Starting phenix.real_space_refine on Thu Mar 5 00:05:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x3w_22035/03_2026/6x3w_22035.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x3w_22035/03_2026/6x3w_22035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x3w_22035/03_2026/6x3w_22035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x3w_22035/03_2026/6x3w_22035.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x3w_22035/03_2026/6x3w_22035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x3w_22035/03_2026/6x3w_22035.map" } resolution = 3.3 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: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 11235 2.51 5 N 2832 2.21 5 O 3235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 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: 17399 Number of models: 1 Model: "" Number of chains: 17 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: 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: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'ABU': 1, 'NAG': 1, 'UQA': 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'UQA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.61, per 1000 atoms: 0.21 Number of scatterers: 17399 At special positions: 0 Unit cell: (141.075, 127.875, 136.125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 97 16.00 O 3235 8.00 N 2832 7.00 C 11235 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=2.02 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=2.03 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-ASN " NAG A 404 " - " ASN A 80 " " NAG C 505 " - " ASN C 80 " " NAG D 401 " - " ASN D 111 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN E 208 " Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 530.4 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: 41 helices and 28 sheets defined 31.1% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 225 through 238 Processing helix chain 'A' and resid 239 through 242 Processing helix chain 'A' and resid 246 through 272 removed outlier: 3.880A pdb=" N ARG A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 305 Processing helix chain 'A' and resid 309 through 339 removed outlier: 4.080A pdb=" N ALA A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 314 " --> pdb=" O PRO A 310 " (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: 3.969A 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: 3.717A 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 244 removed outlier: 3.993A pdb=" N ILE B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix removed outlier: 4.117A 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 277 removed outlier: 3.658A pdb=" N ARG B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 311 Processing helix chain 'B' and resid 314 through 345 removed outlier: 3.928A pdb=" N ALA B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA B 319 " --> pdb=" O PRO B 315 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 218 through 236 removed outlier: 5.203A 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: 4.148A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 268 removed outlier: 4.373A pdb=" N ARG C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 305 Processing helix chain 'C' and resid 309 through 339 removed outlier: 4.004A pdb=" N ALA C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 3.662A 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 11 through 23 Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 223 through 230 removed outlier: 3.840A 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: 3.592A pdb=" N ARG D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 310 Processing helix chain 'D' and resid 314 through 346 removed outlier: 3.505A pdb=" N ARG D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.908A 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: 4.154A pdb=" N MET E 102 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE E 106 " --> pdb=" O VAL E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 253 removed outlier: 4.151A pdb=" N ILE E 238 " --> pdb=" O GLY E 234 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix removed outlier: 3.572A pdb=" N VAL E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 296 through 324 removed outlier: 4.394A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 357 removed outlier: 3.590A pdb=" N ALA E 328 " --> pdb=" O GLN E 324 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET E 331 " --> pdb=" O ARG E 327 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP E 332 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE E 337 " --> pdb=" O SER E 333 " (cutoff:3.500A) Proline residue: E 340 - end of helix removed outlier: 3.793A pdb=" N LEU E 357 " --> pdb=" O SER E 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.742A pdb=" N ASP J 90 " --> pdb=" O THR J 87 " (cutoff:3.500A) removed outlier: 3.939A 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: 3.716A 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: 4.573A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.396A 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: 6.928A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N THR A 176 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.662A 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: 3.816A pdb=" N CYS A 150 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.428A 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: 4.207A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.360A 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: 7.262A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.360A 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: 4.064A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.560A 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: 3.786A pdb=" N LEU C 83 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.268A 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: 6.829A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.762A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.539A 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: 4.485A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N GLU D 59 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.391A 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: 7.316A pdb=" N GLU D 59 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.391A 