Starting phenix.real_space_refine on Sun Jun 29 19:19:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8si9_40503/06_2025/8si9_40503_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8si9_40503/06_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_40503/06_2025/8si9_40503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8si9_40503/06_2025/8si9_40503.map" model { file = "/net/cci-nas-00/data/ceres_data/8si9_40503/06_2025/8si9_40503_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8si9_40503/06_2025/8si9_40503_trim.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.65, per 1000 atoms: 0.57 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: 10.11 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 3.62 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: 15.07 Time building geometry restraints manager: 12.17 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 340 or resid 401)) selection = (chain 'C' and (resid 7 through 340 or resid 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: 2.200 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: 0.610 Extract box with map and model: 1.370 Check model and map are aligned: 0.470 Set scattering table: 0.590 Process input model: 80.740 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.150 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:15.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.280 ------------------------------------------------------------------------------- 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 : 3.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.001 TRP E 134 HIS 0.005 0.001 HIS B 110 PHE 0.017 0.002 PHE D 226 TYR 0.019 0.002 TYR D 129 ARG 0.010 0.001 ARG E 231 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 7) link_NAG-ASN : angle 1.91593 ( 21) 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_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) hydrogen bonds : bond 0.11642 ( 765) hydrogen bonds : angle 6.27925 ( 2451) SS BOND : bond 0.00886 ( 9) SS BOND : angle 1.44444 ( 18) covalent geometry : bond 0.00518 (17860) covalent geometry : angle 0.68996 (24300) *********************** 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 : 2.501 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 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: 0.7152 (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: 0.8205 (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: 0.8356 (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: 0.8291 (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: 2.5852 time to fit residues: 1202.3901 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 : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.091513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.062304 restraints weight = 101353.734| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.60 r_work: 0.2699 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 17892 Z= 0.269 Angle : 0.635 8.430 24387 Z= 0.328 Chirality : 0.045 0.294 2821 Planarity : 0.005 0.052 2980 Dihedral : 7.599 63.765 2943 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.91 % Allowed : 12.81 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.17), residues: 2101 helix: 0.73 (0.21), residues: 589 sheet: -1.91 (0.18), residues: 691 loop : -1.67 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 134 HIS 0.005 0.001 HIS C 267 PHE 0.019 0.001 PHE E 236 TYR 0.016 0.002 TYR D 129 ARG 0.009 0.001 ARG E 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 7) link_NAG-ASN : angle 1.71868 ( 21) link_ALPHA1-6 : bond 0.00109 ( 2) link_ALPHA1-6 : angle 2.51128 ( 6) link_BETA1-4 : bond 0.00141 ( 9) link_BETA1-4 : angle 2.33142 ( 27) link_ALPHA1-2 : bond 0.00196 ( 3) link_ALPHA1-2 : angle 2.10435 ( 9) link_ALPHA1-3 : bond 0.00605 ( 2) link_ALPHA1-3 : angle 1.39603 ( 6) hydrogen bonds : bond 0.04272 ( 765) hydrogen bonds : angle 4.97607 ( 2451) SS BOND : bond 0.00743 ( 9) SS BOND : angle 1.41855 ( 18) covalent geometry : bond 0.00603 (17860) covalent geometry : angle 0.62497 (24300) *********************** 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 307 