Starting phenix.real_space_refine on Tue Aug 26 07:50:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8si9_40503/08_2025/8si9_40503_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8si9_40503/08_2025/8si9_40503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8si9_40503/08_2025/8si9_40503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8si9_40503/08_2025/8si9_40503.map" model { file = "/net/cci-nas-00/data/ceres_data/8si9_40503/08_2025/8si9_40503_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8si9_40503/08_2025/8si9_40503_trim.cif" } resolution = 2.98 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 97 5.16 5 C 11259 2.51 5 N 2827 2.21 5 O 3237 1.98 5 H 16954 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34374 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 5473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5473 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5443 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 321} Chain: "C" Number of atoms: 5473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5473 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5443 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 321} Chain: "E" Number of atoms: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5443 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "I" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1573 Classifications: {'peptide': 105} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1784 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1595 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1798 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'Y4B': 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: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {'ABU': 1, 'NAG': 1, 'Y4B': 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 Time building chain proxies: 6.06, per 1000 atoms: 0.18 Number of scatterers: 34374 At special positions: 0 Unit cell: (149.8, 127.33, 126.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 97 16.00 O 3237 8.00 N 2827 7.00 C 11259 6.00 H 16954 1.00 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=2.05 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=2.03 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=2.05 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 M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 401 " - " ASN A 80 " " NAG C 401 " - " ASN C 80 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN D 111 " " NAG N 1 " - " ASN E 208 " Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 798.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4016 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 31 sheets defined 31.9% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.557A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 226 removed outlier: 3.560A pdb=" N TYR A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 238 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 246 through 271 removed outlier: 3.832A pdb=" N ARG A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR A 271 " --> pdb=" O HIS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 305 Processing helix chain 'A' and resid 311 through 320 removed outlier: 3.977A pdb=" N ALA A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASP A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 340 Processing helix chain 'B' and resid 12 through 23 removed outlier: 3.532A pdb=" N LEU B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 76 removed outlier: 3.689A pdb=" N LYS B 76 " --> pdb=" O GLU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 223 through 230 removed outlier: 3.585A pdb=" N ILE B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 244 removed outlier: 4.022A 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 273 removed outlier: 3.504A pdb=" N ARG B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 277 removed outlier: 3.556A pdb=" N LEU B 277 " --> pdb=" O ARG B 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 274 through 277' Processing helix chain 'B' and resid 284 through 311 Processing helix chain 'B' and resid 314 through 346 removed outlier: 4.436A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix removed outlier: 3.590A pdb=" N ASN B 346 " --> pdb=" O ALA B 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 70 through 73 removed outlier: 3.638A pdb=" N SER C 73 " --> pdb=" O LYS C 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 73' Processing helix chain 'C' and resid 86 through 91 removed outlier: 3.528A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 225 through 238 removed outlier: 3.982A pdb=" N SER C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 247 through 272 removed outlier: 3.686A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 305 Processing helix chain 'C' and resid 309 through 339 Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 12 through 24 Processing helix chain 'D' and resid 72 through 76 removed outlier: 3.575A pdb=" N LEU D 75 " --> pdb=" O ASP D 72 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS D 76 " --> pdb=" O GLU D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 72 through 76' Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.648A pdb=" N SER D 92 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 223 through 243 removed outlier: 4.531A pdb=" N LEU D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 251 through 275 removed outlier: 3.530A pdb=" N ARG D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 311 removed outlier: 3.665A pdb=" N ILE D 302 " --> pdb=" O PHE D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 346 removed outlier: 4.016A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (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 102 through 106 removed outlier: 3.787A pdb=" N LYS E 105 " --> pdb=" O MET E 102 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE E 106 " --> pdb=" O VAL E 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 102 through 106' Processing helix chain 'E' and resid 234 through 240 Processing helix