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: 3.925A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.036A 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: 3.925A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.648A 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: 3.794A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ARG E 144 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA E 121 " --> pdb=" O ARG E 144 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 7.040A 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: 3.794A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N THR E 51 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLN E 182 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE E 53 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS E 184 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N THR E 55 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER E 186 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N MET E 57 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL E 188 " --> pdb=" O MET E 57 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL E 59 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL E 190 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 8.578A 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: 3.617A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.448A 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: 6.435A pdb=" N MET I 11 " --> pdb=" O GLU I 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.592A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N TYR I 49 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 3.599A 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: 6.803A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.779A pdb=" N TYR J 107 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.588A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.606A pdb=" N THR L 96 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.721A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 10 through 12 removed outlier: 4.307A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 926 hydrogen bonds defined for protein. 2637 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4373 1.33 - 1.46: 4820 1.46 - 1.58: 8475 1.58 - 1.71: 0 1.71 - 1.83: 167 Bond restraints: 17835 Sorted by residual: bond pdb=" CD ABU A 405 " pdb=" OE2 ABU A 405 " ideal model delta sigma weight residual 1.250 1.333 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" CD ABU C 506 " pdb=" OE2 ABU C 506 " ideal model delta sigma weight residual 1.250 1.333 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C MET D 114 " pdb=" N PRO D 115 " ideal model delta sigma weight residual 1.332 1.374 -0.042 1.12e-02 7.97e+03 1.41e+01 bond pdb=" C VAL D 252 " pdb=" N PRO D 253 " ideal model delta sigma weight residual 1.335 1.373 -0.039 1.28e-02 6.10e+03 9.07e+00 bond pdb=" C THR E 125 " pdb=" N THR E 126 " ideal model delta sigma weight residual 1.333 1.292 0.042 1.39e-02 5.18e+03 8.99e+00 ... (remaining 17830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 23358 2.70 - 5.40: 786 5.40 - 8.10: 92 8.10 - 10.79: 16 10.79 - 13.49: 4 Bond angle restraints: 24256 Sorted by residual: angle pdb=" N ARG C 269 " pdb=" CA ARG C 269 " pdb=" C ARG C 269 " ideal model delta sigma weight residual 113.41 104.73 8.68 1.22e+00 6.72e-01 5.07e+01 angle pdb=" C THR C 271 " pdb=" N LEU C 272 " pdb=" CA LEU C 272 " ideal model delta sigma weight residual 123.96 133.94 -9.98 1.44e+00 4.82e-01 4.80e+01 angle pdb=" N ILE C 322 " pdb=" CA ILE C 322 " pdb=" C ILE C 322 " ideal model delta sigma weight residual 112.96 107.97 4.99 1.00e+00 1.00e+00 2.49e+01 angle pdb=" CA GLU C 147 " pdb=" CB GLU C 147 " pdb=" CG GLU C 147 " ideal model delta sigma weight residual 114.10 123.27 -9.17 2.00e+00 2.50e-01 2.10e+01 angle pdb=" N LEU C 152 " pdb=" CA LEU C 152 " pdb=" C LEU C 152 " ideal model delta sigma weight residual 108.34 100.95 7.39 1.64e+00 3.72e-01 2.03e+01 ... (remaining 24251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.87: 10093 21.87 - 43.73: 601 43.73 - 65.60: 64 65.60 - 87.47: 34 87.47 - 109.33: 14 Dihedral angle restraints: 10806 sinusoidal: 4550 harmonic: 6256 Sorted by residual: dihedral pdb=" CB CYS A 136 " pdb=" SG CYS A 136 " pdb=" SG CYS A 150 " pdb=" CB CYS A 150 " ideal model delta sinusoidal sigma weight residual -86.00 -9.25 -76.75 1 1.00e+01 1.00e-02 7.40e+01 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 -12.15 -73.85 1 1.00e+01 1.00e-02 6.93e+01 dihedral pdb=" CA CYS C 150 " pdb=" C CYS C 150 " pdb=" N THR C 151 " pdb=" CA THR C 151 " ideal model delta harmonic sigma weight residual -180.00 -151.89 -28.11 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 10803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.283: 2784 0.283 - 0.565: 9 0.565 - 0.848: 4 0.848 - 1.130: 1 1.130 - 1.413: 1 Chirality restraints: 2799 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.99 -1.41 2.00e-02 2.50e+03 4.99e+03 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-02 2.50e+03 1.52e+03 chirality pdb=" C1 MAN G 9 " pdb=" O2 MAN G 8 " pdb=" C2 MAN G 9 " pdb=" O5 MAN G 9 " both_signs ideal model delta sigma weight residual False 2.40 1.64 0.76 2.00e-02 2.50e+03 1.46e+03 ... (remaining 2796 not shown) Planarity restraints: 2992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " 0.193 2.00e-02 2.50e+03 1.59e-01 3.17e+02 pdb=" C7 NAG M 2 " -0.052 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " 0.140 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " -0.258 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " -0.180 2.00e-02 2.50e+03 1.53e-01 2.93e+02 pdb=" C7 NAG M 1 " 0.037 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " 0.036 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " 0.249 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " -0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " -0.129 2.00e-02 2.50e+03 1.06e-01 1.41e+02 pdb=" C7 NAG G 2 " 0.034 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " -0.096 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " 0.171 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " 0.020 2.00e-02 2.50e+03 ... (remaining 2989 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1974 2.75 - 3.29: 15879 3.29 - 3.82: 29623 3.82 - 4.36: 36151 4.36 - 4.90: 63776 Nonbonded interactions: 147403 Sorted by model distance: nonbonded pdb=" OD1 ASP