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 271 time to evaluate : 2.702 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 235 LEU cc_start: 0.9180 (mt) cc_final: 0.8980 (tt) REVERT: A 247 SER cc_start: 0.7960 (m) cc_final: 0.7692 (p) REVERT: B 40 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8224 (tm-30) REVERT: C 224 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8508 (tm-30) REVERT: C 250 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7071 (mtm180) REVERT: C 283 MET cc_start: 0.8947 (tpp) cc_final: 0.8623 (tpp) REVERT: C 312 ARG cc_start: 0.7072 (mtp-110) cc_final: 0.6354 (ttm-80) REVERT: D 114 MET cc_start: 0.9223 (mmm) cc_final: 0.8962 (mmp) REVERT: E 162 GLU cc_start: 0.8612 (tt0) cc_final: 0.7815 (tm-30) REVERT: E 238 ILE cc_start: 0.9191 (pp) cc_final: 0.8937 (tt) REVERT: L 56 THR cc_start: 0.9362 (m) cc_final: 0.9100 (p) REVERT: L 105 LEU cc_start: 0.8726 (tp) cc_final: 0.8512 (tp) REVERT: K 73 ASP cc_start: 0.8139 (t70) cc_final: 0.7868 (t0) REVERT: K 101 LEU cc_start: 0.8721 (mp) cc_final: 0.8399 (mm) outliers start: 36 outliers final: 12 residues processed: 285 average time/residue: 2.6525 time to fit residues: 860.8675 Evaluate side-chains 257 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 243 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 264 ILE 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 D residue 242 GLN 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 K residue 55 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 169 optimal weight: 0.6980 chunk 156 optimal weight: 6.9990 chunk 123 optimal weight: 0.0980 chunk 73 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 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 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 = 0.3421 r_free = 0.3421 target = 0.092981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.063385 restraints weight = 100926.560| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.65 r_work: 0.2724 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2699 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= 0.142 Angle : 0.560 7.331 24387 Z= 0.285 Chirality : 0.043 0.167 2821 Planarity : 0.004 0.052 2980 Dihedral : 6.205 61.627 2943 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.81 % Allowed : 14.14 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.18), residues: 2101 helix: 1.52 (0.21), residues: 587 sheet: -1.57 (0.18), residues: 695 loop : -1.31 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 67 HIS 0.006 0.001 HIS C 267 PHE 0.017 0.001 PHE C 307 TYR 0.011 0.001 TYR E 314 ARG 0.004 0.000 ARG C 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00111 ( 7) link_NAG-ASN : angle 1.40637 ( 21) link_ALPHA1-6 : bond 0.00205 ( 2) link_ALPHA1-6 : angle 1.87656 ( 6) link_BETA1-4 : bond 0.00263 ( 9) link_BETA1-4 : angle 1.87331 ( 27) link_ALPHA1-2 : bond 0.00343 ( 3) link_ALPHA1-2 : angle 1.63222 ( 9) link_ALPHA1-3 : bond 0.00616 ( 2) link_ALPHA1-3 : angle 1.30706 ( 6) hydrogen bonds : bond 0.03738 ( 765) hydrogen bonds : angle 4.63222 ( 2451) SS BOND : bond 0.00631 ( 9) SS BOND : angle 0.99765 ( 18) covalent geometry : bond 0.00314 (17860) covalent geometry : angle 0.55286 (24300) *********************** 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 291 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 257 time to evaluate : 3.063 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: 0.7942 (pp20) cc_final: 0.7732 (pp20) REVERT: A 218 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8425 (pp) REVERT: A 235 LEU cc_start: 0.9178 (mt) cc_final: 0.8959 (tt) REVERT: A 247 SER cc_start: 0.7986 (m) cc_final: 0.7763 (p) REVERT: B 40 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8196 (tm-30) REVERT: C 224 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8556 (tm-30) REVERT: C 250 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7031 (mtm180) REVERT: C 312 ARG cc_start: 0.7109 (mtp-110) cc_final: 0.6466 (ttm-80) REVERT: D 114 MET cc_start: 0.9198 (mmm) cc_final: 0.8935 (mmp) REVERT: D 312 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8764 (ttpp) REVERT: E 162 GLU cc_start: 0.8570 (tt0) cc_final: 0.7843 (tm-30) REVERT: E 346 PHE cc_start: 0.8541 (t80) cc_final: 0.8250 (t80) REVERT: I 13 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7535 (pp-130) REVERT: L 56 THR cc_start: 0.9370 (m) cc_final: 0.9123 (p) REVERT: K 73 ASP cc_start: 0.8088 (t70) cc_final: 0.7747 (t0) REVERT: K 101 LEU cc_start: 0.8681 (mp) cc_final: 0.8362 (mm) outliers start: 34 outliers final: 15 residues processed: 275 average time/residue: 2.5141 time to fit residues: 782.7919 Evaluate side-chains 260 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 240 time to evaluate : 2.648 ------------------------------------------------------------------------------- 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 149 ASN Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 312 LYS 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 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: 0.7980 chunk 123 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 196 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 D 88 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.092734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.063131 restraints weight = 101129.816| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.65 r_work: 0.2718 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17892 Z= 0.158 Angle : 0.548 7.017 24387 Z= 0.278 Chirality : 0.042 0.196 2821 Planarity : 0.004 0.053 2980 Dihedral : 5.559 54.645 2943 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.86 % Allowed : 15.20 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.18), residues: 2101 helix: 1.87 (0.21), residues: 585 sheet: -1.33 (0.19), residues: 688 loop : -1.04 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 67 HIS 0.006 0.001 HIS C 267 PHE 0.012 0.001 PHE C 307 TYR 0.013 0.001 TYR E 314 ARG 0.005 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 7) link_NAG-ASN : angle 1.43107 ( 21) link_ALPHA1-6 : bond 0.00107 ( 2) link_ALPHA1-6 : angle 2.00164 ( 6) link_BETA1-4 : bond 0.00267 ( 9) link_BETA1-4 : angle 1.77689 ( 27) link_ALPHA1-2 : bond 0.00229 ( 3) link_ALPHA1-2 : angle 1.78092 ( 9) link_ALPHA1-3 : bond 0.00551 ( 2) link_ALPHA1-3 : angle 1.34416 ( 6) hydrogen bonds : bond 0.03542 ( 765) hydrogen bonds : angle 4.49487 ( 2451) SS BOND : bond 0.00581 ( 9) SS BOND : angle 0.98064 ( 18) covalent geometry : bond 0.00354 (17860) covalent geometry : angle 0.54104 (24300) *********************** 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 290 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 255 time to evaluate : 2.424 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: 0.8750 (OUTLIER) cc_final: 0.8385 (pp) REVERT: A 235 LEU cc_start: 0.9161 (mt) cc_final: 0.8952 (tt) REVERT: A 323 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7427 (t80) REVERT: B 40 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8214 (tm-30) REVERT: C 224 GLN cc_start: 0.8920 (tm-30) cc_final: 0.8594 (tm-30) REVERT: C 250 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7072 (mtm180) REVERT: C 312 ARG cc_start: 0.7095 (mtp-110) cc_final: 0.6517 (ttm-80) REVERT: D 114 MET cc_start: 0.9227 (mmm) cc_final: 0.9000 (mmp) REVERT: D 131 MET cc_start: 0.9346 (mtp) cc_final: 0.9066 (mtp) REVERT: E 162 GLU cc_start: 0.8561 (tt0) cc_final: 0.7853 (tm-30) REVERT: E 238 ILE cc_start: 0.9115 (pp) cc_final: 0.8892 (tt) REVERT: E 346 PHE cc_start: 0.8551 (t80) cc_final: 0.8273 (t80) REVERT: I 13 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7544 (pp-130) REVERT: I 102 LYS cc_start: 0.9053 (tptm) cc_final: 0.8776 (tppt) REVERT: L 56 THR cc_start: 0.9378 (m) cc_final: 0.9149 (p) REVERT: K 73 ASP cc_start: 0.8109 (t70) cc_final: 0.7762 (t0) REVERT: K 101 LEU cc_start: 0.8661 (mp) cc_final: 0.8342 (mm) outliers start: 35 outliers final: 15 residues processed: 272 average time/residue: 2.4955 time to fit residues: 770.3741 Evaluate side-chains 258 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 238 time to evaluate : 2.440 ------------------------------------------------------------------------------- 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 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 118 LEU Chi-restraints