Starting phenix.real_space_refine on Thu Mar 5 00:15:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x3x_22036/03_2026/6x3x_22036.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x3x_22036/03_2026/6x3x_22036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x3x_22036/03_2026/6x3x_22036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x3x_22036/03_2026/6x3x_22036.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x3x_22036/03_2026/6x3x_22036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x3x_22036/03_2026/6x3x_22036.map" } resolution = 2.92 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 97 5.16 5 Cl 4 4.86 5 C 11289 2.51 5 N 2837 2.21 5 O 3243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17470 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2729 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "I" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'ABU': 1, 'DZP': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'ABU': 1, 'DZP': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'DZP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'DZP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.15, per 1000 atoms: 0.24 Number of scatterers: 17470 At special positions: 0 Unit cell: (145.775, 147.441, 98.294, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 97 16.00 O 3243 8.00 N 2837 7.00 C 11289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.06 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " " MAN G 8 " - " MAN G 9 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 10 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 404 " - " ASN A 80 " " NAG C 404 " - " ASN C 80 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN D 111 " " NAG N 1 " - " ASN E 208 " Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 655.3 milliseconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 27 sheets defined 32.0% alpha, 40.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 Processing helix chain 'A' and resid 70 through 73 removed outlier: 3.664A pdb=" N SER A 73 " --> pdb=" O LYS A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 73' Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 139 through 143 removed outlier: 4.556A pdb=" N ARG A 142 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 238 removed outlier: 3.734A pdb=" N LEU A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N MET A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix Processing helix chain 'A' and resid 239 through 242 Processing helix chain 'A' and resid 246 through 270 removed outlier: 3.787A pdb=" N ARG A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 309 removed outlier: 4.837A pdb=" N PHE A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER A 308 " --> pdb=" O TYR A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 340 removed outlier: 3.660A pdb=" N ALA A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 73 through 76 removed outlier: 4.016A pdb=" N LYS B 76 " --> pdb=" O GLU B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 73 through 76' Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.770A pdb=" N ILE B 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 223 through 230 removed outlier: 4.051A pdb=" N ILE B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 244 removed outlier: 4.177A pdb=" N SER B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 251 through 274 removed outlier: 3.626A pdb=" N ARG B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 311 Processing helix chain 'B' and resid 314 through 345 removed outlier: 3.735A pdb=" N ALA B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA B 319 " --> pdb=" O PRO B 315 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix removed outlier: 3.705A pdb=" N LEU B 345 " --> pdb=" O TRP B 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 20 removed outlier: 3.972A pdb=" N VAL C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.529A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 236 removed outlier: 5.251A pdb=" N MET C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix Processing helix chain 'C' and resid 237 through 242 removed outlier: 4.258A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 270 removed outlier: 4.134A pdb=" N ARG C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 305 removed outlier: 3.551A pdb=" N ILE C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 339 removed outlier: 3.964A pdb=" N ALA C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C 322 " --> pdb=" O ARG C 318 " (cutoff:3.500A) Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 12 through 23 removed outlier: 3.527A pdb=" N LEU D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 removed outlier: 4.054A pdb=" N LYS D 76 " --> pdb=" O GLU D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 76' Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 223 through 230 removed outlier: 3.765A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 243 Processing helix chain 'D' and resid 244 through 247 Processing helix chain 'D' and resid 251 through 275 removed outlier: 3.554A pdb=" N ARG D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 275 " --> pdb=" O ILE D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 311 Processing helix chain 'D' and resid 314 through 346 removed outlier: 3.712A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Proline residue: D 330 - end of helix Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 99 through 106 removed outlier: 4.114A pdb=" N MET E 102 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL E 103 " --> pdb=" O SER E 100 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLY E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE E 106 " --> pdb=" O VAL E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 253 removed outlier: 4.045A pdb=" N ILE E 238 " --> pdb=" O GLY E 234 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 261 through 285 removed outlier: 3.944A pdb=" N LYS E 285 " --> pdb=" O THR E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 324 removed outlier: 3.957A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 357 removed outlier: 3.875A pdb=" N ALA E 328 " --> pdb=" O GLN E 324 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LYS E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET E 331 " --> pdb=" O ARG E 327 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASP E 332 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE E 337 " --> pdb=" O SER E 333 " (cutoff:3.500A) Proline residue: E 340 - end of helix removed outlier: 3.851A pdb=" N LEU E 357 " --> pdb=" O SER E 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.646A pdb=" N ASP J 90 " --> pdb=" O THR J 87 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 87 through 91' Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.690A pdb=" N THR K 32 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83 removed outlier: 4.559A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.763A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR A 176 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A 42 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.675A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 86 removed outlier: 