E 120 " pdb=" O4 MAN G 10 " model vdw 2.211 3.040 nonbonded pdb=" OD2 ASP A 121 " pdb=" OG1 THR A 123 " model vdw 2.269 3.040 nonbonded pdb=" O ALA E 295 " pdb=" OH TYR E 350 " model vdw 2.281 3.040 nonbonded pdb=" OH TYR D 26 " pdb=" OD2 ASP D 72 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR B 99 " pdb=" OH TYR B 169 " model vdw 2.289 3.040 ... (remaining 147398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 340) selection = (chain 'C' and resid 7 through 340) } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 10 through 347) } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 2.000 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.740 Find NCS groups from input model: 0.310 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: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 : 0.008 0.168 17865 Z= 0.388 Angle : 1.259 42.964 24337 Z= 0.662 Chirality : 0.082 1.413 2799 Planarity : 0.008 0.159 2985 Dihedral : 14.582 109.332 6759 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.85 % Allowed : 6.80 % Favored : 92.35 % Cbeta Deviations : 0.05 % 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: -2.06 (0.16), residues: 2103 helix: -0.16 (0.20), residues: 581 sheet: -1.01 (0.19), residues: 623 loop : -2.41 (0.17), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 85 TYR 0.040 0.003 TYR A 157 PHE 0.031 0.004 PHE C 221 TRP 0.020 0.003 TRP K 103 HIS 0.008 0.002 HIS D 56 Details of bonding type rmsd covalent geometry : bond 0.00787 (17835) covalent geometry : angle 1.15849 (24256) SS BOND : bond 0.00551 ( 9) SS BOND : angle 4.06589 ( 18) hydrogen bonds : bond 0.14792 ( 821) hydrogen bonds : angle 5.96692 ( 2637) link_ALPHA1-2 : bond 0.02269 ( 3) link_ALPHA1-2 : angle 7.82193 ( 9) link_ALPHA1-3 : bond 0.00489 ( 2) link_ALPHA1-3 : angle 4.17328 ( 6) link_ALPHA1-6 : bond 0.00707 ( 2) link_ALPHA1-6 : angle 2.61630 ( 6) link_BETA1-4 : bond 0.04982 ( 7) link_BETA1-4 : angle 13.17379 ( 21) link_NAG-ASN : bond 0.06399 ( 7) link_NAG-ASN : angle 8.05655 ( 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 427 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 411 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 95 ASP cc_start: 0.8036 (p0) cc_final: 0.7053 (t0) REVERT: A 142 ARG cc_start: 0.7557 (mtp180) cc_final: 0.7157 (mtt180) REVERT: A 274 LYS cc_start: 0.7994 (mttt) cc_final: 0.7761 (mttm) REVERT: A 323 PHE cc_start: 0.7139 (t80) cc_final: 0.6765 (t80) REVERT: C 52 GLU cc_start: 0.7965 (mp0) cc_final: 0.7669 (mp0) REVERT: C 142 ARG cc_start: 0.7661 (mtp180) cc_final: 0.7411 (mtp85) REVERT: C 303 ASN cc_start: 0.8725 (t0) cc_final: 0.8519 (t0) REVERT: D 93 LYS cc_start: 0.8503 (tptp) cc_final: 0.7776 (tptp) REVERT: D 98 ASP cc_start: 0.8287 (p0) cc_final: 0.8048 (p0) REVERT: D 156 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8195 (mtmt) REVERT: E 296 MET cc_start: 0.7496 (ttp) cc_final: 0.7282 (ttp) REVERT: E 298 LEU cc_start: 0.8952 (tp) cc_final: 0.8721 (tt) REVERT: E 301 SER cc_start: 0.8822 (m) cc_final: 0.8179 (m) REVERT: E 305 ILE cc_start: 0.8045 (mm) cc_final: 0.7610 (mm) REVERT: E 337 ILE cc_start: 0.8683 (tp) cc_final: 0.8421 (tp) outliers start: 16 outliers final: 10 residues processed: 421 average time/residue: 0.1489 time to fit residues: 90.9150 Evaluate side-chains 340 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 330 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 274 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- 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 185 GLN A 303 ASN B 68 GLN B 142 HIS B 189 ASN B 275 ASN B 308 ASN C 41 ASN C 54 ASN C 65 GLN C 185 GLN C 303 ASN D 68 GLN D 102 HIS E 60 ASN E 128 ASN E 163 HIS E 258 ASN E 318 HIS I 79 GLN J 6 GLN L 42 GLN K 6 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.132947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.103336 restraints weight = 21330.157| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.85 r_work: 0.2853 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17865 Z= 0.207 Angle : 0.642 9.575 24337 Z= 0.326 Chirality : 0.045 0.285 2799 Planarity : 0.005 0.043 2985 Dihedral : 8.282 76.769 2830 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.39 % Allowed : 10.94 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.17), residues: 2103 helix: 0.54 (0.21), residues: 588 sheet: -0.79 (0.19), residues: 629 loop : -1.73 (0.18), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 102 TYR 0.023 0.002 TYR A 299 PHE 0.019 0.002 PHE A 221 TRP 0.010 0.001 TRP K 103 HIS 0.004 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00453 (17835) covalent geometry : angle 0.63272 (24256) SS BOND : bond 0.00232 ( 9) SS BOND : angle 2.09406 ( 18) hydrogen bonds : bond 0.03939 ( 821) hydrogen bonds : angle 4.75000 ( 2637) link_ALPHA1-2 : bond 0.00498 ( 3) link_ALPHA1-2 : angle 1.80471 ( 9) link_ALPHA1-3 : bond 0.01451 ( 2) link_ALPHA1-3 : angle 1.23504 ( 6) link_ALPHA1-6 : bond 0.00819 ( 2) link_ALPHA1-6 : angle 1.51230 ( 6) link_BETA1-4 : bond 0.00398 ( 7) link_BETA1-4 : angle 2.39793 ( 21) link_NAG-ASN : bond 0.00301 ( 7) link_NAG-ASN : angle 1.81035 ( 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 402 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 357 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 54 ASN cc_start: 0.8926 (m-40) cc_final: 0.8676 (m110) REVERT: A 142 ARG cc_start: 0.8149 (mtp180) cc_final: 0.7503 (mtt180) REVERT: A 323 PHE cc_start: 0.7097 (t80) cc_final: 0.6571 (t80) REVERT: B 17 ARG cc_start: 0.8229 (mtm-85) cc_final: 0.7819 (mtt-85) REVERT: B 142 HIS cc_start: 0.7529 (t-90) cc_final: 0.7325 (t-90) REVERT: B 202 ILE cc_start: 0.9378 (mm) cc_final: 0.9112 (mt) REVERT: B 266 MET cc_start: 0.9070 (mmm) cc_final: 0.8868 (mmm) REVERT: C 52 GLU cc_start: 0.8250 (mp0) cc_final: 0.7933 (mp0) REVERT: C 142 ARG cc_start: 0.8384 (mtp180) cc_final: 0.8071 (mtp-110) REVERT: D 93 LYS cc_start: 0.8766 (tptp) cc_final: 0.8046 (mmmm) REVERT: D 156 LYS cc_start: 0.9019 (mtmm) cc_final: 0.8757 (mtmt) REVERT: D 209 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8169 (mm-30) REVERT: D 310 PHE cc_start: 0.8531 (m-10) cc_final: 0.8170 (m-10) REVERT: E 296 MET cc_start: 0.8433 (ttp) cc_final: 0.8097 (ttp) REVERT: E 301 SER cc_start: 0.9112 (m) cc_final: 0.8755 (m) REVERT: E 305 ILE cc_start: 0.8455 (mm) cc_final: 0.7993 (mm) REVERT: E 337 ILE cc_start: 0.8774 (tp) cc_final: 0.8426 (tp) REVERT: I 13 MET cc_start: 0.5284 (OUTLIER) cc_final: 