp80) REVERT: X 45 LYS cc_start: 0.9333 (mtmm) cc_final: 0.9068 (mtmm) REVERT: Y 41 MET cc_start: 0.8423 (ptm) cc_final: 0.7962 (pmm) outliers start: 82 outliers final: 62 residues processed: 338 average time/residue: 0.0971 time to fit residues: 49.2279 Evaluate side-chains 342 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 274 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 431 ILE Chi-restraints excluded: chain R residue 454 VAL Chi-restraints excluded: chain R residue 458 THR Chi-restraints excluded: chain R residue 496 LEU Chi-restraints excluded: chain R residue 502 LEU Chi-restraints excluded: chain R residue 529 LEU Chi-restraints excluded: chain R residue 530 THR Chi-restraints excluded: chain R residue 534 LEU Chi-restraints excluded: chain R residue 536 VAL Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 547 ILE Chi-restraints excluded: chain R residue 549 ILE Chi-restraints excluded: chain R residue 575 ILE Chi-restraints excluded: chain R residue 602 THR Chi-restraints excluded: chain R residue 606 VAL Chi-restraints excluded: chain R residue 610 LEU Chi-restraints excluded: chain R residue 614 ILE Chi-restraints excluded: chain R residue 637 LEU Chi-restraints excluded: chain X residue 51 LYS Chi-restraints excluded: chain X residue 53 VAL Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 38 CYS Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 42 THR Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 56 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 120 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 400 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 = 0.3970 r_free = 0.3970 target = 0.126715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.091838 restraints weight = 26875.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.095796 restraints weight = 12768.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.096947 restraints weight = 7829.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.097580 restraints weight = 6923.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.097440 restraints weight = 6364.745| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 13118 Z= 0.161 Angle : 0.721 14.008 17800 Z= 0.365 Chirality : 0.044 0.292 2038 Planarity : 0.004 0.039 2270 Dihedral : 5.744 52.185 1884 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.49 % Allowed : 19.67 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.21), residues: 1616 helix: 0.69 (0.23), residues: 508 sheet: -1.15 (0.26), residues: 344 loop : -0.19 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 88 TYR 0.024 0.001 TYR A 69 PHE 0.037 0.001 PHE B 241 TRP 0.022 0.002 TRP N 47 HIS 0.004 0.001 HIS X 90 Details of bonding type rmsd covalent geometry : bond 0.00361 (13096) covalent geometry : angle 0.71163 (17751) SS BOND : bond 0.00488 ( 17) SS BOND : angle 2.50998 ( 34) hydrogen bonds : bond 0.04089 ( 566) hydrogen bonds : angle 5.26902 ( 1599) link_NAG-ASN : bond 0.00111 ( 5) link_NAG-ASN : angle 1.79966 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 302 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4426 (ptt) cc_final: 0.2718 (mtt) REVERT: A 172 GLN cc_start: 0.8362 (pm20) cc_final: 0.8023 (pp30) REVERT: A 206 ASP cc_start: 0.8119 (t0) cc_final: 0.7710 (t0) REVERT: A 241 LYS cc_start: 0.9277 (tttt) cc_final: 0.9034 (ttpt) REVERT: A 244 TRP cc_start: 0.9403 (t-100) cc_final: 0.8799 (t-100) REVERT: A 359 GLU cc_start: 0.8094 (mp0) cc_final: 0.7789 (mp0) REVERT: B 15 LYS cc_start: 0.9036 (tmmt) cc_final: 0.8753 (pptt) REVERT: B 45 MET cc_start: 0.8192 (mtt) cc_final: 0.7779 (mtp) REVERT: B 82 TRP cc_start: 0.9120 (OUTLIER) cc_final: 0.8846 (m-10) REVERT: B 99 TRP cc_start: 0.8509 (m100) cc_final: 0.8304 (m100) REVERT: B 111 TYR cc_start: 0.8383 (m-80) cc_final: 0.8012 (m-80) REVERT: B 130 GLU cc_start: 0.8548 (mt-10) cc_final: 0.7975 (pm20) REVERT: B 243 THR cc_start: 0.9081 (p) cc_final: 0.8863 (p) REVERT: B 246 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8128 (t70) REVERT: B 262 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7769 (ttp) REVERT: B 292 PHE cc_start: 0.8590 (m-10) cc_final: 0.8225 (m-10) REVERT: B 296 VAL cc_start: 0.9375 (OUTLIER) cc_final: 0.9065 (p) REVERT: B 308 LEU cc_start: 0.9037 (mt) cc_final: 0.7856 (mt) REVERT: B 325 MET cc_start: 0.8777 (mmt) cc_final: 0.8481 (mmm) REVERT: B 339 TRP cc_start: 0.8110 (m100) cc_final: 0.7248 (m100) REVERT: G 11 GLN cc_start: 0.9488 (tp40) cc_final: 0.9135 (tm-30) REVERT: G 16 VAL cc_start: 0.9519 (t) cc_final: 0.9083 (p) REVERT: G 17 GLU cc_start: 