4.223A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 108 through 109 removed outlier: 7.242A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.241A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N LEU B 193 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 81 through 83 removed outlier: 3.729A pdb=" N LEU C 83 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.669A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N THR C 176 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE C 42 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.612A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 83 through 86 removed outlier: 4.437A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLU D 59 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 108 through 109 removed outlier: 7.295A pdb=" N GLU D 59 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.891A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.891A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.626A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ARG E 144 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ALA E 121 " --> pdb=" O ARG E 144 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.626A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N THR E 51 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N GLN E 182 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE E 53 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LYS E 184 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR E 55 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N SER E 186 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N MET E 57 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL E 188 " --> pdb=" O MET E 57 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL E 59 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL E 190 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N SER E 61 " --> pdb=" O VAL E 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 111 through 113 removed outlier: 3.683A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.828A pdb=" N MET I 11 " --> pdb=" O GLU I 104 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TYR I 49 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.828A pdb=" N MET I 11 " --> pdb=" O GLU I 104 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR I 96 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.523A pdb=" N ALA J 92 " --> pdb=" O VAL J 114 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.614A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.761A pdb=" N THR L 96 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.696A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 10 through 12 removed outlier: 4.366A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 916 hydrogen bonds defined for protein. 2613 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.22 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 4970 1.34 - 1.47: 5180 1.47 - 1.60: 7584 1.60 - 1.73: 7 1.73 - 1.87: 171 Bond restraints: 17912 Sorted by residual: bond pdb=" C5 DZP A 406 " pdb=" N15 DZP A 406 " ideal model delta sigma weight residual 1.272 1.517 -0.245 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C5 DZP C 406 " pdb=" N15 DZP C 406 " ideal model delta sigma weight residual 1.272 1.515 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C5 DZP D 404 " pdb=" N15 DZP D 404 " ideal model delta sigma weight residual 1.272 1.513 -0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C5 DZP E 403 " pdb=" N15 DZP E 403 " ideal model delta sigma weight residual 1.272 1.512 -0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C18 DZP E 403 " pdb=" N2 DZP E 403 " ideal model delta sigma weight residual 1.368 1.523 -0.155 2.00e-02 2.50e+03 6.01e+01 ... (remaining 17907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 24076 4.02 - 8.04: 254 8.04 - 12.06: 23 12.06 - 16.08: 7 16.08 - 20.10: 2 Bond angle restraints: 24362 Sorted by residual: angle pdb=" CA GLU J 42 " pdb=" CB GLU J 42 " pdb=" CG GLU J 42 " ideal model delta sigma weight residual 114.10 126.14 -12.04 2.00e+00 2.50e-01 3.62e+01 angle pdb=" CA LEU E 287 " pdb=" CB LEU E 287 " pdb=" CG LEU E 287 " ideal model delta sigma weight residual 116.30 136.40 -20.10 3.50e+00 8.16e-02 3.30e+01 angle pdb=" C CYS A 150 " pdb=" CA CYS A 150 " pdb=" CB CYS A 150 " ideal model delta sigma weight residual 109.71 120.22 -10.51 1.83e+00 2.99e-01 3.30e+01 angle pdb=" CA LYS B 78 " pdb=" CB LYS B 78 " pdb=" CG LYS B 78 " ideal model delta sigma weight residual 114.10 125.05 -10.95 2.00e+00 2.50e-01 3.00e+01 angle pdb=" C GLY C 170 " pdb=" N ASP C 171 " pdb=" CA ASP C 171 " ideal model delta sigma weight residual 121.54 130.90 -9.36 1.91e+00 2.74e-01 2.40e+01 ... (remaining 24357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.47: 10494 29.47 - 58.93: 288 58.93 - 88.40: 56 88.40 - 117.86: 27 117.86 - 147.33: 11 Dihedral angle restraints: 10876 sinusoidal: 4620 harmonic: 6256 Sorted by residual: dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 165 " pdb=" CB CYS E 165 " ideal model delta sinusoidal sigma weight residual -86.00 -13.37 -72.63 1 1.00e+01 1.00e-02 6.73e+01 dihedral pdb=" CA VAL D 64 " pdb=" C VAL D 64 " pdb=" N PHE D 65 " pdb=" CA PHE D 65 " ideal model delta harmonic sigma weight residual 180.00 154.63 25.37 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA CYS E 165 " pdb=" C CYS E 165 " pdb=" N PRO E 166 " pdb=" CA PRO E 166 " ideal model delta harmonic sigma weight residual 180.00 -155.27 -24.73 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 10873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.913: 2799 0.913 - 1.825: 6 1.825 - 2.738: 0 2.738 - 3.650: 0 3.650 - 4.563: 2 Chirality restraints: 2807 Sorted by residual: chirality pdb=" C1 MAN G 4 " pdb=" O3 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 1.12 1.28 2.00e-02 2.50e+03 4.10e+03 chirality pdb=" C1 MAN G 10 " pdb=" O3 MAN G 7 " pdb=" C2 MAN G 10 " pdb=" O5 MAN G 10 " both_signs ideal model delta sigma weight residual False 2.40 1.24 1.16 2.00e-02 2.50e+03 3.36e+03 chirality pdb=" C1 MAN G 5 " pdb=" O2 MAN G 4 " pdb=" C2 MAN G 5 " pdb=" O5 MAN G 5 " both_signs ideal model delta sigma weight residual False 2.40 1.27 1.13 2.00e-02 2.50e+03 3.19e+03 ... (remaining 2804 not shown) Planarity restraints: 3001 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.155 2.00e-02 2.50e+03 1.32e-01 2.17e+02 pdb=" C7 NAG F 1 " -0.038 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.111 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.221 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.147 2.00e-02 2.50e+03 1.22e-01 1.85e+02 pdb=" C7 NAG F 2 " 0.040 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.110 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.195 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " -0.077 2.00e-02 2.50e+03 6.30e-02 4.96e+01 pdb=" C7 NAG H 2 " 0.021 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.058 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " 0.099 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.015 2.00e-02 2.50e+03 ... (remaining 2998 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3066 2.77 - 3.30: 14995 3.30 - 3.84: 29261 3.84 - 4.37: 35234 4.37 - 4.90: 62311 Nonbonded