Starting phenix.real_space_refine on Fri Mar 6 21:22:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t0w_25583/03_2026/7t0w_25583_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t0w_25583/03_2026/7t0w_25583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t0w_25583/03_2026/7t0w_25583_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t0w_25583/03_2026/7t0w_25583_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t0w_25583/03_2026/7t0w_25583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t0w_25583/03_2026/7t0w_25583.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 95 5.16 5 C 11221 2.51 5 N 2856 2.21 5 O 3255 1.98 5 H 16968 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34395 Number of models: 1 Model: "" Number of chains: 16 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: 5454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5454 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} 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: 5454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5454 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} 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: "L2" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1582 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 1821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1821 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "H2" Number of atoms: 1821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1821 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "L" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1568 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "F" 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: "G" 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: "I" 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: "J" 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: "K" 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: "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: 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 Time building chain proxies: 6.00, per 1000 atoms: 0.17 Number of scatterers: 34395 At special positions: 0 Unit cell: (144.586, 108.979, 143.507, 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 95 16.00 O 3255 8.00 N 2856 7.00 C 11221 6.00 H 16968 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYSH2 22 " - pdb=" SG CYSH2 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " 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 N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN N 8 " - " MAN N 9 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " MAN N 7 " - " MAN N 10 " ALPHA1-6 " BMA N 3 " - " MAN N 7 " " MAN N 7 " - " MAN N 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG F 1 " - " ASN A 80 " " NAG G 1 " - " ASN C 80 " " NAG I 1 " - " ASN C 149 " " NAG J 1 " - " ASN D 111 " " NAG K 1 " - " ASN E 208 " " NAG M 1 " - " ASN A 149 " " NAG N 1 " - " ASN B 111 " Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 801.8 milliseconds 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4024 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 21 sheets defined 34.0% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 Processing helix chain 'A' and resid 70 through 73 removed outlier: 3.518A pdb=" N SER A 73 " --> pdb=" O LYS A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 73' Processing helix chain 'A' and resid 84 through 90 removed outlier: 3.527A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 242 removed outlier: 4.675A pdb=" N MET A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix removed outlier: 4.009A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TRP A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 242 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 272 removed outlier: 3.509A pdb=" N ARG A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 306 Processing helix chain 'A' and resid 309 through 339 Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 11 through 22 removed outlier: 3.621A pdb=" N PHE B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 76 removed outlier: 3.633A pdb=" N LYS B 76 " --> pdb=" O GLU B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 73 through 76' Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 223 through 244 removed outlier: 4.712A pdb=" N LEU B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix 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 275 removed outlier: 3.501A pdb=" N ASN B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 311 Processing helix chain 'B' and resid 314 through 346 removed outlier: 3.775A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix removed outlier: 3.954A pdb=" N ILE B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.727A 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: 3.544A 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 84 through 90 removed outlier: 3.592A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 238 removed outlier: 4.672A pdb=" N MET C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 246 through 272 removed outlier: 4.160A pdb=" N GLU C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 307 removed outlier: 4.785A pdb=" N PHE C 307 " --> pdb=" O ASN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 339 Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 12 through 23 removed outlier: 4.498A pdb=" N LEU D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 removed outlier: 3.550A pdb=" N LYS D 76 " --> pdb=" O GLU D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 76' Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.614A pdb=" N ASP D 145 " --> pdb=" O HIS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 183 through 186 removed outlier: 4.466A pdb=" N SER D 186 " --> pdb=" O GLU D 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 183 through 186' Processing helix chain 'D' and resid 223 through 230 removed outlier: 3.639A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.581A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 251 through 277 Processing helix chain 'D' and resid 284 through 