0.9023 (tp30) cc_final: 0.8456 (tp30) REVERT: G 20 LYS cc_start: 0.9366 (mttt) cc_final: 0.9128 (mttm) REVERT: G 21 MET cc_start: 0.8654 (mmm) cc_final: 0.8407 (mmm) REVERT: G 40 TYR cc_start: 0.8716 (t80) cc_final: 0.8318 (t80) REVERT: G 44 HIS cc_start: 0.8873 (m-70) cc_final: 0.8271 (m90) REVERT: G 51 LEU cc_start: 0.9056 (mt) cc_final: 0.8845 (mp) REVERT: N 34 MET cc_start: 0.8807 (mmm) cc_final: 0.8389 (mmm) REVERT: N 36 TRP cc_start: 0.8709 (m100) cc_final: 0.7348 (m100) REVERT: N 38 ARG cc_start: 0.7010 (ptm-80) cc_final: 0.6562 (ptm-80) REVERT: N 47 TRP cc_start: 0.7801 (t60) cc_final: 0.7545 (t60) REVERT: N 72 ARG cc_start: 0.7781 (ptm160) cc_final: 0.7349 (ptm160) REVERT: N 85 SER cc_start: 0.8480 (m) cc_final: 0.7930 (p) REVERT: N 87 LYS cc_start: 0.9200 (ptpt) cc_final: 0.8803 (ptpp) REVERT: N 109 ASP cc_start: 0.6135 (m-30) cc_final: 0.5918 (m-30) REVERT: N 117 TYR cc_start: 0.7825 (m-10) cc_final: 0.7523 (m-80) REVERT: R 102 GLU cc_start: 0.8058 (mp0) cc_final: 0.7682 (mp0) REVERT: R 108 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8371 (p) REVERT: R 157 ASP cc_start: 0.9120 (m-30) cc_final: 0.8693 (m-30) REVERT: R 170 GLN cc_start: 0.6870 (tp40) cc_final: 0.6509 (tp40) REVERT: R 200 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8339 (t) REVERT: R 228 ASP cc_start: 0.8110 (t0) cc_final: 0.7780 (t0) REVERT: R 230 SER cc_start: 0.9322 (m) cc_final: 0.9009 (t) REVERT: R 240 TYR cc_start: 0.8394 (t80) cc_final: 0.8185 (t80) REVERT: R 359 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.8084 (m-80) REVERT: R 372 LEU cc_start: 0.9470 (tt) cc_final: 0.9190 (tp) REVERT: R 377 ASN cc_start: 0.7458 (m-40) cc_final: 0.7090 (m-40) REVERT: R 384 LEU cc_start: 0.9322 (mt) cc_final: 0.9037 (mt) REVERT: R 399 CYS cc_start: 0.8623 (m) cc_final: 0.8159 (t) REVERT: R 405 ASP cc_start: 0.8611 (m-30) cc_final: 0.8340 (t0) REVERT: R 410 LEU cc_start: 0.9215 (mt) cc_final: 0.8876 (tt) REVERT: R 433 TRP cc_start: 0.8166 (t-100) cc_final: 0.7327 (t-100) REVERT: R 529 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8917 (tp) REVERT: R 534 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8475 (mp) REVERT: R 571 MET cc_start: 0.8689 (ttp) cc_final: 0.8343 (ttt) REVERT: X 6 ASP cc_start: 0.8569 (m-30) cc_final: 0.8026 (p0) REVERT: X 18 PHE cc_start: 0.8480 (m-80) cc_final: 0.8079 (m-80) REVERT: X 20 GLN cc_start: 0.7683 (tp40) cc_final: 0.7418 (tp40) REVERT: X 27 GLN cc_start: 0.8097 (tt0) cc_final: 0.7553 (tm-30) REVERT: X 29 MET cc_start: 0.7928 (ptm) cc_final: 0.7346 (ptt) REVERT: X 35 ARG cc_start: 0.8877 (ttt180) cc_final: 0.8611 (ttp-170) REVERT: X 42 ARG cc_start: 0.8496 (mmp-170) cc_final: 0.8291 (mmp-170) REVERT: X 45 LYS cc_start: 0.9327 (mtmm) cc_final: 0.9051 (mtmm) REVERT: X 51 LYS cc_start: 0.9647 (OUTLIER) cc_final: 0.9228 (mmmt) REVERT: Y 41 MET cc_start: 0.8409 (ptm) cc_final: 0.7937 (pmm) REVERT: Y 61 ASP cc_start: 0.8672 (p0) cc_final: 0.8436 (p0) outliers start: 77 outliers final: 53 residues processed: 347 average time/residue: 0.0993 time to fit residues: 51.0467 Evaluate side-chains 347 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 284 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 359 TYR Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 431 ILE Chi-restraints excluded: chain R residue 454 VAL Chi-restraints excluded: chain R residue 458 THR Chi-restraints excluded: chain R residue 496 LEU Chi-restraints excluded: chain R residue 502 LEU Chi-restraints excluded: chain R residue 529 LEU Chi-restraints excluded: chain R residue 530 THR Chi-restraints excluded: chain R residue 534 LEU Chi-restraints excluded: chain R residue 536 VAL Chi-restraints excluded: chain R residue 547 ILE Chi-restraints excluded: chain R residue 549 ILE Chi-restraints excluded: chain R residue 575 ILE Chi-restraints excluded: chain R residue 602 THR Chi-restraints excluded: chain R residue 606 VAL Chi-restraints excluded: chain R residue 610 LEU Chi-restraints excluded: chain R residue 637 LEU Chi-restraints excluded: chain X residue 51 LYS Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 38 CYS Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 128 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 142 optimal weight: 20.0000 chunk 16 optimal weight: 0.0050 chunk 89 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS G 18 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 400 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 = 0.3979 r_free = 0.3979 target = 0.127223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.092133 restraints weight = 26980.