interactions: 144867 Sorted by model distance: nonbonded pdb=" OG SER L 67 " pdb=" O ASP L 70 " model vdw 2.241 3.040 nonbonded pdb=" O ALA E 295 " pdb=" OH TYR E 350 " model vdw 2.255 3.040 nonbonded pdb=" OD2 ASP K 73 " pdb=" OG SER K 76 " model vdw 2.269 3.040 nonbonded pdb=" ND2 ASN C 243 " pdb=" OD2 ASP C 245 " model vdw 2.293 3.120 nonbonded pdb=" O VAL B 257 " pdb=" OG1 THR B 261 " model vdw 2.299 3.040 ... (remaining 144862 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 10 through 347) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 1 through 105) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 2 through 117) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.990 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 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 : 0.010 0.245 17944 Z= 0.482 Angle : 1.330 41.637 24449 Z= 0.627 Chirality : 0.146 4.563 2807 Planarity : 0.007 0.132 2994 Dihedral : 16.355 147.328 6829 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.58 % Allowed : 4.94 % Favored : 94.48 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -2.15 (0.16), residues: 2103 helix: -0.61 (0.19), residues: 584 sheet: -0.90 (0.19), residues: 615 loop : -2.33 (0.17), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 37 TYR 0.027 0.003 TYR C 157 PHE 0.052 0.004 PHE B 258 TRP 0.037 0.002 TRP A 241 HIS 0.004 0.001 HIS E 156 Details of bonding type rmsd covalent geometry : bond 0.00965 (17912) covalent geometry : angle 1.11034 (24362) SS BOND : bond 0.01007 ( 9) SS BOND : angle 4.44650 ( 18) hydrogen bonds : bond 0.14681 ( 817) hydrogen bonds : angle 6.21237 ( 2613) link_ALPHA1-2 : bond 0.06528 ( 3) link_ALPHA1-2 : angle 12.83913 ( 9) link_ALPHA1-3 : bond 0.06527 ( 2) link_ALPHA1-3 : angle 27.70927 ( 6) link_ALPHA1-6 : bond 0.06582 ( 2) link_ALPHA1-6 : angle 24.75990 ( 6) link_BETA1-4 : bond 0.05329 ( 9) link_BETA1-4 : angle 9.97789 ( 27) link_NAG-ASN : bond 0.00491 ( 7) link_NAG-ASN : angle 4.32997 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 487 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 ASP cc_start: 0.7643 (t70) cc_final: 0.7398 (t70) REVERT: A 231 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7691 (mp) REVERT: A 319 TRP cc_start: 0.7387 (t60) cc_final: 0.7180 (t60) REVERT: B 20 ASP cc_start: 0.7792 (m-30) cc_final: 0.7496 (m-30) REVERT: B 138 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7589 (mt-10) REVERT: B 156 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8275 (mtpt) REVERT: C 41 ASN cc_start: 0.8035 (m110) cc_final: 0.7781 (m-40) REVERT: C 215 LYS cc_start: 0.8415 (ttpp) cc_final: 0.8035 (tptt) REVERT: C 294 MET cc_start: 0.6428 (ptt) cc_final: 0.6084 (ptt) REVERT: D 83 VAL cc_start: 0.9067 (p) cc_final: 0.8826 (t) REVERT: D 126 THR cc_start: 0.8624 (t) cc_final: 0.8322 (m) REVERT: J 80 TYR cc_start: 0.8262 (m-80) cc_final: 0.7998 (m-80) REVERT: J 87 THR cc_start: 0.8599 (t) cc_final: 0.8390 (p) REVERT: L 72 THR cc_start: 0.8776 (m) cc_final: 0.8555 (p) outliers start: 11 outliers final: 7 residues processed: 496 average time/residue: 0.6715 time to fit residues: 367.6784 Evaluate side-chains 350 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 342 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 255 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0070 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 65 GLN A 113 ASN A 224 GLN B 68 GLN B 189 ASN B 229 GLN B 242 GLN B 346 ASN C 65 GLN C 148 GLN D 68 GLN E 80 GLN E 90 ASN E 128 ASN E 258 ASN J 6 GLN J 110 GLN L 42 GLN K 6 GLN K 43 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.146826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.116856 restraints weight = 20376.203| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.92 r_work: 0.3160 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17944 Z= 0.143 Angle : 0.715 25.453 24449 Z= 0.339 Chirality : 0.053 1.123 2807 Planarity : 0.004 0.040 2994 Dihedral : 14.377 149.118 2902 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.82 % Allowed : 15.35 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.95 (0.17), residues: 2103 helix: 0.63 (0.21), residues: 585 sheet: -0.43 (0.19), residues: 655 loop : -1.61 (0.19), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 40 TYR 0.030 0.001 TYR C 299 PHE 0.018 0.001 PHE B 258 TRP 0.011 0.001 TRP K 103 HIS 0.004 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00309 (17912) covalent geometry : angle 0.65181 (24362) SS BOND : bond 0.00460 ( 9) SS BOND : angle 3.41287 ( 18) hydrogen bonds : bond 0.03850 ( 817) hydrogen bonds : angle 4.71681 ( 2613) link_ALPHA1-2 : bond 0.00627 ( 3) link_ALPHA1-2 : angle 1.89887 ( 9) link_ALPHA1-3 : bond 0.00578 ( 2) link_ALPHA1-3 : angle 1.67561 ( 6) link_ALPHA1-6 : bond 0.00917 ( 2) link_ALPHA1-6 : angle 1.95728 ( 6) link_BETA1-4 : bond 0.00530 ( 9) link_BETA1-4 : angle 2.82603 ( 27) link_NAG-ASN : bond 0.00286 ( 7) link_NAG-ASN : angle 8.90249 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 364 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7840 (tmtt) REVERT: A 227 MET cc_start: 0.7606 (mmp) cc_final: 0.7201 (mmp) REVERT: A 298 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8751 (tm-30) REVERT: A 318 ARG cc_start: 0.6933 (mtp-110) cc_final: 0.6104 (ppt170) REVERT: B 20 ASP cc_start: 0.8082 (m-30) cc_final: 0.7693 (m-30) REVERT: B 88 ASN cc_start: 0.7451 (p0) cc_final: 0.7234 (p0) REVERT: B 138 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8530 (mt-10) REVERT: B 156 LYS cc_start: 0.8944 (mtmm) cc_final: 0.8611 (mtpt) REVERT: B 236 MET cc_start: 0.8132 (mmt) cc_final: 0.7843 (mmp) REVERT: B 249 ARG cc_start: 0.8038 (mtm-85) cc_final: 0.7837 (mtm180) REVERT: B 301 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7430 (tt) REVERT: C 17 ASP cc_start: 0.8234 (m-30) cc_final: 0.7925 (m-30) REVERT: C 40 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.7852 (mpt) REVERT: C 49 MET cc_start: 0.6567 (pp-130) cc_final: 0.6357 (pp-130) REVERT: C 89 ASP cc_start: 0.8314 (m-30) cc_final: 0.8084 (m-30) REVERT: C 215 LYS cc_start: 0.8559 (ttpp) cc_final: 0.8120 (tptt) REVERT: C 245 ASP cc_start: 0.7736 (p0) cc_final: 0.7244 (m-30) REVERT: D 83 VAL cc_start: 0.9367 (p) cc_final: 0.8920 (t) REVERT: D 93 LYS cc_start: 0.8319 (mmpt) cc_final: 0.7925 (mmmt) REVERT: D 338 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8192 (tp) REVERT: E 189 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: E 211 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: E 334 TYR cc_start: 0.7670 (m-10) cc_final: 0.7381 (m-10) REVERT: I 11 MET cc_start: 0.7353 (ptm) cc_final: 0.7089 (ptp) REVERT: J 43 GLN cc_start: 0.7885 (mt0) cc_final: 0.7611 (mt0) REVERT: J 80 TYR cc_start: 0.8577 (m-80) cc_final: 0.8296 (m-80) REVERT: J 82 GLN cc_start: 0.8508 (tt0) cc_final: 0.7568 (tp40) REVERT: J 84 SER cc_start: 0.7575 (p) cc_final: 0.7222 (m) REVERT: J 87 THR cc_start: 0.8387 (t) cc_final: 0.8100 (p) REVERT: L 72 THR cc_start: 0.8977 (m) cc_final: 0.8745 (p) outliers start: 72 outliers final: 28 residues processed: 396 average time/residue: 0.6329 time to fit residues: 278.0225 Evaluate side-chains 366 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 331 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain K residue 71 