chain 'E' and resid 240 through 253 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 287 removed outlier: 3.699A pdb=" N ARG E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU E 287 " --> pdb=" O ALA E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 324 removed outlier: 3.592A pdb=" N PHE E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 357 removed outlier: 3.790A pdb=" N ALA E 328 " --> pdb=" O GLN E 324 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE E 337 " --> pdb=" O SER E 333 " (cutoff:3.500A) Proline residue: E 340 - end of helix Processing helix chain 'J' and resid 87 through 91 removed outlier: 4.120A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.681A pdb=" N GLN K 65 " --> pdb=" O PRO K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.751A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 130 through 132 removed outlier: 6.843A pdb=" N ASP A 56 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL A 50 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR A 58 " --> pdb=" O ASP A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.839A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 86 removed outlier: 4.116A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 46 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 108 through 109 removed outlier: 7.142A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 46 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.165A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.165A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TYR B 210 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE B 202 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 212 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER B 200 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR B 214 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL B 198 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N HIS B 216 " --> pdb=" O GLN B 196 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLN B 196 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N HIS B 218 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.622A pdb=" N LEU C 83 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.622A pdb=" N LEU C 83 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N THR C 176 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE C 42 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.854A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.854A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL C 199 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N TYR C 205 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS C 197 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG C 207 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR C 195 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER C 209 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU C 193 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER C 211 " --> pdb=" O TYR C 191 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR C 191 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS C 213 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 83 through 86 removed outlier: 4.218A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 108 through 109 removed outlier: 6.954A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.170A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.170A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 61 through 66 removed outlier: 3.633A pdb=" N SER E 61 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR E 73 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N VAL E 65 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU E 71 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ARG E 144 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA E 121 " --> pdb=" O ARG E 144 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 95 through 98 removed outlier: 4.630A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS E 184 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N MET E 57 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N SER E 186 " --> pdb=" O MET E 57 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 111 through 113 removed outlier: 3.562A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.424A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.734A pdb=" N THR I 96 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.044A pdb=" N GLU J 10 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.044A pdb=" N GLU J 10 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR J 107 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC9, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.781A pdb=" N MET L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR L 101 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR L 86 " --> pdb=" O THR L 101 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.781A pdb=" N MET L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR L 101 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR L 86 " --> pdb=" O THR L 101 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR L 96 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.560A pdb=" N VAL K 18 " --> pdb=" O LEU K 83 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.736A pdb=" N GLU K 10 " --> pdb=" O SER K 113 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR K 94 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.736A pdb=" N GLU K 10 " --> pdb=" O SER K 113 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR K 94 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 862 hydrogen bonds defined for protein. 