excluded: chain D residue 242 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 I residue 13 MET Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain K residue 55 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 7 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN B 242 GLN C 267 HIS D 56 HIS D 88 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.093056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.063566 restraints weight = 100983.152| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.65 r_work: 0.2724 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17892 Z= 0.130 Angle : 0.533 7.478 24387 Z= 0.269 Chirality : 0.042 0.207 2821 Planarity : 0.004 0.062 2980 Dihedral : 5.209 48.539 2943 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.70 % Allowed : 15.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.19), residues: 2101 helix: 2.09 (0.21), residues: 585 sheet: -1.11 (0.19), residues: 654 loop : -0.89 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 67 HIS 0.007 0.001 HIS C 267 PHE 0.010 0.001 PHE E 236 TYR 0.014 0.001 TYR E 314 ARG 0.009 0.000 ARG E 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00104 ( 7) link_NAG-ASN : angle 1.23717 ( 21) link_ALPHA1-6 : bond 0.00151 ( 2) link_ALPHA1-6 : angle 1.90800 ( 6) link_BETA1-4 : bond 0.00272 ( 9) link_BETA1-4 : angle 1.56620 ( 27) link_ALPHA1-2 : bond 0.00276 ( 3) link_ALPHA1-2 : angle 1.66440 ( 9) link_ALPHA1-3 : bond 0.00731 ( 2) link_ALPHA1-3 : angle 1.30112 ( 6) hydrogen bonds : bond 0.03361 ( 765) hydrogen bonds : angle 4.36563 ( 2451) SS BOND : bond 0.01010 ( 9) SS BOND : angle 0.89699 ( 18) covalent geometry : bond 0.00290 (17860) covalent geometry : angle 0.52736 (24300) *********************** 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 288 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 256 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.7985 (pp20) cc_final: 0.7687 (pp20) REVERT: A 218 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8367 (pp) REVERT: A 235 LEU cc_start: 0.9188 (mt) cc_final: 0.8981 (tt) REVERT: A 323 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7427 (t80) REVERT: B 242 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8069 (mt0) REVERT: C 224 GLN cc_start: 0.8911 (tm-30) cc_final: 0.8642 (tm-30) REVERT: C 250 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7077 (mtm180) REVERT: C 312 ARG cc_start: 0.7110 (mtp-110) cc_final: 0.6619 (ttm-80) REVERT: D 114 MET cc_start: 0.9262 (mmm) cc_final: 0.9047 (mmp) REVERT: D 131 MET cc_start: 0.9343 (mtp) cc_final: 0.9054 (mtp) REVERT: E 152 GLN cc_start: 0.7727 (mm-40) cc_final: 0.7483 (mm-40) REVERT: E 162 GLU cc_start: 0.8561 (tt0) cc_final: 0.7926 (tm-30) REVERT: I 13 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7501 (pp-130) REVERT: L 56 THR cc_start: 0.9383 (m) cc_final: 0.9158 (p) REVERT: L 83 LEU cc_start: 0.8797 (mm) cc_final: 0.8515 (pp) REVERT: L 104 GLU cc_start: 0.5223 (tm-30) cc_final: 0.4947 (tm-30) REVERT: K 10 GLU cc_start: 0.8395 (mp0) cc_final: 0.8018 (mp0) REVERT: K 73 ASP cc_start: 0.8141 (t70) cc_final: 0.7797 (t0) REVERT: K 101 LEU cc_start: 0.8671 (mp) cc_final: 0.8355 (mm) outliers start: 32 outliers final: 17 residues processed: 271 average time/residue: 2.4598 time to fit residues: 760.6043 Evaluate side-chains 271 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 249 time to evaluate : 2.579 ------------------------------------------------------------------------------- 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 63 ASP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 247 LEU 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 C residue 309 GLN Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 298 PHE 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 I residue 45 LYS Chi-restraints excluded: chain L residue 70 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 146 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 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 = 0.3394 r_free = 0.3394 target = 0.091482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.061837 restraints weight = 