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 35 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 180 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 201 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 332 ASN D 314 GLN E 69 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.147290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.118395 restraints weight = 20873.683| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.80 r_work: 0.3152 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17944 Z= 0.126 Angle : 0.632 22.380 24449 Z= 0.303 Chirality : 0.048 1.037 2807 Planarity : 0.004 0.034 2994 Dihedral : 13.404 154.801 2892 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.04 % Allowed : 17.05 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.27 (0.18), residues: 2103 helix: 1.20 (0.21), residues: 585 sheet: -0.05 (0.19), residues: 661 loop : -1.21 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 68 TYR 0.025 0.001 TYR C 299 PHE 0.015 0.001 PHE B 258 TRP 0.010 0.001 TRP K 103 HIS 0.003 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00275 (17912) covalent geometry : angle 0.58971 (24362) SS BOND : bond 0.00605 ( 9) SS BOND : angle 2.55596 ( 18) hydrogen bonds : bond 0.03466 ( 817) hydrogen bonds : angle 4.38469 ( 2613) link_ALPHA1-2 : bond 0.00535 ( 3) link_ALPHA1-2 : angle 1.63005 ( 9) link_ALPHA1-3 : bond 0.00650 ( 2) link_ALPHA1-3 : angle 1.34624 ( 6) link_ALPHA1-6 : bond 0.00542 ( 2) link_ALPHA1-6 : angle 1.72053 ( 6) link_BETA1-4 : bond 0.00928 ( 9) link_BETA1-4 : angle 3.20400 ( 27) link_NAG-ASN : bond 0.00306 ( 7) link_NAG-ASN : angle 6.38646 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 345 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 49 MET cc_start: 0.6823 (ptt) cc_final: 0.5798 (pp-130) REVERT: A 52 GLU cc_start: 0.7382 (mp0) cc_final: 0.7040 (mp0) REVERT: A 163 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8001 (m-30) REVERT: A 227 MET cc_start: 0.7511 (mmp) cc_final: 0.7234 (mmp) REVERT: A 234 ILE cc_start: 0.8366 (mt) cc_final: 0.8166 (mp) REVERT: A 298 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8633 (tm-30) REVERT: A 318 ARG cc_start: 0.7076 (mtp-110) cc_final: 0.6120 (ppt170) REVERT: A 324 PHE cc_start: 0.7297 (m-10) cc_final: 0.6999 (m-80) REVERT: B 138 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8537 (mt-10) REVERT: B 156 LYS cc_start: 0.8948 (mtmm) cc_final: 0.8608 (mtpt) REVERT: B 236 MET cc_start: 0.8241 (mmt) cc_final: 0.7930 (mmp) REVERT: B 301 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7398 (tt) REVERT: C 17 ASP cc_start: 0.8252 (m-30) cc_final: 0.7963 (m-30) REVERT: C 40 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.7872 (mpt) REVERT: C 89 ASP cc_start: 0.8370 (m-30) cc_final: 0.8136 (m-30) REVERT: C 215 LYS cc_start: 0.8602 (ttpp) cc_final: 0.8110 (tptt) REVERT: C 245 ASP cc_start: 0.7821 (p0) cc_final: 0.7447 (m-30) REVERT: D 83 VAL cc_start: 0.9393 (OUTLIER) cc_final: 0.8894 (t) REVERT: D 93 LYS cc_start: 0.8377 (mmpt) cc_final: 0.7981 (mmmt) REVERT: D 246 TRP cc_start: 0.8872 (m100) cc_final: 0.8508 (m-90) REVERT: D 338 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8242 (tp) REVERT: E 105 LYS cc_start: 0.8581 (mttp) cc_final: 0.8341 (mmtp) REVERT: E 189 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: E 197 ARG cc_start: 0.8419 (mmm-85) cc_final: 0.8188 (mmm-85) REVERT: E 214 LYS cc_start: 0.8601 (mppt) cc_final: 0.8375 (mppt) REVERT: E 334 TYR cc_start: 0.7736 (m-10) cc_final: 0.7462 (m-10) REVERT: I 11 MET cc_start: 0.7243 (ptm) cc_final: 0.7028 (ptp) REVERT: J 43 GLN cc_start: 0.7812 (mt0) cc_final: 0.7571 (mt0) REVERT: J 80 TYR cc_start: 0.8617 (m-80) cc_final: 0.8196 (m-80) REVERT: J 82 GLN cc_start: 0.8521 (tt0) cc_final: 0.7609 (tp40) REVERT: J 87 THR cc_start: 0.8377 (t) cc_final: 0.8086 (p) REVERT: L 72 THR cc_start: 0.8977 (m) cc_final: 0.8716 (p) REVERT: K 43 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.7154 (mp10) REVERT: K 90 ASP cc_start: 0.7586 (m-30) cc_final: 0.6362 (p0) outliers start: 76 outliers final: 31 residues processed: 375 average time/residue: 0.6409 time to fit residues: 267.4468 Evaluate side-chains 365 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 326 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain K residue 43 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 0.3980 chunk 68 optimal weight: 0.0070 chunk 169 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 201 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 229 GLN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN D 151 HIS D 190 GLN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN K 5 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.144540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.115572 restraints weight = 20845.524| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.80 r_work: 0.3086 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17944 Z= 0.166 Angle : 0.623 12.580 24449 Z= 0.304 Chirality : 0.044 0.394 2807 Planarity : 0.004 0.032 2994 Dihedral : 12.910 154.204 2892 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.62 % Allowed : 18.00 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.03 (0.18), residues: 2103 helix: 1.48 (0.21), residues: 581 sheet: 0.09 (0.19), residues: 646 loop : -0.98 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 323 TYR 0.024 0.002 TYR C 299 PHE 0.016 0.002 PHE B 258 TRP 0.013 0.001 TRP C 241 HIS 0.005 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00382 (17912) covalent geometry : angle 0.59501 (24362) SS BOND : bond 0.00605 ( 9) SS BOND : angle 2.57514 ( 18) hydrogen bonds : bond 0.03514 ( 817) hydrogen bonds : angle 4.34672 ( 2613) link_ALPHA1-2 : bond 0.00495 ( 3) link_ALPHA1-2 : angle 1.59452 ( 9) link_ALPHA1-3 : bond 0.00852 ( 2) link_ALPHA1-3 : angle 1.32462 ( 6) link_ALPHA1-6 : bond 0.00322 ( 2) link_ALPHA1-6 : angle 1.98827 ( 6) link_BETA1-4 : bond 0.00948 ( 9) link_BETA1-4 : angle 2.87862 ( 27) link_NAG-ASN : bond 0.00198 ( 7) link_NAG-ASN : angle 4.77443 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 337 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.6750 (ptt) cc_final: 0.5803 (pp-130) REVERT: A 294 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7970 (mmm) REVERT: A 298 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8705 (tm-30) REVERT: A 318 ARG cc_start: 0.7185 (mtp-110) cc_final: 0.6189 (ppt170) REVERT: B 138 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8624 (mt-10) REVERT: B 156 LYS cc_start: 0.8941 (mtmm) cc_final: 0.8588 (mtpt) REVERT: B 236 MET cc_start: 0.8257 (mmt) cc_final: 0.7961 (mmp) REVERT: B 258 PHE cc_start: 0.6815 (OUTLIER) cc_final: 0.4512 (t80) REVERT: B 301 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7515 (tt) REVERT: B 327 ILE cc_start: 0.8123 (mt) cc_final: 0.7819 (mm) REVERT: C 17 ASP cc_start: 0.8292 (m-30) cc_final: 0.8005 (m-30) REVERT: C 215 LYS cc_start: 0.8591 (ttpp) cc_final: 0.8084 (tptt) REVERT: C 243 ASN cc_start: 0.7412 (t0) cc_final: 0.7079 (t0) REVERT: C 245 ASP cc_start: 0.7851 (p0) cc_final: 0.7493 (m-30) REVERT: C 318 ARG cc_start: 0.7608 (mtp85) cc_final: 0.7237 (mtt-85) REVERT: D 93 LYS cc_start: 0.8453 (mmpt) cc_final: 0.8138 (mmpt) REVERT: D 213 MET cc_start: 0.8865 (mmm) cc_final: 0.8385 (mtm) REVERT: D 246 TRP