2451 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: 8.62 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 16924 1.00 - 1.21: 32 1.21 - 1.42: 7519 1.42 - 1.62: 10172 1.62 - 1.83: 167 Bond restraints: 34814 Sorted by residual: bond pdb=" N ARG A 269 " pdb=" H ARG A 269 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N GLN D 242 " pdb=" H GLN D 242 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.74e+01 bond pdb=" NE2 GLN D 242 " pdb="HE22 GLN D 242 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.10e+01 bond pdb=" NE2 GLN D 242 " pdb="HE21 GLN D 242 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.09e+01 bond pdb=" NH1 ARG A 269 " pdb="HH12 ARG A 269 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.07e+01 ... (remaining 34809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.35: 62546 7.35 - 14.71: 8 14.71 - 22.06: 6 22.06 - 29.41: 4 29.41 - 36.76: 2 Bond angle restraints: 62566 Sorted by residual: angle pdb=" CD GLN A 309 " pdb=" NE2 GLN A 309 " pdb="HE22 GLN A 309 " ideal model delta sigma weight residual 120.00 156.76 -36.76 3.00e+00 1.11e-01 1.50e+02 angle pdb="HE21 GLN A 309 " pdb=" NE2 GLN A 309 " pdb="HE22 GLN A 309 " ideal model delta sigma weight residual 120.00 86.81 33.19 3.00e+00 1.11e-01 1.22e+02 angle pdb=" CD GLN A 309 " pdb=" NE2 GLN A 309 " pdb="HE21 GLN A 309 " ideal model delta sigma weight residual 120.00 91.85 28.15 3.00e+00 1.11e-01 8.81e+01 angle pdb=" CG ASN E 347 " pdb=" ND2 ASN E 347 " pdb="HD22 ASN E 347 " ideal model delta sigma weight residual 120.00 147.24 -27.24 3.00e+00 1.11e-01 8.24e+01 angle pdb="HD21 ASN E 347 " pdb=" ND2 ASN E 347 " pdb="HD22 ASN E 347 " ideal model delta sigma weight residual 120.00 94.78 25.22 3.00e+00 1.11e-01 7.07e+01 ... (remaining 62561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.80: 15855 21.80 - 43.60: 840 43.60 - 65.39: 199 65.39 - 87.19: 46 87.19 - 108.99: 16 Dihedral angle restraints: 16956 sinusoidal: 9274 harmonic: 7682 Sorted by residual: dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 165 " pdb=" CB CYS E 165 " ideal model delta sinusoidal sigma weight residual -86.00 -19.11 -66.89 1 1.00e+01 1.00e-02 5.83e+01 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 -27.42 -58.58 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CD ARG E 232 " pdb=" NE ARG E 232 " pdb=" CZ ARG E 232 " pdb=" NH1 ARG E 232 " ideal model delta sinusoidal sigma weight residual 0.00 -53.72 53.72 1 1.00e+01 1.00e-02 3.92e+01 ... (remaining 16953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2296 0.057 - 0.114: 455 0.114 - 0.171: 60 0.171 - 0.228: 6 0.228 - 0.285: 4 Chirality restraints: 2821 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN E 208 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 2818 not shown) Planarity restraints: 5010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 321 " -0.436 9.50e-02 1.11e+02 2.19e-01 6.21e+02 pdb=" NE ARG A 321 " -0.191 2.00e-02 2.50e+03 pdb=" CZ ARG A 321 " -0.052 2.00e-02 2.50e+03 pdb=" NH1 ARG A 321 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 321 " 0.031 2.00e-02 2.50e+03 pdb="HH11 ARG A 321 " 0.322 2.00e-02 2.50e+03 pdb="HH12 ARG A 321 " -0.231 2.00e-02 2.50e+03 pdb="HH21 ARG A 321 " 0.195 2.00e-02 2.50e+03 pdb="HH22 ARG A 321 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 232 " 0.910 9.50e-02 1.11e+02 3.09e-01 1.71e+02 pdb=" NE ARG E 232 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG E 232 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG E 232 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG E 232 " -0.011 2.00e-02 2.50e+03 pdb="HH11 ARG E 232 " -0.091 2.00e-02 2.50e+03 pdb="HH12 ARG E 232 " 0.113 2.00e-02 2.50e+03 pdb="HH21 ARG E 232 " 0.052 2.00e-02 2.50e+03 pdb="HH22 ARG E 232 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 231 " 0.635 9.50e-02 1.11e+02 2.24e-01 1.67e+02 pdb=" NE ARG E 231 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG E 231 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG E 231 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG E 231 " -0.018 2.00e-02 2.50e+03 pdb="HH11 ARG E 231 " -0.154 2.00e-02 2.50e+03 pdb="HH12 ARG E 231 " 0.145 2.00e-02 2.50e+03 pdb="HH21 ARG E 231 " -0.009 2.00e-02 2.50e+03 pdb="HH22 ARG E 231 " -0.047 2.00e-02 2.50e+03 ... (remaining 5007 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1002 2.13 - 2.74: 62855 2.74 - 3.36: 94219 3.36 - 3.98: 127529 3.98 - 4.60: 200358 Nonbonded interactions: 485963 Sorted by model distance: nonbonded pdb=" HE2 HIS C 107 " pdb=" OG1 THR C 131 " model vdw 1.507 2.450 nonbonded pdb=" OE2 GLU C 270 " pdb="HE22 GLN D 229 " model vdw 1.512 2.450 nonbonded pdb=" OE1 GLU C 155 " pdb="HH21 ARG C 207 " model vdw 1.513 2.450 nonbonded pdb=" H GLY K 100 " pdb=" O ALA K 104 " model vdw 1.547 2.450 nonbonded pdb=" OG1 THR B 207 " pdb=" HH TYR B 210 " model vdw 1.563 2.450 ... (remaining 485958 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 401) selection = (chain 'C' and resid 7 through 401) } ncs_group { reference = (chain 'B' and resid 11 through 347) selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 1 through 105) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 2 through 117) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 0.180 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 31.950 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 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:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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 : 0.005 0.040 17892 Z= 0.249 Angle : 0.698 8.952 24387 Z= 0.373 Chirality : 0.047 0.285 2821 Planarity : 0.010 0.387 2980 Dihedral : 14.194 108.991 6879 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.43 % Favored : 95.53 % Rotamer: Outliers : 0.05 % Allowed : 0.11 % Favored : 99.84 % 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 aren not related in a simple way. whole: -3.17 (0.16), residues: 2101 helix: -1.01 (0.20), residues: 582 sheet: -2.51 (0.17), residues: 668 loop : -2.36 (0.18), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 231 TYR 0.019 0.002 TYR D 129 PHE 0.017 0.002 PHE D 226 TRP 0.015 0.001 TRP E 134 HIS 0.005 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00518 (17860) covalent geometry : angle 0.68996 (24300) SS BOND : bond 0.00886 ( 9) SS BOND : angle 1.44444 ( 18) hydrogen bonds : bond 0.11642 ( 765) hydrogen bonds : angle 6.27925 ( 2451) link_ALPHA1-2 : bond 0.00257 ( 3) link_ALPHA1-2 : angle 2.08378 ( 9) link_ALPHA1-3 : bond 0.00201 ( 2) link_ALPHA1-3 : angle 2.53095 ( 