101451.881| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.63 r_work: 0.2681 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17892 Z= 0.242 Angle : 0.572 7.484 24387 Z= 0.293 Chirality : 0.043 0.222 2821 Planarity : 0.004 0.062 2980 Dihedral : 5.320 51.340 2943 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.91 % Allowed : 16.11 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.19), residues: 2101 helix: 2.11 (0.21), residues: 585 sheet: -0.99 (0.19), residues: 664 loop : -0.85 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 103 HIS 0.010 0.001 HIS C 267 PHE 0.021 0.001 PHE E 346 TYR 0.014 0.001 TYR E 172 ARG 0.008 0.001 ARG E 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 7) link_NAG-ASN : angle 1.54139 ( 21) link_ALPHA1-6 : bond 0.00333 ( 2) link_ALPHA1-6 : angle 2.15167 ( 6) link_BETA1-4 : bond 0.00263 ( 9) link_BETA1-4 : angle 1.64727 ( 27) link_ALPHA1-2 : bond 0.00188 ( 3) link_ALPHA1-2 : angle 2.01927 ( 9) link_ALPHA1-3 : bond 0.00534 ( 2) link_ALPHA1-3 : angle 1.43382 ( 6) hydrogen bonds : bond 0.03537 ( 765) hydrogen bonds : angle 4.46702 ( 2451) SS BOND : bond 0.00751 ( 9) SS BOND : angle 1.13530 ( 18) covalent geometry : bond 0.00543 (17860) covalent geometry : angle 0.56510 (24300) *********************** 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 288 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 252 time to evaluate : 2.732 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: 0.8751 (OUTLIER) cc_final: 0.8428 (pp) REVERT: A 235 LEU cc_start: 0.9191 (mt) cc_final: 0.8808 (tt) REVERT: A 253 LEU cc_start: 0.9017 (tp) cc_final: 0.8800 (tt) REVERT: A 323 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7519 (t80) REVERT: C 224 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8576 (tm-30) REVERT: C 250 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7160 (mtm180) REVERT: C 312 ARG cc_start: 0.7101 (mtp-110) cc_final: 0.6551 (ttm-80) REVERT: D 114 MET cc_start: 0.9281 (mmm) cc_final: 0.9066 (mmp) REVERT: D 131 MET cc_start: 0.9396 (mtp) cc_final: 0.9171 (mtp) REVERT: E 162 GLU cc_start: 0.8612 (tt0) cc_final: 0.7974 (tm-30) REVERT: I 13 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7510 (pp-130) REVERT: L 56 THR cc_start: 0.9375 (m) cc_final: 0.9152 (p) REVERT: L 104 GLU cc_start: 0.5263 (tm-30) cc_final: 0.4961 (tm-30) REVERT: K 10 GLU cc_start: 0.8401 (mp0) cc_final: 0.7987 (mp0) REVERT: K 73 ASP cc_start: 0.8155 (t70) cc_final: 0.7790 (t0) REVERT: K 101 LEU cc_start: 0.8727 (mp) cc_final: 0.8416 (mm) outliers start: 36 outliers final: 20 residues processed: 263 average time/residue: 2.4914 time to fit residues: 744.2560 Evaluate side-chains 269 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 245 time to evaluate : 2.726 ------------------------------------------------------------------------------- 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 283 MET Chi-restraints excluded: chain A residue 323 PHE 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 B residue 298 PHE 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 C residue 309 GLN Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 264 LEU 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 11 MET Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain K residue 55 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 134 optimal weight: 0.0670 chunk 30 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.9120 ------------------------------------------------------------------------------- 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** C 267 HIS 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 = 0.3418 r_free = 0.3418 target = 0.092823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.063291 restraints weight = 101007.827| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.64 r_work: 0.2717 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3335 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= 0.123 Angle : 0.534 6.858 24387 Z= 0.270 Chirality : 0.042 0.217 2821 Planarity : 0.004 0.066 2980 Dihedral : 4.999 47.901 2943 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.75 % Allowed : 16.