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.096339 restraints weight = 13023.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.096733 restraints weight = 8173.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.097298 restraints weight = 7370.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.097362 restraints weight = 6778.523| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 13118 Z= 0.160 Angle : 0.734 16.979 17800 Z= 0.369 Chirality : 0.044 0.178 2038 Planarity : 0.004 0.039 2270 Dihedral : 5.706 50.947 1884 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.92 % Allowed : 21.10 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -0.24 (0.21), residues: 1616 helix: 0.72 (0.23), residues: 508 sheet: -1.14 (0.27), residues: 338 loop : -0.13 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 13 TYR 0.023 0.001 TYR A 69 PHE 0.029 0.001 PHE N 29 TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00364 (13096) covalent geometry : angle 0.72041 (17751) SS BOND : bond 0.00568 ( 17) SS BOND : angle 3.07971 ( 34) hydrogen bonds : bond 0.04015 ( 566) hydrogen bonds : angle 5.23644 ( 1599) link_NAG-ASN : bond 0.00108 ( 5) link_NAG-ASN : angle 1.69636 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 305 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4345 (ptt) cc_final: 0.2682 (mtt) REVERT: A 172 GLN cc_start: 0.8391 (pm20) cc_final: 0.8054 (pp30) REVERT: A 206 ASP cc_start: 0.8092 (t0) cc_final: 0.7661 (t0) REVERT: A 224 VAL cc_start: 0.9426 (t) cc_final: 0.9156 (m) REVERT: A 241 LYS cc_start: 0.9242 (tttt) cc_final: 0.8998 (ttpt) REVERT: A 244 TRP cc_start: 0.9451 (t-100) cc_final: 0.8798 (t-100) REVERT: A 359 GLU cc_start: 0.8130 (mp0) cc_final: 0.7807 (mp0) REVERT: B 82 TRP cc_start: 0.9130 (OUTLIER) cc_final: 0.8840 (m-10) REVERT: B 111 TYR cc_start: 0.8318 (m-80) cc_final: 0.8005 (m-80) REVERT: B 118 ASP cc_start: 0.8403 (t0) cc_final: 0.8092 (p0) REVERT: B 130 GLU cc_start: 0.8578 (mt-10) cc_final: 0.7982 (pm20) REVERT: B 243 THR cc_start: 0.9116 (p) cc_final: 0.8868 (p) REVERT: B 246 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8110 (t70) REVERT: B 292 PHE cc_start: 0.8537 (m-10) cc_final: 0.8207 (m-10) REVERT: B 296 VAL cc_start: 0.9365 (OUTLIER) cc_final: 0.8988 (p) REVERT: B 308 LEU cc_start: 0.8957 (mt) cc_final: 0.7797 (mt) REVERT: B 325 MET cc_start: 0.8712 (mmt) cc_final: 0.8405 (mmm) REVERT: B 339 TRP cc_start: 0.8105 (m100) cc_final: 0.7314 (m100) REVERT: G 11 GLN cc_start: 0.9515 (tp40) cc_final: 0.9099 (tm-30) REVERT: G 17 GLU cc_start: 0.9074 (tp30) cc_final: 0.8393 (tp30) REVERT: G 20 LYS cc_start: 0.9332 (mttt) cc_final: 0.9121 (mttm) REVERT: G 21 MET cc_start: 0.8621 (mmm) cc_final: 0.8403 (mmm) REVERT: G 40 TYR cc_start: 0.8721 (t80) cc_final: 0.8301 (t80) REVERT: G 44 HIS cc_start: 0.8827 (m-70) cc_final: 0.8235 (m90) REVERT: G 48 ASP cc_start: 0.8495 (t0) cc_final: 0.8242 (t0) REVERT: G 51 LEU cc_start: 0.9057 (mt) cc_final: 0.8857 (mp) REVERT: N 34 MET cc_start: 0.8735 (mmm) cc_final: 0.8294 (mmm) REVERT: N 36 TRP cc_start: 0.8683 (m100) cc_final: 0.7396 (m100) REVERT: N 38 ARG cc_start: 0.7052 (ptm-80) cc_final: 0.6557 (ptm-80) REVERT: N 46 GLU cc_start: 0.7604 (mp0) cc_final: 0.7372 (mp0) REVERT: N 85 SER cc_start: 0.8497 (m) cc_final: 0.7936 (p) REVERT: N 87 LYS cc_start: 0.9250 (ptpt) cc_final: 0.8893 (ptpp) REVERT: N 109 ASP cc_start: 0.6561 (m-30) cc_final: 0.6232 (m-30) REVERT: N 117 TYR cc_start: 0.7939 (m-10) cc_final: 0.7655 (m-80) REVERT: R 79 GLU cc_start: 0.8037 (pp20) cc_final: 0.7771 (pp20) REVERT: R 102 GLU cc_start: 0.8012 (mp0) cc_final: 0.7663 (mp0) REVERT: R 108 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8378 (p) REVERT: R 157 ASP cc_start: 0.8949 (m-30) cc_final: 0.8691 (m-30) REVERT: R 200 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8138 (t) REVERT: R 228 ASP cc_start: 0.8041 (t0) cc_final: 0.7739 (t0) REVERT: R 230 SER cc_start: 0.9309 (m) cc_final: 0.8983 (t) REVERT: R 240 TYR cc_start: 0.8351 (t80) cc_final: 0.8143 (t80) REVERT: R 359 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.8076 (m-80) REVERT: R 375 MET cc_start: 0.6979 (tmm) cc_final: 0.6729 (tmm) REVERT: R 384 LEU cc_start: 0.9323 (mt) cc_final: 0.9052 (mt) REVERT: R 399 CYS cc_start: 0.8474 (m) cc_final: 0.8158 (t) REVERT: R 410 LEU cc_start: 0.9230 (mt) cc_final: 0.8910 (tt) REVERT: R 433 TRP cc_start: 0.8131 (t-100) cc_final: 0.7269 (t-100) REVERT: R 529 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8879 (tp) REVERT: R 534 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8478 (mp) REVERT: R 559 MET cc_start: 0.5451 (mpp) cc_final: 0.3954 (mpp) REVERT: R 571 MET cc_start: 0.8549 (ttp) cc_final: 0.8348 (ttt) REVERT: X 6 ASP cc_start: 0.8577 (m-30) cc_final: 0.8155 (p0) REVERT: X 18 PHE cc_start: 0.8068 (m-80) cc_final: 0.7818 (m-80) REVERT: X 27 GLN cc_start: 0.8125 (tt0) cc_final: 0.7438 (tm-30) REVERT: X 29 MET cc_start: 0.7987 (ptm) cc_final: 0.7419 (ptt) REVERT: X 35 ARG cc_start: 0.8915 (ttt180) cc_final: 0.8636 (ttp-170) REVERT: X 42 ARG cc_start: 0.8465 (mmp-170) cc_final: 0.8246 (mmp-170) REVERT: X 45 LYS cc_start: 0.9328 (mtmm) cc_final: 0.9017 (mtmm) REVERT: X 51 LYS cc_start: 0.9607 (OUTLIER) cc_final: 0.9264 (mmmt) REVERT: Y 41 MET cc_start: 0.8396 (ptm) cc_final: 0.7922 (pmm) REVERT: Y 61 ASP cc_start: 0.8642 (p0) cc_final: 0.8407 (p0) outliers start: 69 outliers final: 49 residues processed: 347 average time/residue: 0.0986 time to fit residues: 51.1495 Evaluate side-chains 345 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 287 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 359 TYR Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 431 ILE Chi-restraints excluded: chain R residue 458 THR Chi-restraints excluded: chain R residue 496 LEU Chi-restraints excluded: chain R residue 502 LEU Chi-restraints excluded: chain R residue 529 LEU Chi-restraints excluded: chain R residue 530 THR Chi-restraints excluded: chain R residue 534 LEU Chi-restraints excluded: chain R residue 536 VAL Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 547 ILE Chi-restraints excluded: chain R residue 549 ILE Chi-restraints excluded: chain R residue 575 ILE Chi-restraints excluded: chain R residue 602 THR Chi-restraints excluded: chain R residue 606 VAL Chi-restraints excluded: chain R residue 610 LEU Chi-restraints excluded: chain R residue 614 ILE Chi-restraints excluded: chain R residue 637 LEU Chi-restraints excluded: chain X residue 51 LYS Chi-restraints excluded: chain X residue 53 VAL Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 38 CYS Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 42 THR Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 110 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 147 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS G 18 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 400 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 = 0.3906 r_free = 0.3906 target = 0.122371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.088960 restraints weight = 27391.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.090058 restraints weight = 12918.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.092151 restraints weight = 9495.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.092272 restraints weight = 8001.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.092281 restraints weight = 7306.242| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 13118 Z= 0.340 Angle : 0.867 17.133 17800 Z= 0.448 Chirality : 0.050 0.238 2038 Planarity : 0.005 0.070 2270 Dihedral : 6.138 51.439 1884 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.77 % Allowed : 21.03 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.21), residues: 1616 helix: 0.50 (0.23), residues: 507 sheet: -1.30 (0.26), residues: 348 loop : -0.28 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 46 TYR 0.025 0.002 TYR A 69 PHE 0.039 0.003 PHE B 241 TRP 0.025 0.003 TRP B 99 HIS 0.008 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00739 (13096) covalent geometry : angle 0.85507 (17751) SS BOND : bond 0.00727 ( 17) SS BOND : angle 3.21350 ( 34) hydrogen bonds : bond 0.04563 ( 566) hydrogen bonds : angle 5.56291 ( 1599) link_NAG-ASN : bond 0.00237 ( 5) link_NAG-ASN : angle 1.88133 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 271 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4496 (ptt) cc_final: 0.2762 (mtt) REVERT: A 206 ASP cc_start: 0.8286 (t0) cc_final: 0.7856 (t0) REVERT: A 241 LYS cc_start: 0.9252 (tttt) cc_final: 0.8987 (ttpt) REVERT: A 244 TRP cc_start: 0.9440 (t-100) cc_final: 0.8740 (t-100) REVERT: A 359 GLU cc_start: 0.8229 (mp0) cc_final: 0.7982 (mp0) REVERT: B 82 TRP cc_start: 0.9197 (OUTLIER) cc_final: 0.8916 (m-10) REVERT: B 105 TYR cc_start: 0.9219 (OUTLIER) cc_final: 0.8535 (t80) REVERT: B 111 TYR cc_start: 0.8499 (m-80) cc_final: 0.7891 (m-80) REVERT: B 120 ILE cc_start: 0.9050 (mt) cc_final: 0.8807 (mt) REVERT: B 130 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7979 (pm20) REVERT: B 204 CYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7887 (t) REVERT: B 243 THR cc_start: 0.9112 (p) cc_final: 0.8908 (p) REVERT: B 246 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8174 (t70) REVERT: B 292 PHE cc_start: 0.8724 (m-10) cc_final: 0.8321 (m-10) REVERT: B 296 VAL cc_start: 0.9214 (OUTLIER) cc_final: 0.8852 (m) REVERT: B 308 LEU cc_start: 0.9026 (mt) cc_final: 0.7802 (mt) REVERT: B 325 MET cc_start: 0.8790 (mmt) cc_final: 0.8464 (mmm) REVERT: B 337 LYS cc_start: 0.8712 (mttt) cc_final: 0.7878 (mtpp) REVERT: B 339 TRP cc_start: 0.8157 (m100) cc_final: 0.7373 (m100) REVERT: G 11 GLN cc_start: 0.9509 (tp40) cc_final: 0.9055 (tm-30) REVERT: G 17 GLU cc_start: 0.9081 (tp30) cc_final: 0.8013 (tp30) REVERT: G 18 GLN cc_start: 0.9061 (tp-100) cc_final: 0.8759 (tp40) REVERT: G 21 MET cc_start: 0.8753 (mmm) cc_final: 0.7945 (mmm) REVERT: G 40 TYR cc_start: 0.8884 (t80) cc_final: 0.8570 (t80) REVERT: G 44 HIS cc_start: 0.8945 (m-70) cc_final: 0.8251 (m90) REVERT: N 29 PHE cc_start: 0.8366 (t80) cc_final: 0.8155 (t80) REVERT: N 34 MET cc_start: 0.8613 (mmm) cc_final: 0.8346 (mmm) REVERT: N 36 TRP cc_start: 0.8807 (m100) cc_final: 0.7441 (m100) REVERT: N 38 ARG cc_start: 0.7231 (ptm-80) cc_final: 0.6790 (ptm-80) REVERT: N 72 ARG cc_start: 0.8109 (ptm160) cc_final: 0.7760 (tmm-80) REVERT: N 85 SER cc_start: 0.8617 (m) cc_final: 0.8044 (p) REVERT: N 87 LYS cc_start: 0.9321 (ptpt) cc_final: 0.8966 (ptpp) REVERT: N 109 ASP cc_start: 0.6735 (m-30) cc_final: 0.6451 (m-30) REVERT: N 117 TYR cc_start: 0.8119 (m-10) cc_final: 0.7834 (m-80) REVERT: R 102 GLU cc_start: 0.8123 (mp0) cc_final: 0.7813 (mp0) REVERT: R 108 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8471 (p) REVERT: R 228 ASP cc_start: 0.8200 (t0) cc_final: 0.7954 (t0) REVERT: R 230 SER cc_start: 0.9363 (m) cc_final: 0.9047 (t) REVERT: R 240 TYR cc_start: 0.8470 (t80) cc_final: 0.8173 (t80) REVERT: R 375 MET cc_start: 0.6848 (tmm) cc_final: 0.6552 (tmm) REVERT: R 377 ASN cc_start: 0.7609 (m-40) cc_final: 0.7177 (t0) REVERT: R 399 CYS cc_start: 0.8589 (m) cc_final: 0.8339 (t) REVERT: R 433 TRP cc_start: 0.8276 (t-100) cc_final: 0.7354 (t-100) REVERT: R 529 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9004 (tp) REVERT: R 534 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8500 (mp) REVERT: R 559 MET cc_start: 0.5603 (mpp) cc_final: 0.4227 (mpp) REVERT: R 571 MET cc_start: 0.8627 (ttp) cc_final: 0.8378 (ttt) REVERT: R 617 CYS cc_start: 0.8476 (m) cc_final: 0.8263 (p) REVERT: X 6 ASP cc_start: 0.8526 (m-30) cc_final: 0.8045 (p0) REVERT: X 27 GLN cc_start: 0.8237 (tt0) cc_final: 0.7689 (tm-30) REVERT: X 29 MET cc_start: 0.7948 (ptm) cc_final: 0.7351 (ptt) REVERT: X 35 ARG cc_start: 0.8924 (ttt180) cc_final: 0.8693 (ttp-170) REVERT: X 42 ARG cc_start: 0.8556 (mmp-170) cc_final: 0.8032 (mmm160) REVERT: X 45 LYS cc_start: 0.9364 (mtmm) cc_final: 0.8927 (mtmm) REVERT: Y 41 MET cc_start: 0.8558 (ptm) cc_final: 0.8022 (pmm) outliers start: 81 outliers final: 59 residues processed: 317 average time/residue: 0.1042 time to fit residues: 48.9398 Evaluate side-chains 323 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 256 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 431 ILE Chi-restraints excluded: chain R residue 496 LEU Chi-restraints excluded: chain R residue 502 LEU Chi-restraints excluded: chain R residue 529 LEU Chi-restraints excluded: chain R residue 530 THR Chi-restraints excluded: chain R residue 534 LEU Chi-restraints excluded: chain R residue 536 VAL Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 547 ILE Chi-restraints excluded: chain R residue 549 ILE Chi-restraints excluded: chain R residue 567 ILE Chi-restraints excluded: chain R residue 575 ILE Chi-restraints excluded: chain R residue 606 VAL Chi-restraints excluded: chain R residue 610 LEU Chi-restraints excluded: chain R residue 614 ILE Chi-restraints excluded: chain R residue 637 LEU Chi-restraints excluded: chain X residue 53 VAL Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain Y residue 9 CYS Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 38 CYS Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 42 THR Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 154 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 400 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 = 0.3948 r_free = 0.3948 target = 0.124904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.089517 restraints weight = 27298.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.093552 restraints weight = 13673.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.094782 restraints weight = 8300.