311 Processing helix chain 'D' and resid 314 through 347 Proline residue: D 330 - end of helix removed outlier: 4.191A pdb=" N ARG D 347 " --> pdb=" O THR D 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 85 through 88 removed outlier: 3.721A pdb=" N LYS E 88 " --> pdb=" O ARG E 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 85 through 88' Processing helix chain 'E' and resid 99 through 105 removed outlier: 4.026A pdb=" N MET E 102 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 240 removed outlier: 4.227A pdb=" N ILE E 238 " --> pdb=" O GLY E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 252 Processing helix chain 'E' and resid 252 through 257 removed outlier: 4.026A pdb=" N TRP E 256 " --> pdb=" O TRP E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 286 removed outlier: 3.684A pdb=" N ILE E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG E 284 " --> pdb=" O SER E 280 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER E 286 " --> pdb=" O ILE E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 322 removed outlier: 4.252A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 356 removed outlier: 3.810A pdb=" N LYS E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET E 331 " --> pdb=" O ARG E 327 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP E 332 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE E 337 " --> pdb=" O SER E 333 " (cutoff:3.500A) Proline residue: E 340 - end of helix removed outlier: 3.529A pdb=" N LEU E 355 " --> pdb=" O TRP E 351 " (cutoff:3.500A) Processing helix chain 'L2' and resid 80 through 84 Processing helix chain 'H' and resid 61 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.747A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H2' and resid 61 through 65 removed outlier: 3.519A pdb=" N GLNH2 65 " --> pdb=" O GLNH2 62 " (cutoff:3.500A) Processing helix chain 'H2' and resid 87 through 91 removed outlier: 3.579A pdb=" N ASPH2 90 " --> pdb=" O ARGH2 87 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THRH2 91 " --> pdb=" O SERH2 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H2' and resid 87 through 91' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.536A pdb=" N ASP L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 51 removed outlier: 6.532A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 56 through 68 current: chain 'A' and resid 123 through 135 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.796A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 49 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 39 through 49 current: chain 'B' and resid 59 through 71 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 59 through 71 current: chain 'B' and resid 126 through 138 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 99 through 101 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 150 through 159 current: chain 'B' and resid 209 through 221 Processing sheet with id=AA5, first strand: chain 'C' and resid 36 through 51 removed outlier: 6.501A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 68 current: chain 'C' and resid 123 through 135 Processing sheet with id=AA6, first strand: chain 'C' and resid 96 through 98 removed outlier: 4.029A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY C 203 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 42 through 49 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 42 through 49 current: chain 'D' and resid 59 through 71 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 71 current: chain 'D' and resid 126 through 138 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.126A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 51 through 59 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 51 through 59 current: chain 'E' and resid 71 through 83 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 71 through 83 current: chain 'E' and resid 138 through 150 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 111 through 112 removed outlier: 4.494A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L2' and resid 9 through 10 removed outlier: 6.316A pdb=" N TRPL2 36 " --> pdb=" O LEUL2 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L2' and resid 18 through 23 Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.610A pdb=" N GLU H 10 " --> pdb=" O VAL H 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AB6, first strand: chain 'H' and resid 45 through 49 removed outlier: 5.000A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 101 through 103 Processing sheet with id=AB8, first strand: chain 'H2' and resid 3 through 6 removed outlier: 3.800A pdb=" N VALH2 20 " --> pdb=" O METH2 81 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H2' and resid 10 through 11 removed outlier: 6.179A pdb=" N GLUH2 10 " --> pdb=" O VALH2 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'H2' and resid 45 through 51 removed outlier: 6.702A pdb=" N TRPH2 36 " --> pdb=" O METH2 48 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N GLYH2 50 " --> pdb=" O ILEH2 34 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILEH2 34 " --> pdb=" O GLYH2 50 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASPH2 33 " --> pdb=" O GLYH2 99 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 12 current: chain 'L' and resid 46 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 46 through 49 current: chain 'L' and resid 99 through 102 No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'L' and resid 18 through 23 650 hydrogen bonds defined for protein. 