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.19), residues: 2101 helix: 2.23 (0.21), residues: 585 sheet: -0.94 (0.19), residues: 662 loop : -0.66 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 237 HIS 0.012 0.001 HIS C 267 PHE 0.020 0.001 PHE C 307 TYR 0.014 0.001 TYR E 314 ARG 0.009 0.000 ARG E 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00105 ( 7) link_NAG-ASN : angle 1.26176 ( 21) link_ALPHA1-6 : bond 0.00227 ( 2) link_ALPHA1-6 : angle 1.83093 ( 6) link_BETA1-4 : bond 0.00306 ( 9) link_BETA1-4 : angle 1.48300 ( 27) link_ALPHA1-2 : bond 0.00329 ( 3) link_ALPHA1-2 : angle 1.59145 ( 9) link_ALPHA1-3 : bond 0.00807 ( 2) link_ALPHA1-3 : angle 1.23490 ( 6) hydrogen bonds : bond 0.03300 ( 765) hydrogen bonds : angle 4.29282 ( 2451) SS BOND : bond 0.00674 ( 9) SS BOND : angle 0.86045 ( 18) covalent geometry : bond 0.00277 (17860) covalent geometry : angle 0.52887 (24300) *********************** 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 282 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 249 time to evaluate : 2.530 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: 0.8708 (OUTLIER) cc_final: 0.8350 (pp) REVERT: B 229 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8623 (tp40) REVERT: C 224 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8583 (tm-30) REVERT: C 312 ARG cc_start: 0.7095 (mtp-110) cc_final: 0.6560 (ttm-80) REVERT: D 114 MET cc_start: 0.9235 (mmm) cc_final: 0.8974 (mmp) REVERT: D 131 MET cc_start: 0.9330 (mtp) cc_final: 0.9097 (mtp) REVERT: E 162 GLU cc_start: 0.8584 (tt0) cc_final: 0.7943 (tm-30) REVERT: L 56 THR cc_start: 0.9367 (m) cc_final: 0.9160 (p) REVERT: K 10 GLU cc_start: 0.8422 (mp0) cc_final: 0.8028 (mp0) REVERT: K 73 ASP cc_start: 0.8120 (t70) cc_final: 0.7775 (t0) outliers start: 33 outliers final: 14 residues processed: 262 average time/residue: 2.4591 time to fit residues: 730.8866 Evaluate side-chains 252 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 2.697 ------------------------------------------------------------------------------- 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 63 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 229 GLN 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 118 LEU 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 L residue 70 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 186 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 154 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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** C 267 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 = 0.3416 r_free = 0.3416 target = 0.092744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.063220 restraints weight = 100809.239| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.64 r_work: 0.2712 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17892 Z= 0.136 Angle : 0.538 7.014 24387 Z= 0.272 Chirality : 0.042 0.217 2821 Planarity : 0.004 0.070 2980 Dihedral : 4.875 48.858 2943 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.28 % Allowed : 17.44 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.19), residues: 2101 helix: 2.31 (0.21), residues: 585 sheet: -0.86 (0.19), residues: 672 loop : -0.59 (0.23), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 237 HIS 0.012 0.001 HIS C 267 PHE 0.012 0.001 PHE E 346 TYR 0.014 0.001 TYR E 314 ARG 0.010 0.000 ARG E 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 7) link_NAG-ASN : angle 1.30130 ( 21) link_ALPHA1-6 : bond 0.00153 ( 2) link_ALPHA1-6 : angle 1.94348 ( 6) link_BETA1-4 : bond 0.00300 ( 9) link_BETA1-4 : angle 1.45148 ( 27) link_ALPHA1-2 : bond 0.00233 ( 3) link_ALPHA1-2 : angle 1.73522 ( 9) link_ALPHA1-3 : bond 0.00778 ( 2) link_ALPHA1-3 : angle 1.31323 ( 6) hydrogen bonds : bond 0.03241 ( 765) hydrogen bonds : angle 4.25342 ( 2451) SS BOND : bond 0.00584 ( 9) SS BOND : angle 1.00507 ( 18) covalent geometry : bond 0.00307 (17860) covalent geometry : angle 0.53249 (24300) *********************** 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 270 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 246 time to evaluate : 2.