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.095401 restraints weight = 7272.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.095347 restraints weight = 6692.703| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 13118 Z= 0.207 Angle : 0.800 14.733 17800 Z= 0.406 Chirality : 0.047 0.320 2038 Planarity : 0.005 0.078 2270 Dihedral : 5.995 52.229 1884 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.85 % Allowed : 22.95 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -0.47 (0.21), residues: 1616 helix: 0.48 (0.23), residues: 507 sheet: -1.29 (0.26), residues: 343 loop : -0.22 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG Y 95 TYR 0.024 0.001 TYR A 69 PHE 0.038 0.002 PHE X 18 TRP 0.021 0.002 TRP B 99 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00462 (13096) covalent geometry : angle 0.79032 (17751) SS BOND : bond 0.00530 ( 17) SS BOND : angle 2.73652 ( 34) hydrogen bonds : bond 0.04286 ( 566) hydrogen bonds : angle 5.45643 ( 1599) link_NAG-ASN : bond 0.00175 ( 5) link_NAG-ASN : angle 1.73430 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 277 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4617 (ptt) cc_final: 0.2763 (mtt) REVERT: A 172 GLN cc_start: 0.8488 (pm20) cc_final: 0.8103 (pp30) REVERT: A 241 LYS cc_start: 0.9240 (tttt) cc_final: 0.9017 (ttpt) REVERT: A 244 TRP cc_start: 0.9457 (t-100) cc_final: 0.8748 (t-100) REVERT: A 359 GLU cc_start: 0.8138 (mp0) cc_final: 0.7846 (mp0) REVERT: B 15 LYS cc_start: 0.8958 (tmmt) cc_final: 0.8609 (pptt) REVERT: B 23 LYS cc_start: 0.9337 (ptpp) cc_final: 0.9085 (ptpp) REVERT: B 82 TRP cc_start: 0.9125 (OUTLIER) cc_final: 0.8865 (m-10) REVERT: B 105 TYR cc_start: 0.9169 (OUTLIER) cc_final: 0.8558 (t80) REVERT: B 111 TYR cc_start: 0.8416 (m-80) cc_final: 0.7837 (m-80) REVERT: B 130 GLU cc_start: 0.8494 (mt-10) cc_final: 0.7991 (pm20) REVERT: B 204 CYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7613 (t) REVERT: B 243 THR cc_start: 0.9075 (p) cc_final: 0.8850 (p) REVERT: B 246 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8252 (t70) REVERT: B 292 PHE cc_start: 0.8691 (m-10) cc_final: 0.8332 (m-10) REVERT: B 296 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8746 (m) REVERT: B 325 MET cc_start: 0.8710 (mmt) cc_final: 0.8419 (mmm) REVERT: B 337 LYS cc_start: 0.8689 (mttt) cc_final: 0.7934 (mtpp) REVERT: B 339 TRP cc_start: 0.8192 (m100) cc_final: 0.7765 (m100) REVERT: G 11 GLN cc_start: 0.9502 (tp40) cc_final: 0.9057 (tm-30) REVERT: G 13 ARG cc_start: 0.9486 (mtp85) cc_final: 0.9133 (mtm-85) REVERT: G 17 GLU cc_start: 0.9068 (tp30) cc_final: 0.8632 (tp30) REVERT: G 40 TYR cc_start: 0.8772 (t80) cc_final: 0.8425 (t80) REVERT: G 44 HIS cc_start: 0.8824 (m-70) cc_final: 0.8162 (m90) REVERT: N 29 PHE cc_start: 0.8395 (t80) cc_final: 0.8023 (t80) REVERT: N 34 MET cc_start: 0.8573 (mmm) cc_final: 0.8123 (mmm) REVERT: N 36 TRP cc_start: 0.8785 (m100) cc_final: 0.7643 (m100) REVERT: N 38 ARG cc_start: 0.7259 (ptm-80) cc_final: 0.6693 (ptm-80) REVERT: N 46 GLU cc_start: 0.7736 (mp0) cc_final: 0.7526 (mp0) REVERT: N 72 ARG cc_start: 0.8113 (ptm160) cc_final: 0.7893 (tmm-80) REVERT: N 85 SER cc_start: 0.8556 (m) cc_final: 0.7989 (p) REVERT: N 87 LYS cc_start: 0.9334 (ptpt) cc_final: 0.8969 (ptpp) REVERT: N 109 ASP cc_start: 0.6597 (m-30) cc_final: 0.6363 (m-30) REVERT: N 117 TYR cc_start: 0.8031 (m-10) cc_final: 0.7691 (m-80) REVERT: R 102 GLU cc_start: 0.8078 (mp0) cc_final: 0.7708 (mp0) REVERT: R 108 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8348 (p) REVERT: R 200 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8199 (t) REVERT: R 230 SER cc_start: 0.9309 (m) cc_final: 0.8954 (t) REVERT: R 240 TYR cc_start: 0.8409 (t80) cc_final: 0.8185 (t80) REVERT: R 375 MET cc_start: 0.6942 (tmm) cc_final: 0.6667 (tmm) REVERT: R 377 ASN cc_start: 0.7492 (m-40) cc_final: 0.7184 (t0) REVERT: R 398 MET cc_start: 0.8449 (tpp) cc_final: 0.8165 (tpp) REVERT: R 399 CYS cc_start: 0.8513 (m) cc_final: 0.8242 (t) REVERT: R 405 ASP cc_start: 0.8748 (m-30) cc_final: 0.8411 (t70) REVERT: R 410 LEU cc_start: 0.9288 (mt) cc_final: 0.8947 (tt) REVERT: R 433 TRP cc_start: 0.8188 (t-100) cc_final: 0.7254 (t-100) REVERT: R 529 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8926 (tp) REVERT: R 534 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8481 (mp) REVERT: R 559 MET cc_start: 0.5269 (mpp) cc_final: 0.3808 (mpp) REVERT: R 571 MET cc_start: 0.8530 (ttp) cc_final: 0.8300 (ttt) REVERT: R 617 CYS cc_start: 0.8300 (m) cc_final: 0.8027 (p) REVERT: X 6 ASP cc_start: 0.8499 (m-30) cc_final: 