0.4842 (ppp) REVERT: J 30 LYS cc_start: 0.8656 (mtmt) cc_final: 0.8422 (mtmm) REVERT: J 80 TYR cc_start: 0.8382 (m-80) cc_final: 0.8172 (m-80) REVERT: K 5 GLN cc_start: 0.7705 (tm-30) cc_final: 0.7266 (tm-30) REVERT: K 102 ARG cc_start: 0.8615 (mmm-85) cc_final: 0.8212 (mmm-85) outliers start: 45 outliers final: 36 residues processed: 378 average time/residue: 0.1434 time to fit residues: 79.3468 Evaluate side-chains 352 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 315 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 SER 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 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 110 GLN Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 120 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 206 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 129 optimal weight: 0.0770 chunk 146 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 185 GLN A 224 GLN B 116 ASN E 200 GLN E 318 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.135128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.105302 restraints weight = 21445.434| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.88 r_work: 0.2926 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 17865 Z= 0.127 Angle : 0.559 9.610 24337 Z= 0.282 Chirality : 0.043 0.260 2799 Planarity : 0.004 0.039 2985 Dihedral : 6.803 66.255 2823 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.50 % Allowed : 12.85 % Favored : 84.65 % 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: -0.69 (0.17), residues: 2103 helix: 0.97 (0.21), residues: 594 sheet: -0.57 (0.19), residues: 624 loop : -1.30 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 141 TYR 0.023 0.001 TYR A 299 PHE 0.018 0.001 PHE D 310 TRP 0.009 0.001 TRP K 103 HIS 0.002 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00279 (17835) covalent geometry : angle 0.55213 (24256) SS BOND : bond 0.00208 ( 9) SS BOND : angle 1.79132 ( 18) hydrogen bonds : bond 0.03299 ( 821) hydrogen bonds : angle 4.35373 ( 2637) link_ALPHA1-2 : bond 0.00425 ( 3) link_ALPHA1-2 : angle 1.47355 ( 9) link_ALPHA1-3 : bond 0.01459 ( 2) link_ALPHA1-3 : angle 1.07136 ( 6) link_ALPHA1-6 : bond 0.00656 ( 2) link_ALPHA1-6 : angle 1.46582 ( 6) link_BETA1-4 : bond 0.00454 ( 7) link_BETA1-4 : angle 2.03570 ( 21) link_NAG-ASN : bond 0.00277 ( 7) link_NAG-ASN : angle 1.26790 ( 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 397 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 350 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8099 (mtp180) cc_final: 0.7461 (mtt180) REVERT: A 323 PHE cc_start: 0.7151 (t80) cc_final: 0.6549 (t80) REVERT: B 17 ARG cc_start: 0.8218 (mtm-85) cc_final: 0.7678 (mtt-85) REVERT: B 202 ILE cc_start: 0.9243 (mm) cc_final: 0.9030 (mt) REVERT: B 240 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.7730 (tp) REVERT: B 258 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7138 (t80) REVERT: B 266 MET cc_start: 0.9052 (mmm) cc_final: 0.8782 (mmm) REVERT: C 141 ARG cc_start: 0.8481 (mtt90) cc_final: 0.8238 (ttm110) REVERT: C 142 ARG cc_start: 0.8213 (mtp180) cc_final: 0.7993 (mtp-110) REVERT: D 89 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8418 (pt) REVERT: D 93 LYS cc_start: 0.8627 (tptp) cc_final: 0.7970 (mmmm) REVERT: D 156 LYS cc_start: 0.8881 (mtmm) cc_final: 0.8624 (mtmt) REVERT: D 202 ILE cc_start: 0.8890 (mt) cc_final: 0.8673 (mt) REVERT: D 266 MET cc_start: 0.8795 (mmm) cc_final: 0.8057 (mpp) REVERT: D 322 ASP cc_start: 0.8115 (t0) cc_final: 0.7788 (t0) REVERT: E 296 MET cc_start: 0.8140 (ttp) cc_final: 0.7821 (ttp) REVERT: E 301 SER cc_start: 0.9043 (m) cc_final: 0.8658 (m) REVERT: E 305 ILE cc_start: 0.8430 (mm) cc_final: 0.7976 (mm) REVERT: E 337 ILE cc_start: 0.8727 (tp) cc_final: 0.8390 (tp) REVERT: I 13 MET cc_start: 0.5139 (OUTLIER) cc_final: 0.4685 (ppp) REVERT: J 30 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8383 (mtmm) REVERT: J 46 GLU cc_start: 0.8722 (tt0) cc_final: 0.8510 (mt-10) REVERT: K 5 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7225 (tm-30) REVERT: K 102 ARG cc_start: 0.8527 (mmm-85) cc_final: 0.8148 (mmm-85) outliers start: 47 outliers final: 29 residues processed: 375 average time/residue: 0.1420 time to fit residues: 78.7368 Evaluate side-chains 352 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 319 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 144 optimal weight: 4.9990 chunk 157 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 155 optimal weight: 0.2980 chunk 60 optimal weight: 0.1980 chunk 147 optimal weight: 2.9990 chunk 136 optimal weight: 0.0980 chunk 32 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 142 HIS B 308 ASN C 41 ASN D 189 ASN E 135 ASN E 318 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.135445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.106007 restraints weight = 21386.851| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.83 r_work: 0.2899 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 17865 Z= 0.113 Angle : 0.532 9.515 24337 Z= 0.269 Chirality : 0.042 0.254 2799 Planarity : 0.004 0.036 2985 Dihedral : 6.126 57.927 2822 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.50 % Allowed : 14.13 % Favored : 83.38 % 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: -0.30 (0.18), residues: 2103 helix: 1.26 (0.21), residues: 595 sheet: -0.35 (0.19), residues: 637 loop : -1.04 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 68 TYR 0.021 0.001 TYR A 299 PHE 0.016 0.001 PHE D 310 TRP 0.009 0.001 TRP K 103 HIS 0.002 0.000 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00249 (17835) covalent geometry : angle 0.52603 (24256) SS BOND : bond 0.00132 ( 9) SS BOND : angle 1.59623 ( 18) hydrogen bonds : bond 0.03057 ( 821) hydrogen bonds : angle 4.20826 ( 2637) link_ALPHA1-2 : bond 0.00416 ( 3) link_ALPHA1-2 : angle 1.51209 ( 9) link_ALPHA1-3 : bond 0.01416 ( 2) link_ALPHA1-3 : angle 1.09924 ( 6) link_ALPHA1-6 : bond 0.00567 ( 2) link_ALPHA1-6 : angle 1.52100 ( 6) link_BETA1-4 : bond 0.00379 ( 7) link_BETA1-4 : angle 1.79861 ( 21) link_NAG-ASN : bond 0.00249 ( 7) link_NAG-ASN : angle 1.19746 ( 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 387 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 340 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8828 (ptt) REVERT: A 142 ARG cc_start: 0.8256 (mtp180) cc_final: 0.7588 (mtt180) REVERT: A 224 GLN cc_start: 0.8691 (tt0) cc_final: 