cc_start: 0.8920 (m100) cc_final: 0.8536 (m-90) REVERT: D 338 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8267 (tp) REVERT: E 189 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7457 (mt-10) REVERT: E 211 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: E 334 TYR cc_start: 0.7777 (m-10) cc_final: 0.7485 (m-10) REVERT: J 43 GLN cc_start: 0.7726 (mt0) cc_final: 0.7506 (mt0) REVERT: J 80 TYR cc_start: 0.8671 (m-80) cc_final: 0.8283 (m-80) REVERT: J 82 GLN cc_start: 0.8477 (tt0) cc_final: 0.7632 (tp40) REVERT: J 87 THR cc_start: 0.8373 (t) cc_final: 0.8101 (p) REVERT: L 72 THR cc_start: 0.9019 (m) cc_final: 0.8736 (p) outliers start: 87 outliers final: 51 residues processed: 378 average time/residue: 0.6231 time to fit residues: 262.4952 Evaluate side-chains 384 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 326 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 135 ASN Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 71 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 182 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 190 GLN B 229 GLN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN E 69 ASN E 163 HIS ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116963 restraints weight = 20592.365| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.80 r_work: 0.3137 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17944 Z= 0.123 Angle : 0.572 11.171 24449 Z= 0.281 Chirality : 0.043 0.234 2807 Planarity : 0.004 0.042 2994 Dihedral : 12.631 155.401 2892 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.46 % Allowed : 18.91 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.18), residues: 2103 helix: 1.76 (0.22), residues: 577 sheet: 0.16 (0.19), residues: 656 loop : -0.79 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 323 TYR 0.026 0.001 TYR A 299 PHE 0.014 0.001 PHE B 258 TRP 0.013 0.001 TRP C 241 HIS 0.002 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00274 (17912) covalent geometry : angle 0.55038 (24362) SS BOND : bond 0.00344 ( 9) SS BOND : angle 2.25298 ( 18) hydrogen bonds : bond 0.03257 ( 817) hydrogen bonds : angle 4.18230 ( 2613) link_ALPHA1-2 : bond 0.00539 ( 3) link_ALPHA1-2 : angle 1.46965 ( 9) link_ALPHA1-3 : bond 0.01038 ( 2) link_ALPHA1-3 : angle 1.21108 ( 6) link_ALPHA1-6 : bond 0.00305 ( 2) link_ALPHA1-6 : angle 1.81283 ( 6) link_BETA1-4 : bond 0.00601 ( 9) link_BETA1-4 : angle 2.07336 ( 27) link_NAG-ASN : bond 0.00713 ( 7) link_NAG-ASN : angle 4.13761 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 347 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.6736 (ptt) cc_final: 0.5851 (pp-130) REVERT: A 52 GLU cc_start: 0.7411 (mp0) cc_final: 0.7014 (mp0) REVERT: A 148 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.6570 (mm-40) REVERT: A 163 ASP cc_start: 0.8844 (m-30) cc_final: 0.8579 (m-30) REVERT: A 196 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8350 (pttm) REVERT: A 294 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8038 (mmm) REVERT: A 298 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8627 (tm-30) REVERT: A 318 ARG cc_start: 0.7120 (mtp-110) cc_final: 0.6247 (ppt170) REVERT: B 138 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8627 (mt-10) REVERT: B 156 LYS cc_start: 0.8934 (mtmm) cc_final: 0.8580 (mtpt) REVERT: B 236 MET cc_start: 0.8278 (mmt) cc_final: 0.7944 (mmp) REVERT: B 258 PHE cc_start: 0.6731 (OUTLIER) cc_final: 0.4387 (t80) REVERT: B 301 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7582 (tt) REVERT: B 327 ILE cc_start: 0.8154 (mt) cc_final: 0.7862 (mm) REVERT: C 17 ASP cc_start: 0.8265 (m-30) cc_final: 0.7954 (m-30) REVERT: C 215 LYS cc_start: 0.8602 (ttpp) cc_final: 0.8079 (tptt) REVERT: C 243 ASN cc_start: 0.7400 (t0) cc_final: 0.6945 (t0) REVERT: C 245 ASP cc_start: 0.7847 (p0) cc_final: 0.7534 (m-30) REVERT: C 318 ARG cc_start: 0.7639 (mtp85) cc_final: 0.7333 (mtt-85) REVERT: D 93 LYS cc_start: 0.8458 (mmpt) cc_final: 0.8056 (mmmt) REVERT: D 246 TRP cc_start: 0.8893 (m100) cc_final: 0.8533 (m-90) REVERT: D 338 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8266 (tp) REVERT: E 189 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7379 (mt-10) REVERT: E 334 TYR cc_start: 0.7797 (m-10) cc_final: 0.7542 (m-10) REVERT: J 82 GLN cc_start: 0.8473 (tt0) cc_final: 0.7624 (tp40) REVERT: J 87 THR cc_start: 0.8350 (t) cc_final: 0.8069 (p) REVERT: L 72 THR cc_start: 0.9009 (m) cc_final: 0.8705 (p) REVERT: L 104 GLU cc_start: 0.3447 (OUTLIER) cc_final: 0.2947 (mt-10) REVERT: K 43 GLN cc_start: 0.7472 (mt0) cc_final: 0.7239 (mp10) outliers start: 84 outliers final: 46 residues processed: 388 average time/residue: 0.6467 time to fit residues: 279.0470 Evaluate side-chains 386 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 331 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain K residue 71 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 106 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 185 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 52 optimal weight: 0.0170 chunk 63 optimal weight: 0.0470 chunk 42 optimal weight: 1.9990 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 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 = 0.3655 r_free = 0.3655 target = 0.146573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117506 restraints weight = 20619.416| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.78 r_work: 0.3152 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17944 Z= 0.106 Angle : 0.551 9.663 24449 Z= 0.271 Chirality : 0.042 0.273 2807 Planarity : 0.004 0.036 2994 Dihedral : 12.351 156.294 2890 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.09 % Allowed : 19.81 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.55 (0.18), residues: 2103 helix: 1.95 (0.22), residues: 577 sheet: 0.37 (0.20), residues: 630 loop : -0.66 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 85 TYR 0.022 0.001 TYR L 49 PHE 0.014 0.001 PHE B 258 TRP 0.015 0.001 TRP C 241 HIS 0.002 0.000 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00231 (17912) covalent geometry : angle 0.53171 (24362) SS BOND : bond 0.00268 ( 9) SS BOND : angle 1.88439 ( 18) hydrogen bonds : bond 0.03071 ( 817) hydrogen bonds : angle 4.04678 ( 2613) link_ALPHA1-2 : bond 0.00530 ( 3) link_ALPHA1-2 : angle 1.46809 ( 9) link_ALPHA1-3 : bond 0.01097 ( 2) link_ALPHA1-3 : angle 1.17206 ( 6) link_ALPHA1-6 : bond 0.00326 ( 2) link_ALPHA1-6 : angle 1.81802 ( 6) link_BETA1-4 : bond 0.00704 ( 9) link_BETA1-4 : angle 1.96875 ( 27) link_NAG-ASN : bond 0.00340 ( 7) link_NAG-ASN : angle 3.96095 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 339 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.6863 (ptt) cc_final: 0.5903 (pp-130) REVERT: A 52 GLU cc_start: 0.7326 (mp0) cc_final: 0.6899 (mp0) REVERT: A 148 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.6060 (mm-40) REVERT: A 163 ASP cc_start: 0.8749 (m-30) cc_final: 0.8365 (m-30) REVERT: A 196 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8327 (pttm) REVERT: A 294 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.8001 (mmm) REVERT: A 298 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8653 (tm-30) REVERT: A 318 ARG cc_start: 0.7187 (mtp-110) cc_final: 0.6213 (ppt170) REVERT: B 78 LYS cc_start: 0.8311 (mmpt) cc_final: 