0.8147 (p0) REVERT: X 20 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7737 (tp40) REVERT: X 27 GLN cc_start: 0.8202 (tt0) cc_final: 0.7693 (tm-30) REVERT: X 29 MET cc_start: 0.7960 (ptm) cc_final: 0.7335 (ptt) REVERT: X 35 ARG cc_start: 0.8793 (ttt180) cc_final: 0.8584 (ttp-170) REVERT: X 42 ARG cc_start: 0.8439 (mmp-170) cc_final: 0.7783 (mmm160) REVERT: X 45 LYS cc_start: 0.9349 (mtmm) cc_final: 0.8822 (mtmm) REVERT: Y 41 MET cc_start: 0.8464 (ptm) cc_final: 0.7992 (pmm) outliers start: 68 outliers final: 50 residues processed: 318 average time/residue: 0.0956 time to fit residues: 45.8156 Evaluate side-chains 323 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 264 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 431 ILE Chi-restraints excluded: chain R residue 496 LEU Chi-restraints excluded: chain R residue 502 LEU Chi-restraints excluded: chain R residue 529 LEU Chi-restraints excluded: chain R residue 530 THR Chi-restraints excluded: chain R residue 534 LEU Chi-restraints excluded: chain R residue 536 VAL Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 547 ILE Chi-restraints excluded: chain R residue 549 ILE Chi-restraints excluded: chain R residue 575 ILE Chi-restraints excluded: chain R residue 606 VAL Chi-restraints excluded: chain R residue 610 LEU Chi-restraints excluded: chain R residue 614 ILE Chi-restraints excluded: chain R residue 637 LEU Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain Y residue 9 CYS Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 38 CYS Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 42 THR Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 130 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 139 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 35 ASN B 75 GLN G 18 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 400 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 = 0.4012 r_free = 0.4012 target = 0.129152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.093929 restraints weight = 27194.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.097148 restraints weight = 14285.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.100157 restraints weight = 8699.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.100284 restraints weight = 6877.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.100339 restraints weight = 6184.353| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 13118 Z= 0.141 Angle : 0.771 13.792 17800 Z= 0.384 Chirality : 0.045 0.224 2038 Planarity : 0.005 0.055 2270 Dihedral : 5.698 51.125 1884 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.78 % Allowed : 25.09 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -0.36 (0.21), residues: 1616 helix: 0.58 (0.23), residues: 508 sheet: -1.29 (0.26), residues: 340 loop : -0.12 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Y 95 TYR 0.022 0.001 TYR A 69 PHE 0.031 0.001 PHE B 241 TRP 0.022 0.002 TRP N 47 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00316 (13096) covalent geometry : angle 0.76365 (17751) SS BOND : bond 0.00401 ( 17) SS BOND : angle 2.41110 ( 34) hydrogen bonds : bond 0.04060 ( 566) hydrogen bonds : angle 5.27798 ( 1599) link_NAG-ASN : bond 0.00158 ( 5) link_NAG-ASN : angle 1.59019 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 296 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4484 (ptt) cc_final: 0.2641 (mtt) REVERT: A 172 GLN cc_start: 0.8478 (pm20) cc_final: 0.8094 (pp30) REVERT: A 241 LYS cc_start: 0.9245 (tttt) cc_final: 0.9030 (ttpt) REVERT: A 244 TRP cc_start: 0.9403 (t-100) cc_final: 0.8632 (t-100) REVERT: A 359 GLU cc_start: 0.8147 (mp0) cc_final: 0.7747 (mp0) REVERT: B 15 LYS cc_start: 0.9099 (tmmt) cc_final: 0.8796 (pptt) REVERT: B 23 LYS cc_start: 0.9391 (ptpp) cc_final: 0.9167 (ptpp) REVERT: B 82 TRP cc_start: 0.9091 (OUTLIER) cc_final: 0.8796 (m-10) REVERT: B 105 TYR cc_start: 0.9163 (OUTLIER) cc_final: 0.8644 (t80) REVERT: B 111 TYR cc_start: 0.8311 (m-80) cc_final: 0.7825 (m-80) REVERT: B 130 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8002 (pm20) REVERT: B 204 CYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7424 (t) REVERT: B 226 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6661 (mm-30) REVERT: B 246 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8173 (t70) REVERT: B 292 PHE cc_start: 0.8500 (m-10) cc_final: 0.8245 (m-10) REVERT: B 308 LEU cc_start: 0.8673 (mt) cc_final: 0.7596 (mt) REVERT: B 325 MET cc_start: 0.8692 (mmt) cc_final: 0.8374 (mmm) REVERT: B 337 LYS cc_start: 0.8667 (mttt) cc_final: 0.8026 (mtpp) REVERT: B 339 TRP cc_start: 0.8059 (m100) cc_final: 0.7130 (m100) REVERT: G 11 GLN cc_start: 0.9485 (tp40) cc_final: 0.9104 (tm-30) REVERT: G 13 ARG cc_start: 0.9507 (mtp85) cc_final: 0.9168 (mtm-85) REVERT: G 17 GLU cc_start: 0.9031 (tp30) cc_final: 0.8494 (tp30) REVERT: G 21 MET cc_start: 0.8629 (mmm) cc_final: 0.8240 (mmm) REVERT: G 32 LYS cc_start: 0.9227 (pttt) cc_final: 0.9007 (ptpp) REVERT: G 40 TYR cc_start: 0.8689 (t80) cc_final: 0.8271 (t80) REVERT: G 44 HIS cc_start: 0.8760 (m-70) cc_final: 0.8109 (m90) REVERT: N 29 PHE cc_start: 0.8280 (t80) cc_final: 0.8006 (t80) REVERT: N 36 TRP cc_start: 0.8746 (m100) cc_final: 0.7530 (m100) REVERT: N 38 ARG cc_start: 0.7180 (ptm-80) cc_final: 0.6730 (ptm-80) REVERT: N 46 GLU cc_start: 0.7679 (mp0) cc_final: 0.7460 (mp0) REVERT: N 85 SER cc_start: 0.8548 (m) cc_final: 0.7994 (p) REVERT: N 87 LYS cc_start: 0.9320 (ptpt) cc_final: 0.8985 (ptpp) REVERT: R 102 GLU cc_start: 0.8021 (mp0) cc_final: 0.7598 (mp0) REVERT: R 230 SER cc_start: 0.9264 (m) cc_final: 0.8918 (t) REVERT: R 240 TYR cc_start: 0.8345 (t80) cc_final: 0.8124 (t80) REVERT: R 375 MET cc_start: 0.6859 (tmm) cc_final: 0.6572 (tmm) REVERT: R 377 ASN cc_start: 0.7252 (m-40) cc_final: 0.6743 (t0) REVERT: R 398 MET cc_start: 0.8512 (tpp) cc_final: 0.8206 (tpp) REVERT: R 399 CYS cc_start: 0.8456 (m) cc_final: 0.8218 (m) REVERT: R 405 ASP cc_start: 0.8585 (m-30) cc_final: 0.7838 (t0) REVERT: R 433 TRP cc_start: 0.8111 (t-100) cc_final: 0.7400 (t-100) REVERT: R 509 MET cc_start: 0.7756 (mmm) cc_final: 0.7473 (mmm) REVERT: R 529 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8837 (tp) REVERT: R 582 MET cc_start: 0.8098 (tmm) cc_final: 0.7861 (tmm) REVERT: R 617 CYS cc_start: 0.8110 (m) cc_final: 0.7821 (p) REVERT: X 6 ASP cc_start: 0.8580 (m-30) cc_final: 0.8254 (p0) REVERT: X 27 GLN cc_start: 0.8105 (tt0) cc_final: 0.7491 (tm-30) REVERT: X 29 MET cc_start: 0.7990 (ptm) cc_final: 0.7382 (ptt) REVERT: X 37 TYR cc_start: 0.8856 (p90) cc_final: 0.8584 (p90) REVERT: X 42 ARG cc_start: 0.8416 (mmp-170) cc_final: 0.8105 (mmp-170) REVERT: X 45 LYS cc_start: 0.9355 (mtmm) cc_final: 0.8964 (mtmm) REVERT: X 47 MET cc_start: 0.7949 (mmm) cc_final: 0.7467 (mmm) REVERT: Y 41 MET cc_start: 0.8300 (ptm) cc_final: 0.7956 (pmm) outliers start: 39 outliers final: 31 residues processed: 321 average time/residue: 0.0952 time to fit residues: 45.8929 Evaluate side-chains 319 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 283 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 496 LEU Chi-restraints excluded: chain R residue 502 LEU Chi-restraints excluded: chain R residue 529 LEU Chi-restraints excluded: chain R residue 536 VAL Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 549 ILE Chi-restraints excluded: chain R residue 637 LEU Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain Y residue 9 CYS Chi-restraints excluded: chain Y residue 38 CYS Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 123 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 400 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 = 0.4002 r_free = 0.4002 target = 0.128573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.093890 restraints weight = 27412.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.097963 restraints weight = 13627.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.098673 restraints weight = 8426.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.099270 restraints weight = 7525.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.099383 restraints weight = 6897.642| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 13118 Z= 0.146 Angle : 0.772 14.094 17800 Z= 0.386 Chirality : 0.045 0.218 2038 Planarity : 0.005 0.055 2270 Dihedral : 5.605 49.345 1884 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.99 % Allowed : 25.37 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -0.28 (0.21), residues: 1616 helix: 0.61 (0.23), residues: 507 sheet: -1.18 (0.27), residues: 339 loop : -0.09 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 129 TYR 0.022 0.001 TYR A 69 PHE 0.025 0.001 PHE B 241 TRP 0.020 0.002 TRP N 47 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00333 (13096) covalent geometry : angle 0.76435 (17751) SS BOND : bond 0.00419 ( 17) SS BOND : angle 2.36344 ( 34) hydrogen bonds : bond 0.04033 ( 566) hydrogen bonds : angle 5.26711 ( 1599) link_NAG-ASN : bond 0.00142 ( 5) link_NAG-ASN : angle 1.71792 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2257.87 seconds wall clock time: 39 minutes 47.94 seconds (2387.94 seconds total)