0.8459 (tt0) REVERT: A 245 ASP cc_start: 0.8351 (m-30) cc_final: 0.8127 (m-30) REVERT: A 323 PHE cc_start: 0.7176 (t80) cc_final: 0.6482 (t80) REVERT: B 240 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.7689 (tp) REVERT: B 258 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7112 (t80) REVERT: B 266 MET cc_start: 0.9116 (mmm) cc_final: 0.8846 (mmm) REVERT: C 142 ARG cc_start: 0.8362 (mtp180) cc_final: 0.8081 (mtp-110) REVERT: C 163 ASP cc_start: 0.8721 (m-30) cc_final: 0.8517 (m-30) REVERT: D 21 ARG cc_start: 0.7557 (ttp-110) cc_final: 0.7274 (ttp-110) REVERT: D 93 LYS cc_start: 0.8685 (tptp) cc_final: 0.8070 (mmmm) REVERT: D 317 ARG cc_start: 0.6741 (ttt180) cc_final: 0.6480 (ttt180) REVERT: D 322 ASP cc_start: 0.8123 (t0) cc_final: 0.7839 (t0) REVERT: E 276 MET cc_start: 0.8870 (tpp) cc_final: 0.8510 (mmm) REVERT: E 296 MET cc_start: 0.8403 (ttp) cc_final: 0.8067 (ttp) REVERT: E 301 SER cc_start: 0.9076 (m) cc_final: 0.8758 (m) REVERT: E 305 ILE cc_start: 0.8498 (mm) cc_final: 0.8028 (mm) REVERT: E 337 ILE cc_start: 0.8754 (tp) cc_final: 0.8410 (tp) REVERT: E 356 TYR cc_start: 0.5491 (OUTLIER) cc_final: 0.5024 (t80) REVERT: I 13 MET cc_start: 0.5339 (OUTLIER) cc_final: 0.4895 (ppp) REVERT: J 46 GLU cc_start: 0.8898 (tt0) cc_final: 0.8651 (mt-10) REVERT: J 112 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8474 (t) REVERT: L 79 GLN cc_start: 0.7255 (mp10) cc_final: 0.6832 (mp10) REVERT: K 5 GLN cc_start: 0.7746 (tm-30) cc_final: 0.7241 (tm-30) REVERT: K 102 ARG cc_start: 0.8549 (mmm-85) cc_final: 0.8149 (mmm-85) outliers start: 47 outliers final: 30 residues processed: 366 average time/residue: 0.1320 time to fit residues: 72.6853 Evaluate side-chains 361 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 325 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 171 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 186 optimal weight: 0.0970 chunk 204 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 199 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 185 GLN B 190 GLN B 308 ASN D 116 ASN E 135 ASN E 318 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.129943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.101203 restraints weight = 21374.083| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.77 r_work: 0.2846 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17865 Z= 0.195 Angle : 0.584 9.577 24337 Z= 0.295 Chirality : 0.044 0.257 2799 Planarity : 0.004 0.041 2985 Dihedral : 5.896 55.163 2822 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.72 % Allowed : 14.39 % Favored : 81.89 % 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: -0.20 (0.18), residues: 2103 helix: 1.31 (0.21), residues: 595 sheet: -0.47 (0.19), residues: 628 loop : -0.78 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 141 TYR 0.021 0.002 TYR A 299 PHE 0.016 0.002 PHE A 221 TRP 0.010 0.001 TRP E 183 HIS 0.004 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00449 (17835) covalent geometry : angle 0.57689 (24256) SS BOND : bond 0.00228 ( 9) SS BOND : angle 1.91671 ( 18) hydrogen bonds : bond 0.03262 ( 821) hydrogen bonds : angle 4.30089 ( 2637) link_ALPHA1-2 : bond 0.00329 ( 3) link_ALPHA1-2 : angle 1.70838 ( 9) link_ALPHA1-3 : bond 0.01459 ( 2) link_ALPHA1-3 : angle 1.13216 ( 6) link_ALPHA1-6 : bond 0.00422 ( 2) link_ALPHA1-6 : angle 1.76362 ( 6) link_BETA1-4 : bond 0.00392 ( 7) link_BETA1-4 : angle 1.61113 ( 21) link_NAG-ASN : bond 0.00268 ( 7) link_NAG-ASN : angle 1.53765 ( 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 405 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 335 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8279 (mtp180) cc_final: 0.7603 (mtt180) REVERT: A 224 GLN cc_start: 0.8731 (tt0) cc_final: 0.8381 (tt0) REVERT: A 323 PHE cc_start: 0.7149 (t80) cc_final: 0.6393 (t80) REVERT: B 24 ASP cc_start: 0.7254 (t0) cc_final: 0.6689 (p0) REVERT: B 266 MET cc_start: 0.9130 (mmm) cc_final: 0.8832 (mmm) REVERT: C 142 ARG cc_start: 0.8409 (mtp180) cc_final: 0.8098 (mtp-110) REVERT: D 21 ARG cc_start: 0.7463 (ttp-110) cc_final: 0.7178 (ttp-110) REVERT: D 93 LYS cc_start: 0.8755 (tptp) cc_final: 0.8210 (mmmt) REVERT: D 310 PHE cc_start: 0.8325 (m-10) cc_final: 0.8111 (m-10) REVERT: E 296 MET cc_start: 0.8334 (ttp) cc_final: 0.7860 (ttp) REVERT: E 301 SER cc_start: 0.9095 (m) cc_final: 0.8754 (m) REVERT: E 305 ILE cc_start: 0.8471 (mm) cc_final: 0.8051 (mm) REVERT: E 337 ILE cc_start: 0.8729 (tp) cc_final: 0.8411 (tp) REVERT: E 356 TYR cc_start: 0.5638 (OUTLIER) cc_final: 0.5081 (t80) REVERT: I 13 MET cc_start: 0.5442 (OUTLIER) cc_final: 0.5047 (ppp) REVERT: I 90 GLN cc_start: 0.9361 (pp30) cc_final: 0.9123 (pp30) REVERT: J 46 GLU cc_start: 0.8846 (tt0) cc_final: 0.8558 (mt-10) REVERT: J 112 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8611 (t) REVERT: L 79 GLN cc_start: 0.7416 (mp10) cc_final: 0.7023 (mp10) REVERT: K 5 GLN cc_start: 0.7726 (tm-30) cc_final: 0.7184 (tm-30) REVERT: K 105 MET cc_start: 0.9085 (mtm) cc_final: 0.8481 (mtt) outliers start: 70 outliers final: 47 residues processed: 379 average time/residue: 0.1297 time to fit residues: 74.3393 Evaluate side-chains 358 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 308 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 88 ASN 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 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 135 ASN Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN B 308 ASN D 190 GLN E 318 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.134507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.105220 restraints weight = 21095.173| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.88 r_work: 0.2945 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17865 Z= 0.133 Angle : 0.546 9.532 24337 Z= 0.275 Chirality : 0.043 0.253 2799 Planarity : 0.004 0.040 2985 Dihedral : 5.778 56.534 2822 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.92 % Allowed : 15.67 % Favored : 81.41 % 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: -0.04 (0.18), residues: 2103 helix: 1.43 (0.21), residues: 595 sheet: -0.39 (0.19), residues: 639 loop : -0.66 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 141 TYR 0.023 0.001 TYR A 299 PHE 0.012 0.001 PHE A 221 TRP 0.008 0.001 TRP E 134 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00296 (17835) covalent geometry : angle 0.53939 (24256) SS BOND : bond 0.00114 ( 9) SS BOND : angle 1.75355 ( 18) hydrogen bonds : bond 0.03065 ( 821) hydrogen bonds : angle 4.20337 ( 2637) link_ALPHA1-2 : bond 0.00426 ( 3) link_ALPHA1-2 : angle 1.54005 ( 9) link_ALPHA1-3 : bond 0.01479 ( 2) link_ALPHA1-3 : angle 1.09297 ( 6) link_ALPHA1-6 : bond 0.00436 ( 2) link_ALPHA1-6 : angle 1.66607 ( 6) link_BETA1-4 : bond 0.00384 ( 7) link_BETA1-4 : angle 1.60936 ( 21) link_NAG-ASN : bond 0.00216 ( 7) link_NAG-ASN : angle 1.27606 ( 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 382 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 327 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8312 (mtp180) cc_final: 0.7647 (mtt180) REVERT: A 224 GLN cc_start: 0.8673 (tt0) cc_final: 0.8292 (tt0) REVERT: A 323 PHE cc_start: 0.7204 (t80) cc_final: 0.6426 (t80) REVERT: B 24 ASP cc_start: 0.7234 (t0) cc_final: 0.6784 (p0) REVERT: B 266 MET cc_start: 0.9080 (mmm) cc_final: 0.8772 (mmm) REVERT: C 142 ARG cc_start: 0.8317 (mtp180) cc_final: 0.8055 (mtp-110) REVERT: D 21 ARG cc_start: 0.7396 (ttp-110) cc_final: 0.7124 (ttp-110) REVERT: D 59 GLU cc_start: 0.8373 (tt0) cc_final: 0.8066 (tt0) REVERT: D 93 LYS cc_start: 0.8686 (tptp) cc_final: 0.8136 (mmmm) REVERT: D 264 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7819 (mm) REVERT: D 310 PHE cc_start: 0.8255 (m-10) cc_final: 0.7985 (m-10) REVERT: E 178 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7949 (mt-10) REVERT: E 276 MET cc_start: 0.8771 (tpp) cc_final: 0.8470 (mmm) REVERT: E 296 MET cc_start: 0.8053 (ttp) cc_final: 0.7677 (ttp) REVERT: E 301 SER cc_start: 0.9103 (m) cc_final: 0.8785 (m) REVERT: E 305 ILE cc_start: 0.8491 (mm) cc_final: 0.8064 (mm) REVERT: E 337 ILE cc_start: 0.8742 (tp) cc_final: 0.8442 (tp) REVERT: E 356 TYR cc_start: 0.5572 (OUTLIER) cc_final: 0.5055 (t80) REVERT: I 13 MET cc_start: 0.5269 (OUTLIER) cc_final: 0.4882 (ppp) REVERT: I 79 GLN cc_start: 0.8025 (mp10) cc_final: 0.7555 (mp10) REVERT: J 46 GLU cc_start: 0.8721 (tt0) cc_final: 0.8518 (mt-10) REVERT: J 112 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8536 (t) REVERT: L 79 GLN cc_start: 0.7418 (mp10) cc_final: 0.7024 (mp10) outliers start: 55 outliers final: 42 residues processed: 359 average time/residue: 0.1315 time to fit residues: 71.5032 Evaluate side-chains 363 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 317 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 55 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN B 308 ASN D 190 GLN E 318 HIS K 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.129840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.101125 restraints weight = 21347.467| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.72 r_work: 0.2847 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17865 Z= 0.187 Angle : 0.581 9.560 24337 Z= 0.292 Chirality : 0.044 0.257 2799 Planarity : 0.004 0.041 2985 Dihedral : 5.741 55.795 2822 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.66 % Allowed : 15.51 % 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: -0.00 (0.18), residues: 2103 helix: 1.42 (0.21), residues: 595 sheet: -0.32 (0.20), residues: 603 loop : -0.65 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 141 TYR 0.023 0.001 TYR A 299 PHE 0.014 0.002 PHE A 221 TRP 0.008 0.001 TRP E 183 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00432 (17835) covalent geometry : angle 0.57372 (24256) SS BOND : bond 0.00149 ( 9) SS BOND : angle 1.94107 ( 18) hydrogen bonds : bond 0.03206 ( 821) hydrogen bonds : angle 4.27930 ( 2637) link_ALPHA1-2 : bond 0.00366 ( 3) link_ALPHA1-2 : angle 1.69717 ( 9) link_ALPHA1-3 : bond 0.01390 ( 2) link_ALPHA1-3 : angle 1.13305 ( 6) link_ALPHA1-6 : bond 0.00328 ( 2) link_ALPHA1-6 : angle 1.82005 ( 6) link_BETA1-4 : bond 0.00350 ( 7) link_BETA1-4 : angle 1.61315 ( 21) link_NAG-ASN : bond 0.00271 ( 7) link_NAG-ASN : angle 1.47875 ( 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 388 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 319 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8319 (mtp180) cc_final: 0.7642 (mtt180) REVERT: A 224 GLN cc_start: 0.8712 (tt0) cc_final: 0.8331 (tt0) REVERT: A 323 PHE cc_start: 0.7132 (t80) cc_final: 0.6335 (t80) REVERT: B 17 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7812 (mtt-85) REVERT: B 24 ASP cc_start: 0.7325 (t0) cc_final: 0.6813 (p0) REVERT: B 209 GLU cc_start: 0.8557 (tt0) cc_final: 0.8329 (tt0) REVERT: C 142 ARG cc_start: 0.8397 (mtp180) cc_final: 0.8084 (mtp-110) REVERT: C 283 MET cc_start: 0.8369 (mmp) cc_final: 0.8043 (tpt) REVERT: D 21 ARG cc_start: 0.7529 (ttp-110) cc_final: 0.7264 (ttp-110) REVERT: D 93 LYS cc_start: 0.8772 (tptp) cc_final: 0.8091 (mmmm) REVERT: D 261 THR cc_start: 0.8571 (m) cc_final: 0.8131 (t) REVERT: D 264 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7967 (mm) REVERT: D 310 PHE cc_start: 0.8313 (m-10) cc_final: 0.8028 (m-10) REVERT: E 178 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8178 (mt-10) REVERT: E 276 MET cc_start: 0.8791 (tpp) cc_final: 0.8496 (mmm) REVERT: E 296 MET cc_start: 0.8199 (ttp) cc_final: 0.7800 (ttp) REVERT: E 301 SER cc_start: 0.9119 (m) cc_final: 0.8791 (m) REVERT: E 305 ILE cc_start: 0.8488 (mm) cc_final: 0.8074 (mm) REVERT: E 337 ILE cc_start: 0.8764 (tp) cc_final: 0.8444 (tp) REVERT: E 356 TYR cc_start: 0.5730 (OUTLIER) cc_final: 0.5109 (t80) REVERT: I 13 MET cc_start: 0.5377 (OUTLIER) cc_final: 0.5009 (ppp) REVERT: I 90 GLN cc_start: 0.9370 (pp30) cc_final: 0.9156 (pp30) REVERT: J 46 GLU cc_start: 0.8878 (tt0) cc_final: 0.8609 (mt-10) REVERT: J 99 LYS cc_start: 0.9128 (tmmt) cc_final: 0.8897 (ttpp) REVERT: J 112 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8623 (t) REVERT: L 79 GLN cc_start: 0.7410 (mp10) cc_final: 0.7066 (mp10) REVERT: K 5 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7990 (mm-40) REVERT: K 105 MET cc_start: 0.9061 (mtm) cc_final: 0.8510 (mtt) outliers start: 69 outliers final: 55 residues processed: 361 average time/residue: 0.1313 time to fit residues: 71.7950 Evaluate side-chains 374 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 315 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 178 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 184 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN B 308 ASN ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 GLN E 318 HIS J 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.130482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.102181 restraints