6) link_ALPHA1-6 : bond 0.00101 ( 2) link_ALPHA1-6 : angle 2.58837 ( 6) link_BETA1-4 : bond 0.00232 ( 9) link_BETA1-4 : angle 1.57465 ( 27) link_NAG-ASN : bond 0.00246 ( 7) link_NAG-ASN : angle 1.91593 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 413 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LEU cc_start: 0.9108 (mt) cc_final: 0.8896 (tt) REVERT: A 299 TYR cc_start: 0.8390 (t80) cc_final: 0.8170 (t80) REVERT: B 314 GLN cc_start: 0.7373 (mt0) cc_final: 0.7151 (tm-30) REVERT: C 283 MET cc_start: 0.8587 (tpp) cc_final: 0.8344 (tpp) REVERT: D 114 MET cc_start: 0.8446 (mmm) cc_final: 0.8204 (mmp) REVERT: E 152 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7354 (mm-40) REVERT: E 162 GLU cc_start: 0.8355 (tt0) cc_final: 0.7800 (tm-30) REVERT: E 317 LEU cc_start: 0.8575 (tt) cc_final: 0.8355 (tt) REVERT: E 331 MET cc_start: 0.7038 (ttm) cc_final: 0.6557 (ttm) REVERT: J 67 LYS cc_start: 0.8546 (tttt) cc_final: 0.8290 (ttmt) REVERT: J 89 GLU cc_start: 0.7989 (pp20) cc_final: 0.7612 (pp20) REVERT: L 56 THR cc_start: 0.9239 (m) cc_final: 0.9010 (p) REVERT: L 105 LEU cc_start: 0.8862 (tp) cc_final: 0.8620 (tp) outliers start: 1 outliers final: 0 residues processed: 413 average time/residue: 1.3721 time to fit residues: 633.8386 Evaluate side-chains 257 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 309 GLN C 267 HIS D 88 ASN K 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.092060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.062950 restraints weight = 101620.332| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.60 r_work: 0.2724 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17892 Z= 0.203 Angle : 0.609 7.939 24387 Z= 0.313 Chirality : 0.044 0.264 2821 Planarity : 0.005 0.055 2980 Dihedral : 7.564 63.612 2943 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.86 % Allowed : 12.49 % Favored : 85.65 % 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 aren not related in a simple way. whole: -1.74 (0.17), residues: 2101 helix: 0.75 (0.21), residues: 587 sheet: -1.95 (0.18), residues: 691 loop : -1.70 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 232 TYR 0.014 0.001 TYR D 129 PHE 0.019 0.001 PHE E 346 TRP 0.009 0.001 TRP E 134 HIS 0.006 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00451 (17860) covalent geometry : angle 0.60062 (24300) SS BOND : bond 0.00700 ( 9) SS BOND : angle 1.25738 ( 18) hydrogen bonds : bond 0.04149 ( 765) hydrogen bonds : angle 4.91790 ( 2451) link_ALPHA1-2 : bond 0.00326 ( 3) link_ALPHA1-2 : angle 1.86959 ( 9) link_ALPHA1-3 : bond 0.01047 ( 2) link_ALPHA1-3 : angle 1.43350 ( 6) link_ALPHA1-6 : bond 0.00094 ( 2) link_ALPHA1-6 : angle 2.20540 ( 6) link_BETA1-4 : bond 0.00240 ( 9) link_BETA1-4 : angle 2.22911 ( 27) link_NAG-ASN : bond 0.00244 ( 7) link_NAG-ASN : angle 1.59465 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 275 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8077 (mmm) cc_final: 0.7803 (mmm) REVERT: A 235 LEU cc_start: 0.9178 (mt) cc_final: 0.8968 (tt) REVERT: A 247 SER cc_start: 0.7933 (m) cc_final: 0.7681 (p) REVERT: B 40 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8196 (tm-30) REVERT: C 250 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7023 (mtm180) REVERT: C 283 MET cc_start: 0.8949 (tpp) cc_final: 0.8644 (tpp) REVERT: C 312 ARG cc_start: 0.7066 (mtp-110) cc_final: 0.6354 (ttm-80) REVERT: D 114 MET cc_start: 0.9229 (mmm) cc_final: 0.8972 (mmp) REVERT: E 162 GLU cc_start: 0.8604 (tt0) cc_final: 0.7836 (tm-30) REVERT: E 238 ILE cc_start: 0.9167 (pp) cc_final: 0.8915 (tt) REVERT: L 56 THR cc_start: 0.9358 (m) cc_final: 0.9099 (p) REVERT: L 104 GLU cc_start: 0.5019 (OUTLIER) cc_final: 0.4775 (tm-30) REVERT: L 105 LEU cc_start: 0.8738 (tp) cc_final: 0.8398 (tp) REVERT: K 73 ASP cc_start: 0.8131 (t70) cc_final: 0.7849 (t0) outliers start: 35 outliers final: 10 residues processed: 289 average time/residue: 1.2119 time to fit residues: 394.2225 Evaluate side-chains 260 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 247 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain K residue 55 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 30 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN C 267 HIS D 88 ASN K 110 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.093318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.063832 restraints weight = 101099.822| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.65 r_work: 0.2732 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17892 Z= 0.147 Angle : 0.554 7.097 24387 Z= 0.283 Chirality : 0.043 0.180 2821 Planarity : 0.004 0.051 2980 Dihedral : 6.087 59.201 2943 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.65 % Allowed : 14.14 % Favored : 84.21 % 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 aren not related in a simple way. whole: -0.97 (0.18), residues: 2101 helix: 1.52 (0.21), residues: 589 sheet: -1.56 (0.18), residues: 680 loop : -1.30 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 18 TYR 0.011 0.001 TYR E 314 PHE 0.017 0.001 PHE C 307 TRP 0.007 0.001 TRP A 67 HIS 0.006 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00326 (17860) covalent geometry : angle 0.54687 (24300) SS BOND : bond 0.00592 ( 9) SS BOND : angle 0.99190 ( 18) hydrogen bonds : bond 0.03697 ( 765) hydrogen bonds : angle 4.61528 ( 2451) link_ALPHA1-2 : bond 0.00319 ( 3) link_ALPHA1-2 : angle 1.70402 ( 9) link_ALPHA1-3 : bond 0.00598 ( 2) link_ALPHA1-3 : angle 1.31193 ( 6) link_ALPHA1-6 : bond 0.00280 ( 2) link_ALPHA1-6 : angle 1.93955 ( 6) link_BETA1-4 : bond 0.00276 ( 9) link_BETA1-4 : angle 1.89762 ( 27) link_NAG-ASN : bond 0.00094 ( 7) link_NAG-ASN : angle 1.41756 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 259 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8204 (mmm) cc_final: 0.7968 (mmm) REVERT: A 218 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8389 (pp) REVERT: A 235 LEU cc_start: 0.9161 (mt) cc_final: 0.8948 (tt) REVERT: A 247 SER cc_start: 0.8007 (m) cc_final: 0.7785 (p) REVERT: B 40 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: C 250 