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8341 (pp) REVERT: A 323 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.7323 (t80) REVERT: C 224 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8581 (tm-30) REVERT: C 312 ARG cc_start: 0.7133 (mtp-110) cc_final: 0.6621 (ttm-80) REVERT: D 114 MET cc_start: 0.9262 (mmm) cc_final: 0.9009 (mmp) REVERT: D 131 MET cc_start: 0.9336 (mtp) cc_final: 0.9037 (mtp) REVERT: E 162 GLU cc_start: 0.8588 (tt0) cc_final: 0.7947 (tm-30) REVERT: L 104 GLU cc_start: 0.4979 (tm-30) cc_final: 0.4714 (tm-30) REVERT: K 10 GLU cc_start: 0.8425 (mp0) cc_final: 0.8022 (mp0) REVERT: K 73 ASP cc_start: 0.8149 (t70) cc_final: 0.7804 (t0) REVERT: K 101 LEU cc_start: 0.8692 (mp) cc_final: 0.8376 (mm) outliers start: 24 outliers final: 14 residues processed: 256 average time/residue: 2.5209 time to fit residues: 739.3584 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 : 2.442 ------------------------------------------------------------------------------- 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 197 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 150 CYS 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 317 LEU Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain K residue 55 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 75 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** C 267 HIS D 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.093129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.063708 restraints weight = 100731.552| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.64 r_work: 0.2722 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17892 Z= 0.118 Angle : 0.534 6.946 24387 Z= 0.269 Chirality : 0.042 0.211 2821 Planarity : 0.004 0.074 2980 Dihedral : 4.709 48.366 2943 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.85 % Allowed : 18.23 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.19), residues: 2101 helix: 2.40 (0.21), residues: 585 sheet: -0.79 (0.19), residues: 662 loop : -0.54 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 237 HIS 0.013 0.001 HIS C 267 PHE 0.026 0.001 PHE E 346 TYR 0.013 0.001 TYR E 314 ARG 0.011 0.000 ARG E 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00102 ( 7) link_NAG-ASN : angle 1.22237 ( 21) link_ALPHA1-6 : bond 0.00201 ( 2) link_ALPHA1-6 : angle 1.86228 ( 6) link_BETA1-4 : bond 0.00310 ( 9) link_BETA1-4 : angle 1.40307 ( 27) link_ALPHA1-2 : bond 0.00297 ( 3) link_ALPHA1-2 : angle 1.63970 ( 9) link_ALPHA1-3 : bond 0.00819 ( 2) link_ALPHA1-3 : angle 1.24203 ( 6) hydrogen bonds : bond 0.03153 ( 765) hydrogen bonds : angle 4.17613 ( 2451) SS BOND : bond 0.00589 ( 9) SS BOND : angle 0.89547 ( 18) covalent geometry : bond 0.00268 (17860) covalent geometry : angle 0.52857 (24300) *********************** 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 260 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 244 time to evaluate : 2.736 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: 0.8681 (OUTLIER) cc_final: 0.8328 (pp) REVERT: C 224 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8578 (tm-30) REVERT: D 131 MET cc_start: 0.9318 (mtp) cc_final: 0.9047 (mtp) REVERT: D 338 LEU cc_start: 0.8566 (mm) cc_final: 0.8304 (tm) REVERT: E 162 GLU cc_start: 0.8573 (tt0) cc_final: 0.7906 (tm-30) REVERT: L 104 GLU cc_start: 0.4996 (tm-30) cc_final: 0.4756 (tm-30) REVERT: K 10 GLU cc_start: 0.8495 (mp0) cc_final: 0.8115 (mp0) REVERT: K 73 ASP cc_start: 0.8181 (t70) cc_final: 0.7914 (t0) outliers start: 16 outliers final: 8 residues processed: 251 average time/residue: 2.5137 time to fit residues: 716.6029 Evaluate side-chains 244 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 235 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain C residue 150 CYS 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 317 LEU Chi-restraints excluded: chain E residue 334 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 108 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** C 267 HIS D 56 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 = 0.3370 r_free = 0.3370 target = 0.090093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.060929 restraints weight = 100774.694| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.57 