0.8104 (mmpt) REVERT: B 138 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8608 (mt-10) REVERT: B 156 LYS cc_start: 0.8877 (mtmm) cc_final: 0.8530 (mtpt) REVERT: B 190 GLN cc_start: 0.8774 (tt0) cc_final: 0.8437 (tt0) REVERT: B 236 MET cc_start: 0.8320 (mmt) cc_final: 0.8030 (mmp) REVERT: B 258 PHE cc_start: 0.6688 (OUTLIER) cc_final: 0.4339 (t80) REVERT: B 301 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7535 (tt) REVERT: B 327 ILE cc_start: 0.8099 (mt) cc_final: 0.7864 (mm) REVERT: C 21 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7233 (ttmm) REVERT: C 40 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.7882 (mpt) REVERT: C 86 ARG cc_start: 0.8544 (mtm110) cc_final: 0.8304 (mtm180) REVERT: C 215 LYS cc_start: 0.8585 (ttpp) cc_final: 0.8073 (tptt) REVERT: C 243 ASN cc_start: 0.7452 (t0) cc_final: 0.6863 (t0) REVERT: C 245 ASP cc_start: 0.7758 (p0) cc_final: 0.7307 (m-30) REVERT: C 318 ARG cc_start: 0.7593 (mtp85) cc_final: 0.7245 (mtt-85) REVERT: D 93 LYS cc_start: 0.8472 (mmpt) cc_final: 0.8065 (mmmt) REVERT: D 204 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7855 (mm-40) REVERT: D 246 TRP cc_start: 0.8883 (m100) cc_final: 0.8544 (m-90) REVERT: D 323 ARG cc_start: 0.7690 (ttp-170) cc_final: 0.6854 (mtp-110) REVERT: D 338 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8297 (tp) REVERT: E 189 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7391 (mt-10) REVERT: E 211 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: E 334 TYR cc_start: 0.7794 (m-10) cc_final: 0.7530 (m-10) REVERT: J 82 GLN cc_start: 0.8492 (tt0) cc_final: 0.7629 (tp40) REVERT: J 87 THR cc_start: 0.8265 (t) cc_final: 0.7985 (p) REVERT: L 72 THR cc_start: 0.8961 (m) cc_final: 0.8697 (p) REVERT: L 104 GLU cc_start: 0.3493 (OUTLIER) cc_final: 0.3060 (mt-10) REVERT: K 43 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7117 (mt0) REVERT: K 90 ASP cc_start: 0.7511 (m-30) cc_final: 0.6671 (p0) outliers start: 77 outliers final: 40 residues processed: 374 average time/residue: 0.6402 time to fit residues: 265.7287 Evaluate side-chains 383 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 330 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 163 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 chunk 144 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 125 optimal weight: 0.1980 chunk 49 optimal weight: 0.3980 chunk 150 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN E 69 ASN E 90 ASN E 135 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN K 5 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.143263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.114261 restraints weight = 20656.168| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.78 r_work: 0.3059 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17944 Z= 0.173 Angle : 0.612 10.975 24449 Z= 0.301 Chirality : 0.044 0.236 2807 Planarity : 0.004 0.044 2994 Dihedral : 12.401 154.295 2889 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.41 % Allowed : 19.60 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.18), residues: 2103 helix: 1.87 (0.22), residues: 581 sheet: 0.13 (0.19), residues: 670 loop : -0.48 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 323 TYR 0.022 0.002 TYR L 49 PHE 0.014 0.002 PHE E 236 TRP 0.023 0.001 TRP C 241 HIS 0.004 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00403 (17912) covalent geometry : angle 0.59170 (24362) SS BOND : bond 0.00376 ( 9) SS BOND : angle 2.22489 ( 18) hydrogen bonds : bond 0.03498 ( 817) hydrogen bonds : angle 4.22231 ( 2613) link_ALPHA1-2 : bond 0.00483 ( 3) link_ALPHA1-2 : angle 1.61710 ( 9) link_ALPHA1-3 : bond 0.01154 ( 2) link_ALPHA1-3 : angle 1.33421 ( 6) link_ALPHA1-6 : bond 0.00173 ( 2) link_ALPHA1-6 : angle 2.19921 ( 6) link_BETA1-4 : bond 0.00566 ( 9) link_BETA1-4 : angle 1.78139 ( 27) link_NAG-ASN : bond 0.00574 ( 7) link_NAG-ASN : angle 4.34490 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 341 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8097 (mpt) REVERT: A 49 MET cc_start: 0.6855 (ptt) cc_final: 0.5941 (pp-130) REVERT: A 163 ASP cc_start: 0.8840 (m-30) cc_final: 0.8481 (m-30) REVERT: A 196 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8299 (pttm) REVERT: A 294 MET cc_start: 0.8326 (mmm) cc_final: 0.8018 (mmm) REVERT: A 298 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8705 (tm-30) REVERT: A 318 ARG cc_start: 0.7225 (mtp-110) cc_final: 0.6253 (ppt170) REVERT: B 37 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7722 (ptt180) REVERT: B 138 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8628 (mt-10) REVERT: B 156 LYS cc_start: 0.8926 (mtmm) cc_final: 0.8615 (mtpt) REVERT: B 236 MET cc_start: 0.8289 (mmt) cc_final: 0.8012 (mmp) REVERT: B 258 PHE cc_start: 0.6792 (OUTLIER) cc_final: 0.4401 (t80) REVERT: B 301 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7539 (tt) REVERT: B 327 ILE cc_start: 0.8100 (mt) cc_final: 0.7842 (mm) REVERT: C 17 ASP cc_start: 0.8384 (m-30) cc_final: 0.8108 (m-30) REVERT: C 215 LYS cc_start: 0.8594 (ttpp) cc_final: 0.8089 (tptt) REVERT: C 245 ASP cc_start: 0.7693 (p0) cc_final: 0.7306 (m-30) REVERT: D 93 LYS cc_start: 0.8503 (mmpt) cc_final: 0.8097 (mmmt) REVERT: D 106 LYS cc_start: 0.8293 (tppt) cc_final: 0.7835 (tptp) REVERT: D 246 TRP cc_start: 0.8937 (m100) cc_final: 0.8556 (m-90) REVERT: D 338 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8311 (tp) REVERT: E 189 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: E 211 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: E 239 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7796 (mm110) REVERT: E 334 TYR cc_start: 0.7807 (m-10) cc_final: 0.7539 (m-10) REVERT: J 52 ASP cc_start: 0.8396 (t0) cc_final: 0.8125 (t0) REVERT: J 82 GLN cc_start: 0.8511 (tt0) cc_final: 0.7633 (tp40) REVERT: J 87 THR cc_start: 0.8316 (t) cc_final: 0.8039 (p) REVERT: L 72 THR cc_start: 0.9018 (m) cc_final: 0.8720 (p) REVERT: L 104 GLU cc_start: 0.3520 (OUTLIER) cc_final: 0.3049 (mt-10) REVERT: K 43 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7249 (mt0) REVERT: K 90 ASP cc_start: 0.7572 (m-30) cc_final: 0.6803 (p0) outliers start: 83 outliers final: 53 residues processed: 378 average time/residue: 0.6333 time to fit residues: 266.3196 Evaluate side-chains 393 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 329 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 108 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 158 optimal weight: 0.0470 chunk 9 optimal weight: 0.8980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN B 248 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN K 5 GLN ** K 77 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 = 0.3643 r_free = 0.3643 target = 0.145474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.116771 restraints weight = 20551.649| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.78 r_work: 0.3136 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17944 Z= 0.114 Angle : 0.567 9.608 24449 Z= 0.279 Chirality : 0.042 0.201 2807 Planarity : 0.004 0.039 2994 Dihedral : 12.213 155.677 2889 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.04 % Allowed : 20.50 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.70 (0.18), residues: 2103 helix: 2.01 (0.22), residues: 