1842 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: 6.87 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 16571 1.03 - 1.23: 701 1.23 - 1.43: 7385 1.43 - 1.63: 10007 1.63 - 1.82: 163 Bond restraints: 34827 Sorted by residual: bond pdb=" N ASP L 94 " pdb=" H ASP L 94 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.83e+01 bond pdb=" N MET H 51 " pdb=" H MET H 51 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.83e+01 bond pdb=" N TYR D 169 " pdb=" H TYR D 169 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.80e+01 bond pdb=" N TYR H 32 " pdb=" H TYR H 32 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.79e+01 bond pdb=" N ASNH2 57 " pdb=" H ASNH2 57 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.79e+01 ... (remaining 34822 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 61414 1.89 - 3.77: 981 3.77 - 5.66: 145 5.66 - 7.54: 27 7.54 - 9.43: 4 Bond angle restraints: 62571 Sorted by residual: angle pdb=" O LEUL2 96 " pdb=" C LEUL2 96 " pdb=" N LYSL2 97 " ideal model delta sigma weight residual 122.81 116.31 6.50 1.42e+00 4.96e-01 2.10e+01 angle pdb=" CA ASPH2 52 " pdb=" C ASPH2 52 " pdb=" O ASPH2 52 " ideal model delta sigma weight residual 119.76 115.69 4.07 8.90e-01 1.26e+00 2.09e+01 angle pdb=" CA LEU L 96 " pdb=" C LEU L 96 " pdb=" O LEU L 96 " ideal model delta sigma weight residual 120.99 115.91 5.08 1.12e+00 7.97e-01 2.06e+01 angle pdb=" CA LEU L 96 " pdb=" C LEU L 96 " pdb=" N LYS L 97 " ideal model delta sigma weight residual 115.61 122.16 -6.55 1.45e+00 4.76e-01 2.04e+01 angle pdb=" N GLY H 56 " pdb=" CA GLY H 56 " pdb=" C GLY H 56 " ideal model delta sigma weight residual 115.21 109.38 5.83 1.30e+00 5.92e-01 2.01e+01 ... (remaining 62566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.27: 15717 21.27 - 42.54: 880 42.54 - 63.80: 235 63.80 - 85.07: 34 85.07 - 106.34: 13 Dihedral angle restraints: 16879 sinusoidal: 9203 harmonic: 7676 Sorted by residual: dihedral pdb=" CB CYSH2 22 " pdb=" SG CYSH2 22 " pdb=" SG CYSH2 96 " pdb=" CB CYSH2 96 " ideal model delta sinusoidal sigma weight residual 93.00 145.43 -52.43 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CA CYS D 153 " pdb=" C CYS D 153 " pdb=" N PRO D 154 " pdb=" CA PRO D 154 " ideal model delta harmonic sigma weight residual 180.00 -158.72 -21.28 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 165 " pdb=" CB CYS E 165 " ideal model delta sinusoidal sigma weight residual 93.00 57.96 35.04 1 1.00e+01 1.00e-02 1.74e+01 ... (remaining 16876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2404 0.066 - 0.133: 373 0.133 - 0.199: 34 0.199 - 0.266: 5 0.266 - 0.332: 1 Chirality restraints: 2817 Sorted by residual: chirality pdb=" CA ASP H 113 " pdb=" N ASP H 113 " pdb=" C ASP H 113 " pdb=" CB ASP H 113 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.71e+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 -2.52 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 2814 not shown) Planarity restraints: 5046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN H 57 " 0.297 2.00e-02 2.50e+03 3.09e-01 1.43e+03 pdb=" CG ASN H 57 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN H 57 " -0.290 2.00e-02 2.50e+03 pdb=" ND2 ASN H 57 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN H 57 " -0.445 2.00e-02 2.50e+03 pdb="HD22 ASN H 57 " 0.451 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASNH2 57 " -0.197 2.00e-02 2.50e+03 1.94e-01 5.64e+02 pdb=" CG ASNH2 57 " 0.007 2.00e-02 2.50e+03 pdb=" OD1 ASNH2 57 " 0.192 2.00e-02 2.50e+03 pdb=" ND2 ASNH2 57 " 0.006 2.00e-02 2.50e+03 pdb="HD21 ASNH2 57 " -0.277 2.00e-02 2.50e+03 pdb="HD22 ASNH2 57 " 0.270 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASPH2 52 " -0.019 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C ASPH2 52 " 0.064 2.00e-02 2.50e+03 pdb=" O ASPH2 52 " -0.023 2.00e-02 2.50e+03 pdb=" N PROH2 53 " -0.022 2.00e-02 2.50e+03 ... (remaining 5043 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 1076 2.11 - 2.74: 62001 2.74 - 3.36: 98731 3.36 - 3.98: 130277 3.98 - 4.60: 203985 Nonbonded interactions: 496070 Sorted by model distance: nonbonded pdb=" OH TYRH2 60 " pdb=" H METH2 70 " model vdw 1.494 2.450 nonbonded pdb=" O THR C 233 " pdb=" HG SER C 236 " model vdw 1.527 2.450 nonbonded pdb=" O ALA E 295 " pdb=" HH TYR E 350 " model vdw 1.541 2.450 nonbonded pdb=" OE1 GLU A 155 " pdb="HH21 ARG A 207 " model vdw 1.562 2.450 nonbonded pdb=" OD1 ASP C 121 " pdb=" HG1 THR C 123 " model vdw 1.574 2.450 ... (remaining 496065 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'H2' } ncs_group { reference = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'L' selection = (chain 'L2' and ((resid 3 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 4 through 21 or (resid 22 \ and (name N or name CA or name C or name O or name CB or name SG or name H or n \ ame HA or name HB2 or name HB3)) or resid 23 through 88 or (resid 89 and (name N \ or name CA or name C or name O or name CB or name SG or name H or name HA or na \ me HB2 or name HB3)) or resid 90 through 96 or (resid 97 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name CE or name NZ or na \ me H or name HA )) or resid 98 through 112)) } 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.180 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 29.330 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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:7.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 17891 Z= 0.325 Angle : 0.806 9.427 24382 Z= 0.448 Chirality : 0.049 0.332 2817 Planarity : 0.006 0.080 2998 Dihedral : 14.131 106.340 6775 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.32 % Allowed : 0.53 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.18), residues: 2121 helix: 1.13 (0.21), residues: 607 sheet: -1.43 (0.19), residues: 661 loop : -1.24 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 107 TYR 0.030 0.002 TYRH2 60 PHE 0.036 0.002 PHE B 146 TRP 0.032 0.002 TRPL2 92 HIS 0.007 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00671 (17859) covalent geometry : angle 0.79040 (24294) SS BOND : bond 0.00371 ( 8) SS BOND : angle 1.83534 ( 16) hydrogen bonds : bond 0.11576 ( 650) hydrogen bonds : angle 5.81920 ( 1842) link_ALPHA1-2 : bond 0.00524 ( 3) link_ALPHA1-2 : angle 2.73845 ( 9) link_ALPHA1-3 : bond 0.00430 ( 2) link_ALPHA1-3 : angle 2.30828 ( 6) link_ALPHA1-6 : bond 0.00311 ( 2) link_ALPHA1-6 : angle 2.64596 ( 6) link_BETA1-4 : bond 0.00631 ( 10) link_BETA1-4 : angle 2.80902 ( 30) link_NAG-ASN : bond 0.01269 ( 7) link_NAG-ASN : angle 3.23520 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 316 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 310 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ILE cc_start: 0.9166 (tt) cc_final: 0.8868 (pt) REVERT: A 241 TRP cc_start: 0.6347 (m-10) cc_final: 0.5763 (m-10) REVERT: A 310 PRO cc_start: 0.7754 (Cg_endo) cc_final: 0.7519 (Cg_exo) REVERT: A 319 TRP cc_start: 0.6582 (t60) cc_final: 0.6290 (t60) REVERT: B 124 ASP cc_start: 0.7783 (t0) cc_final: 0.7553 (t0) REVERT: B 174 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: C 231 LEU cc_start: 0.8395 (mt) cc_final: 0.8081 (mt) REVERT: C 283 MET cc_start: 0.8250 (mmm) cc_final: 0.7925 (mmm) REVERT: C 286 MET cc_start: 0.7884 (tpp) cc_final: 0.7680 (tpt) REVERT: C 305 ILE cc_start: 0.8301 (tp) cc_final: 0.8001 (tp) REVERT: E 52 LEU cc_start: 0.8962 (tp) cc_final: 0.8759 (tp) REVERT: E 152 GLN cc_start: 0.6901 (mm-40) cc_final: 0.6589 (mm-40) REVERT: E 313 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6658 (tp30) REVERT: H 51 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7990 (ttp) REVERT: H 62 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7739 (tm-30) REVERT: H2 62 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7865 (tm-30) REVERT: H2 81 MET cc_start: 0.8477 (ptm) cc_final: 0.8080 (ptm) REVERT: L 84 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7809 (tm-30) outliers start: 6 outliers final: 4 residues processed: 314 average time/residue: 1.1860 time to fit residues: 421.3060 Evaluate side-chains 253 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 247 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 175 PRO Chi-restraints excluded: chain H residue 51 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.0010 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 overall best weight: 1.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN B 56 HIS B 229 GLN D 56 HIS E 135 ASN L2 16 GLN L2 80 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.117734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.086346 restraints weight = 77201.687| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.47 r_work: 0.2981 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17891 Z= 0.183 Angle : 0.605 9.207 24382 Z= 0.311 Chirality : 0.043 0.202 2817 Planarity : 0.005 0.063 2998 Dihedral : 8.522 74.971 2874 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.54 % Allowed : 8.70 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.18), residues: 2121 helix: 1.33 (0.21), residues: 611 sheet: -1.38 (0.20), residues: 641 loop : -1.18 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 87 TYR 0.022 0.002 TYR A 299 PHE 0.019 0.001 PHE A 306 TRP 0.009 0.001 TRP L 36 HIS 0.004 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00421 (17859) covalent geometry : angle 0.59290 (24294) SS BOND : bond 0.00264 ( 8) SS BOND : angle 1.42152 ( 16) hydrogen bonds : bond 0.04091 ( 650) hydrogen bonds : angle 5.03479 ( 1842) link_ALPHA1-2 : bond 0.00219 ( 3) link_ALPHA1-2 : angle 2.10936 ( 9) link_ALPHA1-3 : bond 0.00586 ( 2) link_ALPHA1-3 : angle 1.90024 ( 6) link_ALPHA1-6 : bond 0.00317 ( 2) link_ALPHA1-6 : angle 1.94040 ( 6) link_BETA1-4 : bond 0.00315 ( 10) link_BETA1-4 : angle 2.08529 ( 30) link_NAG-ASN : bond 0.00508 ( 7) link_NAG-ASN : angle 2.53108 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 299 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 270 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ILE cc_start: 0.9142 (tt) cc_final: 0.8819 (pt) REVERT: A 164 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8755 (mt) REVERT: A 241 TRP cc_start: 0.6400 (m-10) cc_final: 0.5820 (m-10) REVERT: A 310 PRO cc_start: 0.7553 (Cg_endo) cc_final: 0.7314 (Cg_exo) REVERT: B 21 ARG cc_start: 0.7735 (mmp80) cc_final: 0.7406 (mmp-170) REVERT: B 73 GLU cc_start: 0.8243 (mp0) cc_final: 0.8013 (mp0) REVERT: B 124 ASP cc_start: 0.8334 (t0) cc_final: 0.8010 (t0) REVERT: B 173 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8477 (mmt90) REVERT: B 174 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: C 283 MET cc_start: 0.8439 (mmm) cc_final: 0.7994 (mmm) REVERT: C 286 MET cc_start: 0.8143 (tpp) cc_final: 0.7907 (tpt) REVERT: C 297 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7526 (mp) REVERT: D 304 PHE cc_start: 0.7838 (t80) cc_final: 0.7610 (t80) REVERT: E 52 LEU cc_start: 0.8998 (tp) cc_final: 0.8774 (tp) REVERT: E 258 ASN cc_start: 0.7773 (t0) cc_final: 0.7377 (t0) REVERT: E 313 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6477 (tp30) REVERT: H 51 MET cc_start: 0.8671 (ppp) cc_final: 0.8433 (ttp) REVERT: H 62 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7826 (tm-30) REVERT: H 80 TYR cc_start: 0.6898 (OUTLIER) cc_final: 0.5801 (p90) REVERT: H2 33 ASP cc_start: 0.8258 (p0) cc_final: 0.8028 (p0) REVERT: H2 62 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8042 (tm-30) REVERT: H2 100 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8189 (mt-10) REVERT: L 84 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8173 (tm-30) outliers start: 29 outliers final: 13 residues processed: 283 average time/residue: 1.1961 time to fit residues: 384.8788 Evaluate side-chains 267 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 249 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H2 residue 23 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 35 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN D 56 HIS E 135 ASN L2 16 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.115839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.084692 restraints weight = 77205.120| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.42 r_work: 0.2952 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17891 Z= 0.232 Angle : 0.600 9.447 24382 Z= 0.308 Chirality : 0.043 0.182 2817 Planarity : 0.005 0.058 2998 Dihedral : 7.134 67.506 2863 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.64 % Allowed : 10.13 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.18), residues: 2121 helix: 1.49 (0.21), residues: 609 sheet: -1.40 (0.20), residues: 628 loop : -1.13 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 269 TYR 0.021 0.002 TYR A 299 PHE 0.019 0.001 PHE A 306 TRP 0.008 0.001 TRP H 36 HIS 0.003 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00536 (17859) covalent geometry : angle 0.58689 (24294) SS BOND : bond 0.00336 ( 8) SS BOND : angle 1.55226 ( 16) hydrogen bonds : bond 0.03897 ( 650) hydrogen bonds : angle 4.84715 ( 1842) link_ALPHA1-2 : bond 0.00457 ( 3) link_ALPHA1-2 : angle 2.29229 ( 9) link_ALPHA1-3 : bond 0.00474 ( 2) link_ALPHA1-3 : angle 2.07629 ( 6) link_ALPHA1-6 : bond 0.00429 ( 2) link_ALPHA1-6 : angle 2.22954 ( 6) link_BETA1-4 : bond 0.00338 ( 10) link_BETA1-4 : angle 1.97981 ( 30) link_NAG-ASN : bond 0.00456 ( 7) link_NAG-ASN : angle 2.60646 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 284 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 253 time to evaluate : 0.954 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: A 164 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8698 (tt) REVERT: A 241 TRP cc_start: 0.6526 (m-10) cc_final: 0.5971 (m-10) REVERT: A 310 PRO cc_start: 0.7587 (Cg_endo) cc_final: 0.7364 (Cg_exo) REVERT: B 21 ARG cc_start: 0.7637 (mmp80) cc_final: 0.7211 (mmp-170) REVERT: B 58 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8616 (mtt) REVERT: B 73 GLU cc_start: 0.8327 (mp0) cc_final: 0.8085 (mp0) REVERT: B 124 ASP cc_start: 0.8320 (t0) cc_final: 0.7947 (t0) REVERT: B 173 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8547 (mmt90) REVERT: B 199 ASP cc_start: 0.8043 (t0) cc_final: 0.7747 (t0) REVERT: B 282 TYR cc_start: 0.7635 (p90) cc_final: 0.7188 (p90) REVERT: C 224 GLN cc_start: 0.8414 (tp40) cc_final: 0.7797 (tm-30) REVERT: C 283 MET cc_start: 0.8409 (mmm) cc_final: 0.7853 (mmm) REVERT: C 286 MET cc_start: 0.7911 (tpp) cc_final: 0.7703 (tpt) REVERT: C 297 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7462 (mp) REVERT: D 63 ASP cc_start: 0.8428 (t0) cc_final: 0.8041 (t0) REVERT: D 83 VAL cc_start: 0.9405 (OUTLIER) cc_final: 0.9177 (t) REVERT: E 152 GLN cc_start: 0.6831 (mm-40) cc_final: 0.6409 (mm-40) REVERT: E 258 ASN cc_start: 0.7751 (t0) cc_final: 0.7348 (t0) REVERT: E 313 GLU cc_start: 0.7063 (tm-30) cc_final: 0.6507 (tp30) REVERT: L2 86 ASP cc_start: 0.8311 (m-30) cc_final: 0.7844 (m-30) REVERT: H 51 MET cc_start: 0.8733 (ppp) cc_final: 0.8515 (ttp) REVERT: H 62 GLN cc_start: 0.8048 (tm-30) cc_final: 0.7754 (tm-30) REVERT: H 80 TYR cc_start: 0.6855 (OUTLIER) cc_final: 0.5777 (p90) REVERT: H 90 ASP cc_start: 0.8007 (m-30) cc_final: 0.7768 (m-30) REVERT: H2 33 ASP cc_start: 0.8298 (p0) cc_final: 0.7922 (p0) REVERT: H2 62 GLN cc_start: 0.8489 (tm-30) cc_final: 0.7980 (tm-30) REVERT: H2 100 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8162 (mt-10) REVERT: L 84 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8214 (tm-30) outliers start: 31 outliers final: 13 residues processed: 269 average time/residue: 1.1743 time to fit residues: 359.2666 Evaluate side-chains 261 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 242 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H2 residue 110 ASP Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 104 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 224 GLN D 56 HIS E 135 ASN L2 16 GLN H 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.116529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.084894 restraints weight = 76805.086| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.47 r_work: 0.2952 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17891 Z= 0.175 Angle : 0.562 9.552 24382 Z= 0.287 Chirality : 0.042 0.197 2817 Planarity : 0.005 0.062 2998 Dihedral : 6.593 62.065 2863 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.54 % Allowed : 11.35 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.19), residues: 2121 helix: 1.58 (0.21), residues: 614 sheet: -1.40 (0.20), residues: 624 loop : -1.04 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 17 TYR 0.020 0.001 TYR A 299 PHE 0.014 0.001 PHE A 306 TRP 0.009 0.001 TRP A 319 HIS 0.003 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00404 (17859) covalent geometry : angle 0.55094 (24294) SS BOND : bond 0.00281 ( 8) SS BOND : angle 1.33851 ( 16) hydrogen bonds : bond 0.03570 ( 650) hydrogen bonds : angle 4.65903 ( 1842) link_ALPHA1-2 : bond 0.00247 ( 3) link_ALPHA1-2 : angle 2.00785 ( 9) link_ALPHA1-3 : bond 0.00634 ( 2) link_ALPHA1-3 : angle 1.80132 ( 6) link_ALPHA1-6 : bond 0.00300 ( 2) link_ALPHA1-6 : angle 2.04348 ( 6) link_BETA1-4 : bond 0.00267 ( 10) link_BETA1-4 : angle 1.75685 ( 30) link_NAG-ASN : bond 0.00424 ( 7) link_NAG-ASN : angle 2.48378 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 280 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 251 time to evaluate : 0.914 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: A 40 MET cc_start: 0.9196 (mpt) cc_final: 0.8184 (mpt) REVERT: A 138 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7602 (mtt) REVERT: A 241 TRP cc_start: 0.6582 (m-10) cc_final: 0.6020 (m-10) REVERT: A 269 ARG cc_start: 0.7010 (mmm160) cc_final: 0.6741 (mmm-85) REVERT: A 286 MET cc_start: 0.7485 (tpp) cc_final: 0.7239 (tpp) REVERT: A 310 PRO cc_start: 0.7626 (Cg_endo) cc_final: 0.7418 (Cg_exo) REVERT: B 21 ARG cc_start: 0.7750 (mmp80) cc_final: 0.7395 (mmp-170) REVERT: B 73 GLU cc_start: 0.8280 (mp0) cc_final: 0.8051 (mp0) REVERT: B 124 ASP cc_start: 0.8323 (t0) cc_final: 0.7906 (t0) REVERT: B 173 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8568 (mmt90) REVERT: B 282 TYR cc_start: 0.7760 (p90) cc_final: 0.7340 (p90) REVERT: C 283 MET cc_start: 0.8438 (mmm) cc_final: 0.7853 (mmm) REVERT: C 286 MET cc_start: 0.7997 (tpp) cc_final: 0.7757 (tpt) REVERT: C 297 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7553 (mp) REVERT: D 83 VAL cc_start: 0.9407 (OUTLIER) cc_final: 0.9174 (t) REVERT: E 152 GLN cc_start: 0.6917 (mm-40) cc_final: 0.6512 (mm-40) REVERT: E 258 ASN cc_start: 0.7853 (t0) cc_final: 0.7444 (t0) REVERT: E 313 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6462 (tp30) REVERT: L2 86 ASP cc_start: 0.8406 (m-30) cc_final: 0.7912 (m-30) REVERT: H 62 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7673 (tm-30) REVERT: H 80 TYR cc_start: 0.7035 (OUTLIER) cc_final: 0.6003 (p90) REVERT: H 90 ASP cc_start: 0.8080 (m-30) cc_final: 0.7783 (m-30) REVERT: H2 10 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: H2 33 ASP cc_start: 0.8270 (p0) cc_final: 0.7884 (p0) REVERT: H2 62 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8015 (tm-30) REVERT: H2 100 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8161 (mt-10) REVERT: L 84 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8173 (tm-30) outliers start: 29 outliers final: 9 residues processed: 266 average time/residue: 1.2141 time to fit residues: 368.0105 Evaluate side-chains 254 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 239 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain L2 residue 57 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H2 residue 10 GLU Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 5 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 210 optimal weight: 0.1980 chunk 127 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN E 135 ASN L2 16 GLN L 80 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.117088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.086081 restraints weight = 76956.511| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.45 r_work: 0.2978 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17891 Z= 0.129 Angle : 0.537 9.210 24382 Z= 0.273 Chirality : 0.041 0.195 2817 Planarity : 0.004 0.063 2998 Dihedral : 6.182 58.935 2863 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.38 % Allowed : 12.20 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.19), residues: 2121 helix: 1.77 (0.21), residues: 614 sheet: -1.35 (0.20), residues: 624 loop : -0.92 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGL2 17 TYR 0.020 0.001 TYR A 299 PHE 0.015 0.001 PHE A 306 TRP 0.011 0.001 TRP A 319 HIS 0.002 0.000 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00299 (17859) covalent geometry : angle 0.52658 (24294) SS BOND : bond 0.00247 ( 8) SS BOND : angle 1.21591 ( 16) hydrogen bonds : bond 0.03318 ( 650) hydrogen bonds : angle 4.50674 ( 1842) link_ALPHA1-2 : bond 0.00142 ( 3) link_ALPHA1-2 : angle 1.93020 ( 9) link_ALPHA1-3 : bond 0.00684 ( 2) link_ALPHA1-3 : angle 1.75118 ( 6) link_ALPHA1-6 : bond 0.00237 ( 2) link_ALPHA1-6 : angle 1.93664 ( 6) link_BETA1-4 : bond 0.00285 ( 10) link_BETA1-4 : angle 1.64919 ( 30) link_NAG-ASN : bond 0.00402 ( 7) link_NAG-ASN : angle 2.45646 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 270 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9150 (mpt) cc_final: 0.8205 (mpt) REVERT: A 138 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7605 (mtt) REVERT: A 241 TRP cc_start: 0.6646 (m-10) cc_final: 0.6096 (m-10) REVERT: A 269 ARG cc_start: 0.6994 (mmm160) cc_final: 0.6766 (mmm-85) REVERT: A 286 MET cc_start: 0.7491 (tpp) cc_final: 0.7177 (tpp) REVERT: A 310 PRO cc_start: 0.7583 (Cg_endo) cc_final: 0.7373 (Cg_exo) REVERT: B 21 ARG cc_start: 0.7786 (mmp80) cc_final: 0.7416 (mmp-170) REVERT: B 58 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8615 (mtt) REVERT: B 73 GLU cc_start: 0.8289 (mp0) cc_final: 0.8050 (mp0) REVERT: B 78 LYS cc_start: 0.9058 (ttmt) cc_final: 0.8667 (mmmm) REVERT: B 124 ASP cc_start: 0.8310 (t0) cc_final: 0.7878 (t0) REVERT: B 173 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8598 (mmt90) REVERT: B 199 ASP cc_start: 0.7939 (t0) cc_final: 0.7679 (t0) REVERT: B 282 TYR cc_start: 0.7803 (p90) cc_final: 0.7216 (p90) REVERT: C 283 MET cc_start: 0.8426 (mmm) cc_final: 0.7834 (mmm) REVERT: C 286 MET cc_start: 0.7968 (tpp) cc_final: 0.7729 (tpt) REVERT: C 297 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7587 (mp) REVERT: D 83 VAL cc_start: 0.9405 (OUTLIER) cc_final: 0.9170 (t) REVERT: E 152 GLN cc_start: 0.7028 (mm-40) cc_final: 0.6627 (mm-40) REVERT: E 258 ASN cc_start: 0.7858 (t0) cc_final: 0.7439 (t0) REVERT: E 313 GLU cc_start: 0.7195 (tm-30) cc_final: 0.6515 (tp30) REVERT: L2 86 ASP cc_start: 0.8400 (m-30) cc_final: 0.7936 (m-30) REVERT: H 62 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7631 (tm-30) REVERT: H 80 TYR cc_start: 0.6943 (OUTLIER) cc_final: 0.5893 (p90) REVERT: H 90 ASP cc_start: 0.8117 (m-30) cc_final: 0.7815 (m-30) REVERT: H2 33 ASP cc_start: 0.8295 (p0) cc_final: 0.7824 (p0) REVERT: H2 62 GLN cc_start: 0.8492 (tm-30) cc_final: 0.7953 (tm-30) REVERT: H2 63 LYS cc_start: 0.8799 (ttmm) cc_final: 0.8560 (ttmt) REVERT: H2 100 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8189 (mt-10) REVERT: L 84 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8135 (tm-30) outliers start: 26 outliers final: 10 residues processed: 258 average time/residue: 1.2463 time to fit residues: 364.3486 Evaluate side-chains 252 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain L2 residue 57 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 163 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN B 116 ASN C 224 GLN E 135 ASN L2 16 GLN L2 80 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.116407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.085315 restraints weight = 77032.050| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.44 r_work: 0.2965 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17891 Z= 0.156 Angle : 0.546 9.042 24382 Z= 0.276 Chirality : 0.042 0.200 2817 Planarity : 0.004 0.063 2998 Dihedral : 6.088 59.916 2863 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.59 % Allowed : 12.73 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.19), residues: 2121 helix: 1.79 (0.21), residues: 614 sheet: -1.34 (0.20), residues: 624 loop : -0.92 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGL2 17 TYR 0.021 0.001 TYR A 244 PHE 0.014 0.001 PHE A 306 TRP 0.014 0.001 TRP A 319 HIS 0.002 0.000 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00360 (17859) covalent geometry : angle 0.53458 (24294) SS BOND : bond 0.00254 ( 8) SS BOND : angle 1.23278 ( 16) hydrogen bonds : bond 0.03324 ( 650) hydrogen bonds : angle 4.46698 ( 1842) link_ALPHA1-2 : bond 0.00174 ( 3) link_ALPHA1-2 : angle 2.04032 ( 9) link_ALPHA1-3 : bond 0.00609 ( 2) link_ALPHA1-3 : angle 1.87862 ( 6) link_ALPHA1-6 : bond 0.00380 ( 2) link_ALPHA1-6 : angle 2.09649 ( 6) link_BETA1-4 : bond 0.00288 ( 10) link_BETA1-4 : angle 1.69745 ( 30) link_NAG-ASN : bond 0.00367 ( 7) link_NAG-ASN : angle 2.52970 