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7015 (mtm180) REVERT: C 283 MET cc_start: 0.8943 (tpp) cc_final: 0.8608 (tpp) REVERT: C 312 ARG cc_start: 0.7102 (mtp-110) cc_final: 0.6472 (ttm-80) REVERT: D 114 MET cc_start: 0.9219 (mmm) cc_final: 0.9010 (mmp) REVERT: E 162 GLU cc_start: 0.8573 (tt0) cc_final: 0.7920 (tm-30) REVERT: E 238 ILE cc_start: 0.9141 (pp) cc_final: 0.8913 (tt) REVERT: E 346 PHE cc_start: 0.8528 (t80) cc_final: 0.8248 (t80) REVERT: I 13 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7556 (pp-130) REVERT: I 102 LYS cc_start: 0.9026 (tptm) cc_final: 0.8794 (tppt) REVERT: I 104 GLU cc_start: 0.6695 (tm-30) cc_final: 0.6119 (tm-30) REVERT: L 56 THR cc_start: 0.9384 (m) cc_final: 0.9144 (p) REVERT: L 104 GLU cc_start: 0.4958 (OUTLIER) cc_final: 0.4747 (tm-30) REVERT: L 105 LEU cc_start: 0.8754 (tp) cc_final: 0.8432 (tp) REVERT: K 73 ASP cc_start: 0.8095 (t70) cc_final: 0.7751 (t0) REVERT: K 101 LEU cc_start: 0.8683 (mp) cc_final: 0.8362 (mm) outliers start: 31 outliers final: 13 residues processed: 275 average time/residue: 1.2611 time to fit residues: 391.9661 Evaluate side-chains 261 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 243 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain K residue 110 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 190 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 chunk 109 optimal weight: 0.0980 chunk 66 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN B 242 GLN C 267 HIS D 56 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.093988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.064647 restraints weight = 100323.769| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.65 r_work: 0.2749 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17892 Z= 0.108 Angle : 0.528 6.393 24387 Z= 0.268 Chirality : 0.042 0.200 2821 Planarity : 0.004 0.051 2980 Dihedral : 5.341 50.853 2943 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.49 % Allowed : 14.89 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.19), residues: 2101 helix: 1.87 (0.21), residues: 589 sheet: -1.38 (0.18), residues: 688 loop : -1.02 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 18 TYR 0.012 0.001 TYR D 294 PHE 0.014 0.001 PHE C 307 TRP 0.007 0.001 TRP A 67 HIS 0.006 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00242 (17860) covalent geometry : angle 0.52226 (24300) SS BOND : bond 0.00535 ( 9) SS BOND : angle 0.77675 ( 18) hydrogen bonds : bond 0.03407 ( 765) hydrogen bonds : angle 4.40753 ( 2451) link_ALPHA1-2 : bond 0.00294 ( 3) link_ALPHA1-2 : angle 1.54699 ( 9) link_ALPHA1-3 : bond 0.00849 ( 2) link_ALPHA1-3 : angle 1.31031 ( 6) link_ALPHA1-6 : bond 0.00217 ( 2) link_ALPHA1-6 : angle 1.86726 ( 6) link_BETA1-4 : bond 0.00318 ( 9) link_BETA1-4 : angle 1.69672 ( 27) link_NAG-ASN : bond 0.00139 ( 7) link_NAG-ASN : angle 1.29235 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 260 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8338 (pp) REVERT: A 224 GLN cc_start: 0.8948 (tp40) cc_final: 0.8660 (mm-40) REVERT: A 235 LEU cc_start: 0.9184 (mt) cc_final: 0.8977 (tt) REVERT: A 247 SER cc_start: 0.8027 (m) cc_final: 0.7823 (p) REVERT: C 224 GLN cc_start: 0.8911 (tp40) cc_final: 0.8586 (tm-30) REVERT: C 250 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7022 (mtm180) REVERT: C 283 MET cc_start: 0.8931 (tpp) cc_final: 0.8561 (tpp) REVERT: C 312 ARG cc_start: 0.7078 (mtp-110) cc_final: 0.6527 (ttm-80) REVERT: D 114 MET cc_start: 0.9242 (mmm) cc_final: 0.9035 (mmp) REVERT: D 131 MET cc_start: 0.9310 (mtp) cc_final: 0.9095 (mtp) REVERT: E 162 GLU cc_start: 0.8540 (tt0) cc_final: 0.7892 (tm-30) REVERT: E 346 PHE cc_start: 0.8532 (t80) cc_final: 0.8280 (t80) REVERT: I 13 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7419 (pp-130) REVERT: I 104 GLU cc_start: 0.6638 (tm-30) cc_final: 0.6407 (tm-30) REVERT: L 56 THR cc_start: 0.9387 (m) cc_final: 0.9157 (p) REVERT: L 105 LEU cc_start: 0.8767 (tp) cc_final: 0.8495 (tp) REVERT: K 73 ASP cc_start: 0.8101 (t70) cc_final: 0.7766 (t0) REVERT: K 101 LEU cc_start: 0.8584 (mp) cc_final: 0.8289 (mm) outliers start: 28 outliers final: 11 residues processed: 273 average time/residue: 1.0927 time to fit residues: 337.5598 Evaluate side-chains 261 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 247 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 45 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 68 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 126 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN B 242 GLN D 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.092121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.062495 restraints weight = 101108.358| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.65 r_work: 0.2700 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17892 Z= 0.207 Angle : 0.559 7.595 24387 Z= 0.285 Chirality : 0.043 0.214 2821 Planarity : 0.004 0.062 2980 Dihedral : 5.242 53.122 2943 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.02 % Allowed : 15.47 % Favored : 82.51 % 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 aren not related in a simple way. whole: -0.26 (0.19), residues: 2101 helix: 2.11 (0.21), residues: 585 sheet: -1.11 (0.19), residues: 664 loop : -0.92 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 18 TYR 0.013 0.001 TYR E 314 PHE 0.012 0.001 PHE D 226 TRP 0.007 0.001 TRP E 134 HIS 0.006 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00470 (17860) covalent geometry : angle 0.55210 (24300) SS BOND : bond 0.01170 ( 9) SS BOND : angle 1.06726 ( 18) hydrogen bonds : bond 0.03492 ( 765) hydrogen bonds : angle 4.44323 ( 2451) link_ALPHA1-2 : bond 0.00174 ( 3) link_ALPHA1-2 : angle 2.00523 ( 9) link_ALPHA1-3 : bond 0.00556 ( 2) link_ALPHA1-3 : angle 1.43971 ( 6) link_ALPHA1-6 : bond 0.00275 ( 2) link_ALPHA1-6 : angle 2.14477 ( 6) link_BETA1-4 : bond 0.00243 ( 9) link_BETA1-4 : angle 1.67621 ( 27) link_NAG-ASN : bond 0.00228 ( 7) link_NAG-ASN : angle 1.55447 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 254 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8016 (pp20) cc_final: 0.7681 (pp20) REVERT: A 218 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8440 (pp) REVERT: A 224 GLN cc_start: 0.8975 (tp40) cc_final: 0.8727 (mm-40) REVERT: A 235 LEU cc_start: 0.9171 (mt) cc_final: 0.8771 (tt) REVERT: A 253 LEU cc_start: 0.9019 (tp) cc_final: 0.8816 (tt) REVERT: A 323 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.7447 (t80) REVERT: B 40 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: B 131 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8924 (mtp) REVERT: C 224 GLN cc_start: 0.8963 (tp40) cc_final: 0.8690 (tm-30) REVERT: C 250 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7119 (mtm180) REVERT: C 283 MET cc_start: 0.8944 (tpp) cc_final: 0.8614 (tpp) REVERT: C 312 ARG cc_start: 0.7099 (mtp-110) cc_final: 0.6526 (ttm-80) REVERT: D 112 MET cc_start: 0.9044 (tpp) cc_final: 0.8819 (tpp) REVERT: D 114 MET cc_start: 0.9278 (mmm) cc_final: 0.9056 (mmp) REVERT: D 131 MET cc_start: 0.9378 (mtp) cc_final: 0.9148 (mtp) REVERT: E 152 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7457 (mm-40) REVERT: E 162 GLU cc_start: 0.8590 (tt0) cc_final: 0.7924 (tm-30) REVERT: I 13 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7522 (pp-130) REVERT: I 102 LYS cc_start: 0.9078 (tptm) cc_final: 0.8863 (tppt) REVERT: L 56 THR cc_start: 0.9386 (m) cc_final: 0.9164 (p) REVERT: L 83 LEU cc_start: 0.8823 (mm) cc_final: 0.8577 (pp) REVERT: L 105 LEU cc_start: 0.8684 (tp) cc_final: 0.8430 (tp) REVERT: K 10 GLU cc_start: 0.8402 (mp0) cc_final: 0.7978 (mp0) REVERT: K 11 LEU cc_start: 0.8925 (mp) cc_final: 0.8679 (tm) REVERT: K 73 ASP cc_start: 0.8163 (t70) cc_final: 0.7811 (t0) REVERT: K 101 LEU cc_start: 0.8723 (mp) cc_final: 0.8405 (mm) outliers start: 38 outliers final: 16 residues processed: 269 average time/residue: 1.1233 time to fit residues: 343.0431 Evaluate side-chains 265 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 243 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain K residue 55 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 188 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 179 optimal weight: 0.5980 chunk 31 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN B 242 GLN D 56 HIS D 88 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.093290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.063845 restraints weight = 100379.832| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.64 r_work: 0.2731 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17892 Z= 0.115 Angle : 0.524 6.858 24387 Z= 0.265 Chirality : 0.042 0.215 2821 Planarity : 0.004 0.060 2980 Dihedral : 4.955 50.686 2943 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.44 % Allowed : 16.53 % Favored : 82.03 % 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 aren not related in a simple way. whole: -0.08 (0.19), residues: 2101 helix: 2.17 (0.21), residues: 585 sheet: -0.99 (0.19), residues: 674 loop : -0.74 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 85 TYR 0.014 0.001 TYR E 314 PHE 0.018 0.001 PHE E 346 TRP 0.007 0.001 TRP C 237 HIS 0.006 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00258 (17860) covalent geometry : angle 0.51877 (24300) SS BOND : bond 0.00697 ( 9) SS BOND : angle 0.86343 ( 18) hydrogen bonds : bond 0.03269 ( 765) hydrogen bonds : angle 4.28391 ( 2451) link_ALPHA1-2 : bond 0.00336 ( 3) link_ALPHA1-2 : angle 1.57285 ( 9) link_ALPHA1-3 : bond 0.00864 ( 2) link_ALPHA1-3 : angle 1.25299 ( 6) link_ALPHA1-6 : bond 0.00234 ( 2) link_ALPHA1-6 : angle 1.84231 ( 6) link_BETA1-4 : bond 0.00305 ( 9) link_BETA1-4 : angle 1.44880 ( 27) link_NAG-ASN : bond 0.00272 ( 7) link_NAG-ASN : angle 1.21390 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 253 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8363 (pp) REVERT: A 235 LEU cc_start: 0.9181 (mt) cc_final: 0.8790 (tt) REVERT: A 253 LEU cc_start: 0.9024 (tp) cc_final: 0.8803 (tt) REVERT: A 323 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7537 (t80) REVERT: B 131 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8890 (mtp) REVERT: C 224 GLN cc_start: 0.8934 (tp40) cc_final: 0.8320 (tp-100) REVERT: C 312 ARG cc_start: 0.7113 (mtp-110) cc_final: 0.6562 (ttm-80) REVERT: D 114 MET cc_start: 0.9244 (mmm) cc_final: 0.9022 (mmp) REVERT: D 131 MET cc_start: 0.9307 (mtp) cc_final: 0.9069 (mtp) REVERT: E 162 GLU cc_start: 0.8558 (tt0) cc_final: 0.7893 (tm-30) REVERT: I 13 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7507 (pp-130) REVERT: I 102 LYS cc_start: 0.9049 (tptm) cc_final: 0.8818 (tppt) REVERT: L 13 MET cc_start: 0.8113 (ppp) cc_final: 0.7907 (ppp) REVERT: L 56 THR cc_start: 0.9370 (m) cc_final: 0.9154 (p) REVERT: L 105 LEU cc_start: 0.8737 (tp) cc_final: 0.8518 (tp) REVERT: K 10 GLU cc_start: 0.8404 (mp0) cc_final: 0.8020 (mp0) REVERT: K 73 ASP cc_start: 0.8142 (t70) cc_final: 0.7819 (t0) REVERT: K 101 LEU cc_start: 0.8658 (mp) cc_final: 0.8336 (mm) outliers start: 27 outliers final: 12 residues processed: 262 average time/residue: 1.1325 time to fit residues: 335.1074 Evaluate side-chains 260 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 244 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 56 HIS Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain I residue 13 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 46 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN B 242 GLN D 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.093100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.063645 restraints weight = 101053.551| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.64 r_work: 0.2726 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17892 Z= 0.138 Angle : 0.527 6.722 24387 Z= 0.267 Chirality : 0.042 0.216 2821 Planarity : 0.004 0.067 2980 Dihedral : 4.804 53.059 2943 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.49 % Allowed : 16.85 % Favored : 81.66 % 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 aren not related in a simple way. whole: 0.09 (0.19), residues: 2101 helix: 2.29 (0.21), residues: 585 sheet: -0.87 (0.19), residues: 671 loop : -0.64 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 