weight = 21360.239| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.74 r_work: 0.2852 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17865 Z= 0.160 Angle : 0.565 9.843 24337 Z= 0.285 Chirality : 0.044 0.256 2799 Planarity : 0.004 0.042 2985 Dihedral : 5.684 56.248 2822 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.72 % Allowed : 15.93 % Favored : 80.35 % 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: 0.05 (0.18), residues: 2103 helix: 1.47 (0.21), residues: 595 sheet: -0.28 (0.20), residues: 613 loop : -0.63 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 68 TYR 0.024 0.001 TYR A 299 PHE 0.014 0.001 PHE A 221 TRP 0.008 0.001 TRP K 103 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00367 (17835) covalent geometry : angle 0.55808 (24256) SS BOND : bond 0.00138 ( 9) SS BOND : angle 1.88830 ( 18) hydrogen bonds : bond 0.03124 ( 821) hydrogen bonds : angle 4.24080 ( 2637) link_ALPHA1-2 : bond 0.00426 ( 3) link_ALPHA1-2 : angle 1.62217 ( 9) link_ALPHA1-3 : bond 0.01370 ( 2) link_ALPHA1-3 : angle 1.06660 ( 6) link_ALPHA1-6 : bond 0.00343 ( 2) link_ALPHA1-6 : angle 1.76479 ( 6) link_BETA1-4 : bond 0.00379 ( 7) link_BETA1-4 : angle 1.61011 ( 21) link_NAG-ASN : bond 0.00252 ( 7) link_NAG-ASN : angle 1.37238 ( 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 401 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 331 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8319 (mtp180) cc_final: 0.7648 (mtt180) REVERT: A 224 GLN cc_start: 0.8689 (tt0) cc_final: 0.8282 (tt0) REVERT: B 24 ASP cc_start: 0.7377 (t0) cc_final: 0.6914 (p0) REVERT: C 142 ARG cc_start: 0.8410 (mtp180) cc_final: 0.8046 (mtp-110) REVERT: C 283 MET cc_start: 0.8359 (mmp) cc_final: 0.8049 (tpt) REVERT: D 21 ARG cc_start: 0.7507 (ttp-110) cc_final: 0.6879 (ttp-110) REVERT: D 76 LYS cc_start: 0.8866 (mttt) cc_final: 0.8598 (mtpp) REVERT: D 93 LYS cc_start: 0.8778 (tptp) cc_final: 0.8100 (mmmm) REVERT: D 261 THR cc_start: 0.8546 (m) cc_final: 0.8067 (t) REVERT: D 264 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7967 (mm) REVERT: D 310 PHE cc_start: 0.8257 (m-10) cc_final: 0.7962 (m-10) REVERT: E 178 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8132 (mt-10) REVERT: E 194 ARG cc_start: 0.7669 (mmm160) cc_final: 0.7449 (mmm160) REVERT: E 296 MET cc_start: 0.8124 (ttp) cc_final: 0.7714 (ttp) REVERT: E 301 SER cc_start: 0.9134 (m) cc_final: 0.8798 (m) REVERT: E 305 ILE cc_start: 0.8483 (mm) cc_final: 0.8098 (mm) REVERT: E 337 ILE cc_start: 0.8784 (tp) cc_final: 0.8465 (tp) REVERT: E 356 TYR cc_start: 0.5716 (OUTLIER) cc_final: 0.5118 (t80) REVERT: I 13 MET cc_start: 0.5528 (OUTLIER) cc_final: 0.5209 (ppp) REVERT: I 79 GLN cc_start: 0.8081 (mp10) cc_final: 0.7594 (mp10) REVERT: I 90 GLN cc_start: 0.9361 (pp30) cc_final: 0.9127 (pp30) REVERT: J 46 GLU cc_start: 0.8850 (tt0) cc_final: 0.8589 (mt-10) REVERT: J 112 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8618 (t) REVERT: L 79 GLN cc_start: 0.7392 (mp10) cc_final: 0.7030 (mp10) REVERT: K 5 GLN cc_start: 0.8347 (mm-40) cc_final: 0.7907 (mm-40) REVERT: K 105 MET cc_start: 0.9027 (mtm) cc_final: 0.8466 (mtt) outliers start: 70 outliers final: 55 residues processed: 373 average time/residue: 0.1328 time to fit residues: 75.3518 Evaluate side-chains 372 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 313 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 170 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 100 optimal weight: 0.4980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN B 308 ASN ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN D 190 GLN J 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.131835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.103545 restraints weight = 21313.742| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.70 r_work: 0.2877 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17865 Z= 0.132 Angle : 0.554 10.912 24337 Z= 0.280 Chirality : 0.043 0.248 2799 Planarity : 0.004 0.040 2985 Dihedral : 5.589 56.631 2822 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.29 % Allowed : 16.78 % Favored : 79.93 % 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: 0.13 (0.18), residues: 2103 helix: 1.56 (0.21), residues: 595 sheet: -0.27 (0.20), residues: 603 loop : -0.57 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 54 TYR 0.024 0.001 TYR A 299 PHE 0.013 0.001 PHE A 221 TRP 0.008 0.001 TRP K 103 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00297 (17835) covalent geometry : angle 0.54826 (24256) SS BOND : bond 0.00146 ( 9) SS BOND : angle 1.76502 ( 18) hydrogen bonds : bond 0.03032 ( 821) hydrogen bonds : angle 4.16533 ( 2637) link_ALPHA1-2 : bond 0.00457 ( 3) link_ALPHA1-2 : angle 1.60044 ( 9) link_ALPHA1-3 : bond 0.01387 ( 2) link_ALPHA1-3 : angle 1.08012 ( 6) link_ALPHA1-6 : bond 0.00346 ( 2) link_ALPHA1-6 : angle 1.71805 ( 6) link_BETA1-4 : bond 0.00364 ( 7) link_BETA1-4 : angle 1.58881 ( 21) link_NAG-ASN : bond 0.00220 ( 7) link_NAG-ASN : angle 1.24218 ( 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 381 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 319 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8308 (mtp180) cc_final: 0.7641 (mtt180) REVERT: A 224 GLN cc_start: 0.8711 (tt0) cc_final: 0.8314 (tt0) REVERT: B 17 ARG cc_start: 0.8198 (mtm-85) cc_final: 0.7855 (mtt90) REVERT: B 24 ASP cc_start: 0.7361 (t0) cc_final: 0.6912 (p0) REVERT: B 142 HIS cc_start: 0.7338 (t70) cc_final: 0.7046 (t-90) REVERT: C 142 ARG cc_start: 0.8336 (mtp180) cc_final: 0.8050 (mtp-110) REVERT: C 283 MET cc_start: 0.8355 (mmp) cc_final: 0.8059 (tpt) REVERT: D 21 ARG cc_start: 0.7362 (ttp-110) cc_final: 0.7145 (ttp-110) REVERT: D 93 LYS cc_start: 0.8772 (tptp) cc_final: 0.8131 (mmmm) REVERT: D 112 MET cc_start: 0.8740 (tpp) cc_final: 0.8314 (tpp) REVERT: D 261 THR cc_start: 0.8545 (m) cc_final: 0.8057 (t) REVERT: D 310 PHE cc_start: 0.8235 (m-10) cc_final: 0.7932 (m-10) REVERT: E 178 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8115 (mt-10) REVERT: E 276 MET cc_start: 0.8812 (tpp) cc_final: 0.8546 (mmm) REVERT: E 296 MET cc_start: 0.8087 (ttp) cc_final: 0.7677 (ttp) REVERT: E 301 SER cc_start: 0.9140 (m) cc_final: 0.8815 (m) REVERT: E 305 ILE cc_start: 0.8463 (mm) cc_final: 0.8061 (mm) REVERT: E 337 ILE cc_start: 0.8792 (tp) cc_final: 0.8468 (tp) REVERT: E 356 TYR cc_start: 0.5699 (OUTLIER) cc_final: 0.5108 (t80) REVERT: I 13 MET cc_start: 0.5497 (OUTLIER) cc_final: 