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 279 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 249 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9154 (mpt) cc_final: 0.8265 (mpt) REVERT: A 138 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7752 (mtt) REVERT: A 241 TRP cc_start: 0.6632 (m-10) cc_final: 0.6068 (m-10) REVERT: A 269 ARG cc_start: 0.7028 (mmm160) cc_final: 0.6783 (mmm-85) REVERT: A 286 MET cc_start: 0.7484 (tpp) cc_final: 0.7198 (tpp) REVERT: B 21 ARG cc_start: 0.7811 (mmp80) cc_final: 0.7426 (mmp-170) REVERT: B 58 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8586 (mtt) REVERT: B 73 GLU cc_start: 0.8297 (mp0) cc_final: 0.8080 (mp0) REVERT: B 124 ASP cc_start: 0.8326 (t0) cc_final: 0.7883 (t0) REVERT: B 174 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: B 199 ASP cc_start: 0.7980 (t0) cc_final: 0.7722 (t0) REVERT: B 282 TYR cc_start: 0.7830 (p90) cc_final: 0.7108 (p90) REVERT: C 224 GLN cc_start: 0.8488 (tp40) cc_final: 0.7870 (tm-30) REVERT: C 283 MET cc_start: 0.8434 (mmm) cc_final: 0.7835 (mmm) REVERT: C 286 MET cc_start: 0.7995 (tpp) cc_final: 0.7734 (tpt) REVERT: C 297 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7602 (mp) REVERT: D 83 VAL cc_start: 0.9403 (OUTLIER) cc_final: 0.9166 (t) REVERT: E 152 GLN cc_start: 0.7126 (mm-40) cc_final: 0.6715 (mm-40) REVERT: E 258 ASN cc_start: 0.7844 (t0) cc_final: 0.7417 (t0) REVERT: E 297 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6800 (t0) REVERT: E 313 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6657 (tp30) REVERT: L2 86 ASP cc_start: 0.8400 (m-30) cc_final: 0.7908 (m-30) REVERT: H 62 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7628 (tm-30) REVERT: H 80 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6086 (p90) REVERT: H 90 ASP cc_start: 0.8086 (m-30) cc_final: 0.7809 (m-30) REVERT: H2 10 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: H2 33 ASP cc_start: 0.8295 (p0) cc_final: 0.7815 (p0) REVERT: H2 80 TYR cc_start: 0.7364 (OUTLIER) cc_final: 0.5639 (p90) REVERT: H2 100 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8185 (mt-10) REVERT: L 84 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8146 (tm-30) outliers start: 30 outliers final: 15 residues processed: 262 average time/residue: 1.1756 time to fit residues: 350.2822 Evaluate side-chains 257 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 233 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain L2 residue 57 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H2 residue 10 GLU Chi-restraints excluded: chain H2 residue 80 TYR Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 117 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 157 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 135 ASN L2 16 GLN L2 38 GLN L2 80 GLN L 80 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.116337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.085192 restraints weight = 77173.087| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.48 r_work: 0.2960 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17891 Z= 0.149 Angle : 0.542 9.223 24382 Z= 0.274 Chirality : 0.042 0.202 2817 Planarity : 0.004 0.064 2998 Dihedral : 5.881 59.088 2859 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.64 % Allowed : 13.21 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.19), residues: 2121 helix: 1.86 (0.21), residues: 615 sheet: -1.34 (0.20), residues: 624 loop : -0.87 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 17 TYR 0.020 0.001 TYR A 299 PHE 0.015 0.001 PHE A 306 TRP 0.015 0.001 TRP A 319 HIS 0.002 0.000 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00345 (17859) covalent geometry : angle 0.53073 (24294) SS BOND : bond 0.00256 ( 8) SS BOND : angle 1.14700 ( 16) hydrogen bonds : bond 0.03244 ( 650) hydrogen bonds : angle 4.42629 ( 1842) link_ALPHA1-2 : bond 0.00150 ( 3) link_ALPHA1-2 : angle 1.97459 ( 9) link_ALPHA1-3 : bond 0.00634 ( 2) link_ALPHA1-3 : angle 1.78760 ( 6) link_ALPHA1-6 : bond 0.00355 ( 2) link_ALPHA1-6 : angle 1.98132 ( 6) link_BETA1-4 : bond 0.00291 ( 10) link_BETA1-4 : angle 1.66299 ( 30) link_NAG-ASN : bond 0.00371 ( 7) link_NAG-ASN : angle 2.51464 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 275 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 244 time to evaluate : 0.858 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: A 40 MET cc_start: 0.9100 (mpt) cc_final: 0.8194 (mpt) REVERT: A 138 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7811 (mtt) REVERT: A 241 TRP cc_start: 0.6638 (m-10) cc_final: 0.6062 (m-10) REVERT: A 269 ARG cc_start: 0.7022 (mmm160) cc_final: 0.6774 (mmm-85) REVERT: A 286 MET cc_start: 0.7484 (tpp) cc_final: 0.7214 (tpp) REVERT: B 21 ARG cc_start: 0.7836 (mmp80) cc_final: 0.7428 (mmp-170) REVERT: B 58 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8572 (mtt) REVERT: B 73 GLU cc_start: 0.8304 (mp0) cc_final: 0.8085 (mp0) REVERT: B 124 ASP cc_start: 0.8317 (t0) cc_final: 0.7910 (t0) REVERT: B 199 ASP cc_start: 0.7936 (t0) cc_final: 0.7693 (t0) REVERT: B 282 TYR cc_start: 0.7843 (p90) cc_final: 0.7163 (p90) REVERT: C 40 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8730 (mtt) REVERT: C 283 MET cc_start: 0.8426 (mmm) cc_final: 0.7822 (mmm) REVERT: C 286 MET cc_start: 0.7977 (tpp) cc_final: 0.7776 (tpt) REVERT: C 297 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7618 (mp) REVERT: D 83 VAL cc_start: 0.9406 (OUTLIER) cc_final: 0.9167 (t) REVERT: E 152 GLN cc_start: 0.7134 (mm-40) cc_final: 0.6714 (mm-40) REVERT: E 258 ASN cc_start: 0.7836 (t0) cc_final: 0.7393 (t0) REVERT: E 297 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.6789 (t0) REVERT: E 313 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6646 (tp30) REVERT: L2 86 ASP cc_start: 0.8448 (m-30) cc_final: 0.7967 (m-30) REVERT: H 62 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7638 (tm-30) REVERT: H 80 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.6097 (p90) REVERT: H 90 ASP cc_start: 0.8050 (m-30) cc_final: 0.7768 (m-30) REVERT: H2 10 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: H2 33 ASP cc_start: 0.8297 (p0) cc_final: 