581 sheet: 0.41 (0.20), residues: 632 loop : -0.50 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 323 TYR 0.023 0.001 TYR L 49 PHE 0.015 0.001 PHE B 258 TRP 0.024 0.001 TRP C 241 HIS 0.002 0.000 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00252 (17912) covalent geometry : angle 0.54940 (24362) SS BOND : bond 0.00256 ( 9) SS BOND : angle 1.95024 ( 18) hydrogen bonds : bond 0.03149 ( 817) hydrogen bonds : angle 4.08297 ( 2613) link_ALPHA1-2 : bond 0.00517 ( 3) link_ALPHA1-2 : angle 1.51063 ( 9) link_ALPHA1-3 : bond 0.01045 ( 2) link_ALPHA1-3 : angle 1.15085 ( 6) link_ALPHA1-6 : bond 0.00221 ( 2) link_ALPHA1-6 : angle 1.84088 ( 6) link_BETA1-4 : bond 0.00563 ( 9) link_BETA1-4 : angle 1.68022 ( 27) link_NAG-ASN : bond 0.00534 ( 7) link_NAG-ASN : angle 3.92681 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 333 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.6782 (ptt) cc_final: 0.5948 (pp-130) REVERT: A 52 GLU cc_start: 0.7306 (mp0) cc_final: 0.6888 (mp0) REVERT: A 163 ASP cc_start: 0.8774 (m-30) cc_final: 0.8416 (m-30) REVERT: A 294 MET cc_start: 0.8300 (mmm) cc_final: 0.7993 (mmm) REVERT: A 298 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8721 (tm-30) REVERT: A 318 ARG cc_start: 0.7315 (mtp-110) cc_final: 0.6413 (ppt170) REVERT: B 37 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7632 (ptt180) REVERT: B 123 GLU cc_start: 0.8601 (pt0) cc_final: 0.8130 (tt0) REVERT: B 138 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8602 (mt-10) REVERT: B 156 LYS cc_start: 0.8896 (mtmm) cc_final: 0.8599 (mtpt) REVERT: B 190 GLN cc_start: 0.8779 (tt0) cc_final: 0.8442 (tt0) REVERT: B 236 MET cc_start: 0.8285 (mmt) cc_final: 0.7997 (mmp) REVERT: B 258 PHE cc_start: 0.6730 (OUTLIER) cc_final: 0.4410 (t80) REVERT: B 301 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7496 (tt) REVERT: B 327 ILE cc_start: 0.8005 (mt) cc_final: 0.7770 (mm) REVERT: C 17 ASP cc_start: 0.8350 (m-30) cc_final: 0.8071 (m-30) REVERT: C 155 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8450 (mm-30) REVERT: C 185 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8151 (tp40) REVERT: C 215 LYS cc_start: 0.8594 (ttpp) cc_final: 0.8085 (tptt) REVERT: C 245 ASP cc_start: 0.7650 (p0) cc_final: 0.7376 (m-30) REVERT: D 93 LYS cc_start: 0.8473 (mmpt) cc_final: 0.8053 (mmmt) REVERT: D 106 LYS cc_start: 0.8227 (tppt) cc_final: 0.7815 (tptp) REVERT: D 204 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7889 (mm-40) REVERT: D 209 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8295 (mt-10) REVERT: D 246 TRP cc_start: 0.8882 (m100) cc_final: 0.8531 (m-90) REVERT: D 323 ARG cc_start: 0.7682 (ttp-170) cc_final: 0.6811 (mtp-110) REVERT: D 338 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8257 (tp) REVERT: E 189 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7425 (mt-10) REVERT: E 197 ARG cc_start: 0.8451 (mmm-85) cc_final: 0.8221 (mtp85) REVERT: E 211 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: E 239 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7743 (mm110) REVERT: E 334 TYR cc_start: 0.7783 (m-10) cc_final: 0.7492 (m-10) REVERT: I 3 VAL cc_start: 0.9332 (OUTLIER) cc_final: 0.9081 (t) REVERT: J 82 GLN cc_start: 0.8488 (tt0) cc_final: 0.7620 (tp40) REVERT: J 87 THR cc_start: 0.8327 (t) cc_final: 0.8032 (p) REVERT: L 72 THR cc_start: 0.8943 (m) cc_final: 0.8659 (p) REVERT: L 104 GLU cc_start: 0.3537 (OUTLIER) cc_final: 0.3104 (mt-10) REVERT: K 43 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7150 (mt0) REVERT: K 90 ASP cc_start: 0.7630 (m-30) cc_final: 0.6801 (p0) outliers start: 76 outliers final: 45 residues processed: 366 average time/residue: 0.6299 time to fit residues: 255.9937 Evaluate side-chains 378 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 322 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 71 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 141 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 158 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN E 69 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN ** K 77 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 = 0.3637 r_free = 0.3637 target = 0.144915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.116157 restraints weight = 20741.025| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.78 r_work: 0.3098 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17944 Z= 0.132 Angle : 0.590 12.521 24449 Z= 0.289 Chirality : 0.043 0.242 2807 Planarity : 0.004 0.042 2994 Dihedral : 12.191 155.627 2889 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.82 % Allowed : 20.82 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.71 (0.18), residues: 2103 helix: 2.01 (0.21), residues: 581 sheet: 0.31 (0.20), residues: 648 loop : -0.38 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 18 TYR 0.025 0.001 TYR L 49 PHE 0.014 0.001 PHE B 258 TRP 0.029 0.001 TRP C 241 HIS 0.002 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00300 (17912) covalent geometry : angle 0.56767 (24362) SS BOND : bond 0.00290 ( 9) SS BOND : angle 1.99052 ( 18) hydrogen bonds : bond 0.03227 ( 817) hydrogen bonds : angle 4.09193 ( 2613) link_ALPHA1-2 : bond 0.00515 ( 3) link_ALPHA1-2 : angle 1.55671 ( 9) link_ALPHA1-3 : bond 0.01163 ( 2) link_ALPHA1-3 : angle 1.22254 ( 6) link_ALPHA1-6 : bond 0.00221 ( 2) link_ALPHA1-6 : angle 1.97658 ( 6) link_BETA1-4 : bond 0.00646 ( 9) link_BETA1-4 : angle 1.74279 ( 27) link_NAG-ASN : bond 0.00511 ( 7) link_NAG-ASN : angle 4.64263 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 322 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.6754 (ptt) cc_final: 0.6021 (pp-130) REVERT: A 52 GLU cc_start: 0.7329 (mp0) cc_final: 0.6900 (mp0) REVERT: A 163 ASP cc_start: 0.8778 (m-30) cc_final: 0.8476 (m-30) REVERT: A 294 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8006 (mmm) REVERT: A 298 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8732 (tm-30) REVERT: A 318 ARG cc_start: 0.7308 (mtp-110) cc_final: 0.6429 (ppt170) REVERT: B 37 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7649 (ptt180) REVERT: B 78 LYS cc_start: 0.8436 (mptt) cc_final: 0.8104 (mmpt) REVERT: B 138 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8603 (mt-10) REVERT: B 156 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8602 (mtpt) REVERT: B 236 MET cc_start: 0.8252 (mmt) cc_final: 0.7969 (mmp) REVERT: B 258 PHE cc_start: 0.6739 (OUTLIER) cc_final: 0.4400 (t80) REVERT: B 301 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7528 (tt) REVERT: B 327 ILE cc_start: 0.8031 (mt) cc_final: 0.7796 (mm) REVERT: C 17 ASP cc_start: 0.8371 (m-30) cc_final: 0.8083 (m-30) REVERT: C 155 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8488 (mm-30) REVERT: C 215 LYS cc_start: 0.8581 (ttpp) cc_final: 0.8071 (tptt) REVERT: C 245 ASP cc_start: 0.7642 (p0) cc_final: 0.7393 (m-30) REVERT: D 93 LYS cc_start: 0.8493 (mmpt) cc_final: 0.8078 (mmmt) REVERT: D 106 LYS cc_start: 0.8268 (tppt) cc_final: 0.7817 (tptp) REVERT: D 246 TRP cc_start: 0.8900 (m100) cc_final: 0.8548 (m-90) REVERT: D 323 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.6853 (mtp-110) REVERT: D 338 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8280 (tp) REVERT: E 148 ASP cc_start: 0.8395 (t70) cc_final: 0.8156 (t0) REVERT: E 189 