r_work: 0.2658 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 17892 Z= 0.318 Angle : 0.636 8.284 24387 Z= 0.324 Chirality : 0.045 0.238 2821 Planarity : 0.005 0.081 2980 Dihedral : 5.244 51.534 2943 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.96 % Allowed : 18.55 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.19), residues: 2101 helix: 2.21 (0.21), residues: 588 sheet: -0.72 (0.19), residues: 674 loop : -0.61 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 237 HIS 0.011 0.002 HIS C 267 PHE 0.015 0.002 PHE D 226 TYR 0.017 0.002 TYR E 172 ARG 0.012 0.001 ARG E 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 7) link_NAG-ASN : angle 1.78178 ( 21) link_ALPHA1-6 : bond 0.00529 ( 2) link_ALPHA1-6 : angle 2.35244 ( 6) link_BETA1-4 : bond 0.00282 ( 9) link_BETA1-4 : angle 1.69977 ( 27) link_ALPHA1-2 : bond 0.00335 ( 3) link_ALPHA1-2 : angle 2.31730 ( 9) link_ALPHA1-3 : bond 0.00374 ( 2) link_ALPHA1-3 : angle 1.46562 ( 6) hydrogen bonds : bond 0.03654 ( 765) hydrogen bonds : angle 4.50899 ( 2451) SS BOND : bond 0.00665 ( 9) SS BOND : angle 1.44000 ( 18) covalent geometry : bond 0.00721 (17860) covalent geometry : angle 0.62814 (24300) ********************** 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 249 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 231 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8480 (pp) REVERT: A 323 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7357 (t80) REVERT: B 229 GLN cc_start: 0.8848 (tp40) cc_final: 0.8529 (tp-100) REVERT: C 224 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8618 (tm-30) REVERT: D 131 MET cc_start: 0.9413 (mtp) cc_final: 0.9174 (mtp) REVERT: E 162 GLU cc_start: 0.8613 (tt0) cc_final: 0.7906 (tm-30) REVERT: L 104 GLU cc_start: 0.5194 (tm-30) cc_final: 0.4769 (tm-30) REVERT: K 10 GLU cc_start: 0.8456 (mp0) cc_final: 0.8047 (mp0) REVERT: K 73 ASP cc_start: 0.8273 (t70) cc_final: 0.7955 (t0) REVERT: K 101 LEU cc_start: 0.8780 (mp) cc_final: 0.8472 (mm) outliers start: 18 outliers final: 10 residues processed: 241 average time/residue: 2.5330 time to fit residues: 694.9269 Evaluate side-chains 240 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 228 time to evaluate : 2.565 ------------------------------------------------------------------------------- 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 197 THR Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 267 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 175 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** C 267 HIS D 56 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 = 0.3409 r_free = 0.3409 target = 0.092416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.062912 restraints weight = 100504.546| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.63 r_work: 0.2701 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: 0.8494 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17892 Z= 0.130 Angle : 0.576 8.974 24387 Z= 0.289 Chirality : 0.043 0.218 2821 Planarity : 0.005 0.076 2980 Dihedral : 5.016 50.353 2943 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.96 % Allowed : 18.61 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 2101 helix: 2.30 (0.21), residues: 590 sheet: -0.70 (0.20), residues: 664 loop : -0.52 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 237 HIS 0.028 0.001 HIS C 267 PHE 0.018 0.001 PHE C 307 TYR 0.013 0.001 TYR E 314 ARG 0.013 0.001 ARG C 312 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 7) link_NAG-ASN : angle 1.32423 ( 21) link_ALPHA1-6 : bond 0.00277 ( 2) link_ALPHA1-6 : angle 1.88104 ( 6) link_BETA1-4 : bond 0.00324 ( 9) link_BETA1-4 : angle 1.48028 ( 27) link_ALPHA1-2 : bond 0.00259 ( 3) link_ALPHA1-2 : angle 1.66399 ( 9) link_ALPHA1-3 : bond 0.00826 ( 2) link_ALPHA1-3 : angle 1.25668 ( 6) hydrogen bonds : bond 0.03379 ( 765) hydrogen bonds : angle 4.32689 ( 2451) SS BOND : bond 0.00613 ( 9) SS BOND : angle 1.04257 ( 18) covalent geometry : bond 0.00292 (17860) covalent geometry : angle 0.57056 (24300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24381.99 seconds wall clock time: 413 minutes 29.76 seconds (24809.76 seconds total)