85 TYR 0.013 0.001 TYR E 314 PHE 0.015 0.001 PHE C 307 TRP 0.009 0.001 TRP C 237 HIS 0.005 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00311 (17860) covalent geometry : angle 0.52173 (24300) SS BOND : bond 0.00612 ( 9) SS BOND : angle 0.82238 ( 18) hydrogen bonds : bond 0.03238 ( 765) hydrogen bonds : angle 4.23556 ( 2451) link_ALPHA1-2 : bond 0.00199 ( 3) link_ALPHA1-2 : angle 1.76918 ( 9) link_ALPHA1-3 : bond 0.00736 ( 2) link_ALPHA1-3 : angle 1.32206 ( 6) link_ALPHA1-6 : bond 0.00129 ( 2) link_ALPHA1-6 : angle 1.99991 ( 6) link_BETA1-4 : bond 0.00290 ( 9) link_BETA1-4 : angle 1.44761 ( 27) link_NAG-ASN : bond 0.00159 ( 7) link_NAG-ASN : angle 1.32859 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 247 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.7986 (pp20) cc_final: 0.7568 (pp20) REVERT: A 218 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8345 (pp) REVERT: A 235 LEU cc_start: 0.9183 (mt) cc_final: 0.8803 (tt) REVERT: A 247 SER cc_start: 0.8333 (m) cc_final: 0.7952 (p) REVERT: A 253 LEU cc_start: 0.9003 (tp) cc_final: 0.8784 (tt) REVERT: A 323 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7548 (t80) REVERT: B 131 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8920 (mtp) REVERT: C 224 GLN cc_start: 0.8900 (tp40) cc_final: 0.8323 (tp-100) REVERT: C 312 ARG cc_start: 0.7094 (mtp-110) cc_final: 0.6588 (ttm-80) REVERT: D 114 MET cc_start: 0.9256 (mmm) cc_final: 0.9039 (mmp) REVERT: D 131 MET cc_start: 0.9336 (mtp) cc_final: 0.9034 (mtp) REVERT: E 162 GLU cc_start: 0.8556 (tt0) cc_final: 0.7926 (tm-30) REVERT: K 10 GLU cc_start: 0.8485 (mp0) cc_final: 0.8094 (mp0) REVERT: K 73 ASP cc_start: 0.8162 (t70) cc_final: 0.7838 (t0) REVERT: K 101 LEU cc_start: 0.8698 (mp) cc_final: 0.8380 (mm) outliers start: 28 outliers final: 12 residues processed: 260 average time/residue: 1.0861 time to fit residues: 320.7840 Evaluate side-chains 253 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 238 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 334 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 71 optimal weight: 2.9990 chunk 123 optimal weight: 0.1980 chunk 191 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS D 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.092649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.063135 restraints weight = 100678.588| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.64 r_work: 0.2717 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17892 Z= 0.155 Angle : 0.540 7.988 24387 Z= 0.272 Chirality : 0.042 0.222 2821 Planarity : 0.004 0.071 2980 Dihedral : 4.793 53.457 2943 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.17 % Allowed : 17.44 % Favored : 81.39 % 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 aren not related in a simple way. whole: 0.19 (0.19), residues: 2101 helix: 2.35 (0.21), residues: 585 sheet: -0.80 (0.20), residues: 662 loop : -0.58 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 85 TYR 0.013 0.001 TYR E 314 PHE 0.014 0.001 PHE C 307 TRP 0.011 0.001 TRP C 237 HIS 0.005 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00350 (17860) covalent geometry : angle 0.53420 (24300) SS BOND : bond 0.00606 ( 9) SS BOND : angle 0.96347 ( 18) hydrogen bonds : bond 0.03240 ( 765) hydrogen bonds : angle 4.23671 ( 2451) link_ALPHA1-2 : bond 0.00201 ( 3) link_ALPHA1-2 : angle 1.76693 ( 9) link_ALPHA1-3 : bond 0.00738 ( 2) link_ALPHA1-3 : angle 1.27880 ( 6) link_ALPHA1-6 : bond 0.00161 ( 2) link_ALPHA1-6 : angle 1.99145 ( 6) link_BETA1-4 : bond 0.00267 ( 9) link_BETA1-4 : angle 1.44452 ( 27) link_NAG-ASN : bond 0.00106 ( 7) link_NAG-ASN : angle 1.30155 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 244 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8344 (pp) REVERT: A 235 LEU cc_start: 0.9181 (mt) cc_final: 0.8805 (tt) REVERT: A 247 SER cc_start: 0.8497 (m) cc_final: 0.8125 (p) REVERT: A 253 LEU cc_start: 0.9017 (tp) cc_final: 0.8791 (tt) REVERT: A 323 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7521 (t80) REVERT: B 131 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8903 (mtp) REVERT: C 224 GLN cc_start: 0.8868 (tp40) cc_final: 0.8305 (tp-100) REVERT: C 312 ARG cc_start: 0.7133 (mtp-110) cc_final: 0.6626 (ttm-80) REVERT: D 112 MET cc_start: 0.8949 (tpp) cc_final: 0.8691 (tpp) REVERT: D 114 MET cc_start: 0.9244 (mmm) cc_final: 0.9026 (mmp) REVERT: D 131 MET cc_start: 0.9337 (mtp) cc_final: 0.9034 (mtp) REVERT: E 162 GLU cc_start: 0.8525 (tt0) cc_final: 0.7932 (tm-30) REVERT: L 104 GLU cc_start: 0.5344 (tm-30) cc_final: 0.5072 (tm-30) REVERT: K 10 GLU cc_start: 0.8486 (mp0) cc_final: 0.8104 (mp0) REVERT: K 73 ASP cc_start: 0.8186 (t70) cc_final: 0.7878 (t0) REVERT: K 101 LEU cc_start: 0.8707 (mp) cc_final: 0.8389 (mm) outliers start: 22 outliers final: 13 residues processed: 253 average time/residue: 1.0411 time to fit residues: 299.2194 Evaluate side-chains 255 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 239 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain L residue 70 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 47 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 75 optimal weight: 0.1980 chunk 153 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.093710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.064358 restraints weight = 100315.200| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.64 r_work: 0.2740 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17892 Z= 0.107 Angle : 0.530 8.434 24387 Z= 0.266 Chirality : 0.042 0.205 2821 Planarity : 0.004 0.074 2980 Dihedral : 4.603 51.003 2943 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.90 % Allowed : 18.02 % Favored : 81.07 % 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 aren not related in a simple way. whole: 0.31 (0.19), residues: 2101 helix: 2.43 (0.21), residues: 585 sheet: -0.76 (0.20), residues: 658 loop : -0.47 (0.23), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 85 TYR 0.013 0.001 TYR E 314 PHE 0.027 0.001 PHE E 346 TRP 0.014 0.001 TRP C 237 HIS 0.005 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00243 (17860) covalent