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: E 197 ARG cc_start: 0.8472 (mmm-85) cc_final: 0.8241 (mtp85) REVERT: E 211 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: E 239 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7749 (mm110) REVERT: E 334 TYR cc_start: 0.7789 (m-10) cc_final: 0.7499 (m-10) REVERT: I 3 VAL cc_start: 0.9323 (OUTLIER) cc_final: 0.9087 (t) REVERT: J 82 GLN cc_start: 0.8456 (tt0) cc_final: 0.7694 (tp40) REVERT: J 87 THR cc_start: 0.8312 (t) cc_final: 0.8005 (p) REVERT: L 72 THR cc_start: 0.8971 (m) cc_final: 0.8685 (p) REVERT: L 104 GLU cc_start: 0.3518 (OUTLIER) cc_final: 0.3097 (mt-10) REVERT: K 43 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.7166 (mt0) REVERT: K 90 ASP cc_start: 0.7644 (m-30) cc_final: 0.6836 (p0) outliers start: 72 outliers final: 49 residues processed: 357 average time/residue: 0.6415 time to fit residues: 254.8591 Evaluate side-chains 380 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 320 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 200 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 191 optimal weight: 0.0050 chunk 68 optimal weight: 0.0010 chunk 190 optimal weight: 0.7980 chunk 179 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN B 204 GLN B 229 GLN B 248 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.115354 restraints weight = 20535.060| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.82 r_work: 0.3071 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17944 Z= 0.123 Angle : 0.582 12.623 24449 Z= 0.286 Chirality : 0.043 0.293 2807 Planarity : 0.004 0.040 2994 Dihedral : 12.152 155.927 2889 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.66 % Allowed : 21.19 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.82 (0.18), residues: 2103 helix: 2.15 (0.21), residues: 575 sheet: 0.34 (0.20), residues: 646 loop : -0.31 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 18 TYR 0.025 0.001 TYR L 49 PHE 0.014 0.001 PHE B 258 TRP 0.035 0.001 TRP C 241 HIS 0.002 0.000 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00278 (17912) covalent geometry : angle 0.56017 (24362) SS BOND : bond 0.00300 ( 9) SS BOND : angle 1.93163 ( 18) hydrogen bonds : bond 0.03167 ( 817) hydrogen bonds : angle 4.06087 ( 2613) link_ALPHA1-2 : bond 0.00499 ( 3) link_ALPHA1-2 : angle 1.55202 ( 9) link_ALPHA1-3 : bond 0.01205 ( 2) link_ALPHA1-3 : angle 1.20426 ( 6) link_ALPHA1-6 : bond 0.00233 ( 2) link_ALPHA1-6 : angle 1.91687 ( 6) link_BETA1-4 : bond 0.00556 ( 9) link_BETA1-4 : angle 1.64793 ( 27) link_NAG-ASN : bond 0.00509 ( 7) link_NAG-ASN : angle 4.55623 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 326 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.6802 (ptt) cc_final: 0.6049 (pp-130) REVERT: A 52 GLU cc_start: 0.7332 (mp0) cc_final: 0.6894 (mp0) REVERT: A 163 ASP cc_start: 0.8824 (m-30) cc_final: 0.8501 (m-30) REVERT: A 294 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.8021 (mmm) REVERT: A 318 ARG cc_start: 0.7319 (mtp-110) cc_final: 0.6417 (ppt170) REVERT: B 37 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7677 (ptt180) REVERT: B 78 LYS cc_start: 0.8396 (mptt) cc_final: 0.8070 (mmpt) REVERT: B 138 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8670 (mt-10) REVERT: B 156 LYS cc_start: 0.8913 (mtmm) cc_final: 0.8626 (mtpt) REVERT: B 190 GLN cc_start: 0.8804 (tt0) cc_final: 0.8534 (tt0) REVERT: B 236 MET cc_start: 0.8308 (mmt) cc_final: 0.8033 (mmp) REVERT: B 258 PHE cc_start: 0.6753 (OUTLIER) cc_final: 0.4438 (t80) REVERT: B 301 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7523 (tt) REVERT: B 327 ILE cc_start: 0.8060 (mt) cc_final: 0.7816 (mm) REVERT: C 155 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8479 (mm-30) REVERT: C 215 LYS cc_start: 0.8627 (ttpp) cc_final: 0.8097 (tptt) REVERT: C 245 ASP cc_start: 0.7624 (p0) cc_final: 0.7419 (m-30) REVERT: D 93 LYS cc_start: 0.8532 (mmpt) cc_final: 0.8095 (mmmt) REVERT: D 106 LYS cc_start: 0.8243 (tppt) cc_final: 0.7796 (tptp) REVERT: D 246 TRP cc_start: 0.8910 (m100) cc_final: 0.8560 (m-90) REVERT: D 323 ARG cc_start: 0.7709 (ttp-170) cc_final: 0.6856 (mtp-110) REVERT: D 338 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8291 (tp) REVERT: E 85 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7959 (ptm160) REVERT: E 105 LYS cc_start: 0.8615 (mmtp) cc_final: 0.8329 (mmtt) REVERT: E 148 ASP cc_start: 0.8470 (t70) cc_final: 0.8154 (t0) REVERT: E 189 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: E 197 ARG cc_start: 0.8478 (mmm-85) cc_final: 0.8258 (mtp85) REVERT: E 211 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: E 239 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7785 (mm110) REVERT: E 305 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8509 (mp) REVERT: E 334 TYR cc_start: 0.7801 (m-10) cc_final: 0.7497 (m-10) REVERT: I 3 VAL cc_start: 0.9303 (OUTLIER) cc_final: 0.9094 (t) REVERT: J 82 GLN cc_start: 0.8463 (tt0) cc_final: 0.7695 (tp40) REVERT: J 87 THR cc_start: 0.8286 (t) cc_final: 0.7958 (p) REVERT: L 72 THR cc_start: 0.8971 (m) cc_final: 0.8689 (p) REVERT: L 104 GLU cc_start: 0.3464 (OUTLIER) cc_final: 0.3078 (mt-10) REVERT: K 43 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.7133 (mt0) REVERT: K 90 ASP cc_start: 0.7580 (m-30) cc_final: 0.6839 (p0) outliers start: 69 outliers final: 48 residues processed: 360 average time/residue: 0.6425 time to fit residues: 256.3368 Evaluate side-chains 376 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 316 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 85 ARG Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN B 248 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 HIS E 69 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 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 = 0.3608 r_free = 0.3608 target = 0.142523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113649 restraints weight = 20762.663| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.78 r_work: 0.3054 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17944 Z= 0.187 Angle : 0.640 12.750 24449 Z= 0.315 Chirality : 0.045 0.243 2807 Planarity : 0.004 0.050 2994 Dihedral : 12.336 153.891 2889 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.56 % Allowed : 21.35 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.66 (0.18), residues: 2103 helix: 1.99 (0.21), residues: 581 sheet: 0.19 (0.20), residues: 641 loop : -0.34 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 323 TYR 0.025 0.002 TYR L 49 PHE 0.016 0.002 PHE E 236 TRP 0.045 0.002 TRP C 241 HIS 0.004 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00438 (17912) covalent geometry : angle 0.61763 (24362) SS BOND : bond 0.00379 ( 9) SS BOND : angle 2.29064 ( 18) hydrogen bonds : bond 0.03573 ( 817) hydrogen bonds : angle 4.26254 ( 2613) link_ALPHA1-2 : bond 0.00425 ( 3) link_ALPHA1-2 : angle 1.67830 ( 9) link_ALPHA1-3 : bond 0.01122 ( 2) link_ALPHA1-3 : angle 1.30751 ( 6) link_ALPHA1-6 : bond 0.00151 ( 2) link_ALPHA1-6 : angle 2.26336 ( 6) link_BETA1-4 : bond 0.00536 ( 9) link_BETA1-4 : angle 1.73353 ( 27) link_NAG-ASN : bond 0.00426 ( 7) link_NAG-ASN : angle 4.80947 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7157.21 seconds wall clock time: 122 minutes 27.40 seconds (7347.40 seconds total)