0.5161 (ppp) REVERT: I 79 GLN cc_start: 0.8105 (mp10) cc_final: 0.7623 (mp10) REVERT: I 90 GLN cc_start: 0.9350 (pp30) cc_final: 0.9121 (pp30) REVERT: J 46 GLU cc_start: 0.8856 (tt0) cc_final: 0.8622 (mt-10) REVERT: J 112 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8582 (t) REVERT: L 60 ASP cc_start: 0.7649 (t0) cc_final: 0.7273 (t70) REVERT: L 79 GLN cc_start: 0.7313 (mp10) cc_final: 0.7009 (mp10) REVERT: K 5 GLN cc_start: 0.8367 (mm-40) cc_final: 0.7967 (mm-40) REVERT: K 102 ARG cc_start: 0.8740 (mmm-85) cc_final: 0.8528 (mmm-85) REVERT: K 105 MET cc_start: 0.8992 (mtm) cc_final: 0.8444 (mtt) outliers start: 62 outliers final: 52 residues processed: 358 average time/residue: 0.1340 time to fit residues: 72.4903 Evaluate side-chains 377 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 322 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 118 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 187 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 171 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 142 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN B 204 GLN B 308 ASN D 151 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.128938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.100740 restraints weight = 21236.840| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.72 r_work: 0.2828 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17865 Z= 0.207 Angle : 0.610 11.506 24337 Z= 0.306 Chirality : 0.045 0.256 2799 Planarity : 0.004 0.042 2985 Dihedral : 5.685 55.502 2822 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.35 % Allowed : 16.68 % Favored : 79.98 % 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: 0.06 (0.18), residues: 2103 helix: 1.48 (0.21), residues: 595 sheet: -0.33 (0.20), residues: 621 loop : -0.58 (0.22), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 17 TYR 0.025 0.002 TYR A 299 PHE 0.015 0.002 PHE A 221 TRP 0.011 0.001 TRP E 183 HIS 0.007 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00480 (17835) covalent geometry : angle 0.60233 (24256) SS BOND : bond 0.00156 ( 9) SS BOND : angle 2.04822 ( 18) hydrogen bonds : bond 0.03251 ( 821) hydrogen bonds : angle 4.31248 ( 2637) link_ALPHA1-2 : bond 0.00345 ( 3) link_ALPHA1-2 : angle 1.76770 ( 9) link_ALPHA1-3 : bond 0.01248 ( 2) link_ALPHA1-3 : angle 1.20996 ( 6) link_ALPHA1-6 : bond 0.00230 ( 2) link_ALPHA1-6 : angle 1.93619 ( 6) link_BETA1-4 : bond 0.00323 ( 7) link_BETA1-4 : angle 1.62165 ( 21) link_NAG-ASN : bond 0.00336 ( 7) link_NAG-ASN : angle 1.56601 ( 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 387 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 324 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8345 (mtp180) cc_final: 0.7651 (mtt180) REVERT: A 224 GLN cc_start: 0.8703 (tt0) cc_final: 0.8294 (tt0) REVERT: B 17 ARG cc_start: 0.8231 (mtm-85) cc_final: 0.7927 (mtt-85) REVERT: B 24 ASP cc_start: 0.7450 (t0) cc_final: 0.7016 (p0) REVERT: B 323 ARG cc_start: 0.7838 (ttp80) cc_final: 0.7585 (ttp80) REVERT: C 52 GLU cc_start: 0.7968 (mp0) cc_final: 0.7677 (mp0) REVERT: C 142 ARG cc_start: 0.8383 (mtp180) cc_final: 0.8015 (mtp-110) REVERT: C 283 MET cc_start: 0.8357 (mmp) cc_final: 0.8060 (tpt) REVERT: D 21 ARG cc_start: 0.7335 (ttp-110) cc_final: 0.7121 (ttp-110) REVERT: D 76 LYS cc_start: 0.8902 (mttt) cc_final: 0.8582 (mtpp) REVERT: D 93 LYS cc_start: 0.8779 (tptp) cc_final: 0.8129 (mmmm) REVERT: D 261 THR cc_start: 0.8585 (m) cc_final: 0.8109 (t) REVERT: D 310 PHE cc_start: 0.8312 (m-10) cc_final: 0.8018 (m-10) REVERT: E 296 MET cc_start: 0.8123 (ttp) cc_final: 0.7688 (ttp) REVERT: E 301 SER cc_start: 0.9155 (m) cc_final: 0.8821 (m) REVERT: E 305 ILE cc_start: 0.8469 (mm) cc_final: 0.8089 (mm) REVERT: E 337 ILE cc_start: 0.8789 (tp) cc_final: 0.8491 (tp) REVERT: E 356 TYR cc_start: 0.5707 (OUTLIER) cc_final: 0.5104 (t80) REVERT: I 13 MET cc_start: 0.5489 (OUTLIER) cc_final: 0.5117 (ppp) REVERT: I 79 GLN cc_start: 0.8120 (mp10) cc_final: 0.7589 (mp10) REVERT: I 90 GLN cc_start: 0.9382 (pp30) cc_final: 0.9163 (pp30) REVERT: J 46 GLU cc_start: 0.8896 (tt0) cc_final: 0.8615 (mt-10) REVERT: J 112 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8628 (t) REVERT: L 60 ASP cc_start: 0.7657 (t0) cc_final: 0.7338 (t70) REVERT: L 79 GLN cc_start: 0.7361 (mp10) cc_final: 0.7047 (mp10) REVERT: K 5 GLN cc_start: 0.8335 (mm-40) cc_final: 0.7941 (mm-40) REVERT: K 102 ARG cc_start: 0.8859 (mmm-85) cc_final: 0.8513 (mmm-85) REVERT: K 105 MET cc_start: 0.9068 (mtm) cc_final: 0.8650 (mtt) outliers start: 63 outliers final: 58 residues processed: 362 average time/residue: 0.1396 time to fit residues: 74.9298 Evaluate side-chains 381 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 320 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 194 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 chunk 65 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 308 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.132749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.103323 restraints weight = 21194.131| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.79 r_work: 0.2875 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17865 Z= 0.127 Angle : 0.562 11.555 24337 Z= 0.283 Chirality : 0.043 0.250 2799 Planarity : 0.004 0.040 2985 Dihedral : 5.551 56.771 2822 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.08 % Allowed : 17.26 % Favored : 79.66 % 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: 0.18 (0.19), residues: 2103 helix: 1.61 (0.21), residues: 595 sheet: -0.28 (0.20), residues: 603 loop : -0.52 (0.22), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 312 TYR 0.025 0.001 TYR A 299 PHE 0.013 0.001 PHE A 221 TRP 0.010 0.001 TRP K 103 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00285 (17835) covalent geometry : angle 0.55606 (24256) SS BOND : bond 0.00099 ( 9) SS BOND : angle 1.80469 ( 18) hydrogen bonds : bond 0.03005 ( 821) hydrogen bonds : angle 4.17440 ( 2637) link_ALPHA1-2 : bond 0.00477 ( 3) link_ALPHA1-2 : angle 1.55031 ( 9) link_ALPHA1-3 : bond 0.01383 ( 2) link_ALPHA1-3 : angle 1.06010 ( 6) link_ALPHA1-6 : bond 0.00375 ( 2) link_ALPHA1-6 : angle 1.68804 ( 6) link_BETA1-4 : bond 0.00384 ( 7) link_BETA1-4 : angle 1.59782 ( 21) link_NAG-ASN : bond 0.00238 ( 7) link_NAG-ASN : angle 1.21813 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4387.59 seconds wall clock time: 75 minutes 49.98 seconds (4549.98 seconds total)