geometry : angle 0.52536 (24300) SS BOND : bond 0.00575 ( 9) SS BOND : angle 0.86827 ( 18) hydrogen bonds : bond 0.03099 ( 765) hydrogen bonds : angle 4.12740 ( 2451) link_ALPHA1-2 : bond 0.00347 ( 3) link_ALPHA1-2 : angle 1.58349 ( 9) link_ALPHA1-3 : bond 0.00875 ( 2) link_ALPHA1-3 : angle 1.22499 ( 6) link_ALPHA1-6 : bond 0.00244 ( 2) link_ALPHA1-6 : angle 1.81358 ( 6) link_BETA1-4 : bond 0.00319 ( 9) link_BETA1-4 : angle 1.38241 ( 27) link_NAG-ASN : bond 0.00129 ( 7) link_NAG-ASN : angle 1.16296 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 240 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8329 (pp) REVERT: A 247 SER cc_start: 0.8555 (m) cc_final: 0.8273 (p) REVERT: A 323 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7563 (t80) REVERT: C 224 GLN cc_start: 0.8844 (tp40) cc_final: 0.8296 (tp-100) REVERT: D 114 MET cc_start: 0.9229 (mmm) cc_final: 0.9013 (mmp) REVERT: D 131 MET cc_start: 0.9291 (mtp) cc_final: 0.9051 (mtp) REVERT: D 338 LEU cc_start: 0.8520 (mm) cc_final: 0.8265 (tm) REVERT: E 162 GLU cc_start: 0.8541 (tt0) cc_final: 0.7931 (tm-30) REVERT: L 104 GLU cc_start: 0.5354 (tm-30) cc_final: 0.5080 (tm-30) REVERT: K 10 GLU cc_start: 0.8476 (mp0) cc_final: 0.8078 (mp0) REVERT: K 73 ASP cc_start: 0.8185 (t70) cc_final: 0.7929 (t0) outliers start: 17 outliers final: 8 residues processed: 246 average time/residue: 1.1331 time to fit residues: 315.7520 Evaluate side-chains 244 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 234 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 317 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 206 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 63 optimal weight: 0.0470 chunk 198 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS D 88 ASN K 110 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.092956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.063515 restraints weight = 100876.640| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.64 r_work: 0.2725 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17892 Z= 0.147 Angle : 0.555 9.208 24387 Z= 0.277 Chirality : 0.042 0.216 2821 Planarity : 0.004 0.077 2980 Dihedral : 4.609 50.458 2943 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.64 % Allowed : 18.71 % Favored : 80.65 % 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 aren not related in a simple way. whole: 0.37 (0.19), residues: 2101 helix: 2.49 (0.21), residues: 585 sheet: -0.71 (0.20), residues: 658 loop : -0.46 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 312 TYR 0.013 0.001 TYR E 314 PHE 0.012 0.001 PHE E 346 TRP 0.014 0.001 TRP C 237 HIS 0.004 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00334 (17860) covalent geometry : angle 0.55006 (24300) SS BOND : bond 0.00564 ( 9) SS BOND : angle 0.89333 ( 18) hydrogen bonds : bond 0.03139 ( 765) hydrogen bonds : angle 4.15378 ( 2451) link_ALPHA1-2 : bond 0.00182 ( 3) link_ALPHA1-2 : angle 1.77153 ( 9) link_ALPHA1-3 : bond 0.00753 ( 2) link_ALPHA1-3 : angle 1.23550 ( 6) link_ALPHA1-6 : bond 0.00171 ( 2) link_ALPHA1-6 : angle 2.01357 ( 6) link_BETA1-4 : bond 0.00285 ( 9) link_BETA1-4 : angle 1.40888 ( 27) link_NAG-ASN : bond 0.00093 ( 7) link_NAG-ASN : angle 1.28701 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 236 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8345 (pp) REVERT: A 247 SER cc_start: 0.8624 (m) cc_final: 0.8404 (p) REVERT: A 323 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7609 (t80) REVERT: C 224 GLN cc_start: 0.8851 (tp40) cc_final: 0.8305 (tp-100) REVERT: D 131 MET cc_start: 0.9311 (mtp) cc_final: 0.9000 (mtp) REVERT: D 338 LEU cc_start: 0.8526 (mm) cc_final: 0.8271 (tm) REVERT: E 162 GLU cc_start: 0.8506 (tt0) cc_final: 0.7884 (tm-30) REVERT: L 104 GLU cc_start: 0.5426 (tm-30) cc_final: 0.5165 (tm-30) REVERT: K 10 GLU cc_start: 0.8474 (mp0) cc_final: 0.8020 (mp0) REVERT: K 73 ASP cc_start: 0.8214 (t70) cc_final: 0.7959 (t0) REVERT: K 101 LEU cc_start: 0.8695 (mp) cc_final: 0.8374 (mm) outliers start: 12 outliers final: 8 residues processed: 242 average time/residue: 1.2724 time to fit residues: 348.4168 Evaluate side-chains 244 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 234 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 317 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 156 optimal weight: 9.9990 chunk 153 optimal weight: 0.8980 chunk 162 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 112 optimal weight: 0.3980 chunk 115 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS D 88 ASN K 110 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.092912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.063475 restraints weight = 100555.141| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.63 r_work: 0.2725 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17892 Z= 0.142 Angle : 0.546 8.389 24387 Z= 0.274 Chirality : 0.042 0.213 2821 Planarity : 0.004 0.075 2980 Dihedral : 4.585 49.253 2943 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.74 % Allowed : 18.50 % Favored : 80.75 % 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 aren not related in a simple way. whole: 0.40 (0.19), residues: 2101 helix: 2.50 (0.21), residues: 585 sheet: -0.68 (0.20), residues: 658 loop : -0.43 (0.23), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 85 TYR 0.013 0.001 TYR E 314 PHE 0.021 0.001 PHE C 307 TRP 0.015 0.001 TRP C 237 HIS 0.004 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00322 (17860) covalent geometry : angle 0.54129 (24300) SS BOND : bond 0.00573 ( 9) SS BOND : angle 0.89067 ( 18) hydrogen bonds : bond 0.03135 ( 765) hydrogen bonds : angle 4.14234 ( 2451) link_ALPHA1-2 : bond 0.00233 ( 3) link_ALPHA1-2 : angle 1.73056 ( 9) link_ALPHA1-3 : bond 0.00848 ( 2) link_ALPHA1-3 : angle 1.21680 ( 6) link_ALPHA1-6 : bond 0.00195 ( 2) link_ALPHA1-6 : angle 1.96242 ( 6) link_BETA1-4 : bond 0.00286 ( 9) link_BETA1-4 : angle 1.40355 ( 27) link_NAG-ASN : bond 0.00083 ( 7) link_NAG-ASN : angle 1.24877 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11072.32 seconds wall clock time: 187 minutes 52.59 seconds (11272.59 seconds total)