0.7809 (p0) REVERT: H2 80 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.5619 (p90) REVERT: H2 100 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8186 (mt-10) REVERT: L 84 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8170 (tm-30) outliers start: 31 outliers final: 16 residues processed: 261 average time/residue: 1.1154 time to fit residues: 333.5759 Evaluate side-chains 259 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 234 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain L2 residue 57 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H2 residue 10 GLU Chi-restraints excluded: chain H2 residue 80 TYR Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 52 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 189 optimal weight: 0.6980 chunk 183 optimal weight: 0.4980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L2 16 GLN L2 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.116461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.085410 restraints weight = 77115.644| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.44 r_work: 0.2967 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17891 Z= 0.141 Angle : 0.540 9.193 24382 Z= 0.273 Chirality : 0.041 0.202 2817 Planarity : 0.004 0.066 2998 Dihedral : 5.805 57.886 2859 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.38 % Allowed : 13.63 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.19), residues: 2121 helix: 1.91 (0.21), residues: 615 sheet: -1.37 (0.20), residues: 642 loop : -0.81 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 17 TYR 0.020 0.001 TYR A 299 PHE 0.014 0.001 PHE A 306 TRP 0.016 0.001 TRP A 319 HIS 0.002 0.000 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00326 (17859) covalent geometry : angle 0.52902 (24294) SS BOND : bond 0.00248 ( 8) SS BOND : angle 1.10982 ( 16) hydrogen bonds : bond 0.03185 ( 650) hydrogen bonds : angle 4.39023 ( 1842) link_ALPHA1-2 : bond 0.00143 ( 3) link_ALPHA1-2 : angle 1.95337 ( 9) link_ALPHA1-3 : bond 0.00635 ( 2) link_ALPHA1-3 : angle 1.76157 ( 6) link_ALPHA1-6 : bond 0.00326 ( 2) link_ALPHA1-6 : angle 1.98054 ( 6) link_BETA1-4 : bond 0.00313 ( 10) link_BETA1-4 : angle 1.64046 ( 30) link_NAG-ASN : bond 0.00371 ( 7) link_NAG-ASN : angle 2.48203 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 270 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9088 (mpt) cc_final: 0.8235 (mpt) REVERT: A 138 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7915 (mtt) REVERT: A 185 GLN cc_start: 0.8112 (tt0) cc_final: 0.7896 (tt0) REVERT: A 241 TRP cc_start: 0.6703 (m-10) cc_final: 0.6052 (m-10) REVERT: A 269 ARG cc_start: 0.7029 (mmm160) cc_final: 0.6779 (mmm-85) REVERT: A 283 MET cc_start: 0.8198 (tpt) cc_final: 0.7967 (mmm) REVERT: A 286 MET cc_start: 0.7485 (tpp) cc_final: 0.7229 (tpp) REVERT: B 21 ARG cc_start: 0.7829 (mmp80) cc_final: 0.7391 (mmp-170) REVERT: B 58 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8558 (mtt) REVERT: B 73 GLU cc_start: 0.8292 (mp0) cc_final: 0.8075 (mp0) REVERT: B 124 ASP cc_start: 0.8322 (t0) cc_final: 0.7915 (t0) REVERT: B 199 ASP cc_start: 0.7955 (t0) cc_final: 0.7742 (t0) REVERT: B 282 TYR cc_start: 0.7865 (p90) cc_final: 0.7154 (p90) REVERT: C 40 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8721 (mtt) REVERT: C 283 MET cc_start: 0.8418 (mmm) cc_final: 0.7808 (mmm) REVERT: C 297 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7667 (mp) REVERT: D 83 VAL cc_start: 0.9402 (OUTLIER) cc_final: 0.9163 (t) REVERT: E 152 GLN cc_start: 0.7163 (mm-40) cc_final: 0.6747 (mm-40) REVERT: E 258 ASN cc_start: 0.7825 (t0) cc_final: 0.7377 (t0) REVERT: E 297 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6814 (t0) REVERT: E 313 GLU cc_start: 0.7327 (tm-30) cc_final: 0.6669 (tp30) REVERT: L2 86 ASP cc_start: 0.8481 (m-30) cc_final: 0.8000 (m-30) REVERT: H 62 GLN cc_start: 0.7873 (tm-30) cc_final: 0.7603 (tm-30) REVERT: H 80 TYR cc_start: 0.7088 (OUTLIER) cc_final: 0.6093 (p90) REVERT: H 90 ASP cc_start: 0.8054 (m-30) cc_final: 0.7775 (m-30) REVERT: H2 10 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: H2 33 ASP cc_start: 0.8282 (p0) cc_final: 0.7755 (p0) REVERT: H2 80 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.5695 (p90) REVERT: H2 100 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8184 (mt-10) REVERT: L 84 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8173 (tm-30) outliers start: 26 outliers final: 14 residues processed: 255 average time/residue: 1.1064 time to fit residues: 322.9487 Evaluate side-chains 259 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain L2 residue 57 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H2 residue 10 GLU Chi-restraints excluded: chain H2 residue 80 TYR Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 179 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 142 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 196 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN L2 16 GLN L 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.115443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.084593 restraints weight = 76754.290| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.39 r_work: 0.2952 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17891 Z= 0.196 Angle : 0.568 9.316 24382 Z= 0.288 Chirality : 0.042 0.211 2817 Planarity : 0.005 0.065 2998 Dihedral : 5.953 57.560 2859 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.17 % Allowed : 13.85 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.19), residues: 2121 helix: 1.88 (0.21), residues: 615 sheet: -1.39 (0.19), residues: 642 loop : -0.84 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGL2 17 TYR 0.019 0.002 TYR A 299 PHE 0.013 0.001 PHE H 112 TRP 0.020 0.001 TRP A 319 HIS 0.003 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00454 (17859) covalent geometry : angle 0.55583 (24294) SS BOND : bond 0.00292 ( 8) SS BOND : angle 1.28963 ( 16) hydrogen bonds : bond 0.03295 ( 650) hydrogen bonds : angle 4.41895 ( 1842) link_ALPHA1-2 : bond 0.00251 ( 3) link_ALPHA1-2 : angle 2.10622 ( 9) link_ALPHA1-3 : bond 0.00530 ( 2) link_ALPHA1-3 : angle 1.87607 ( 6) link_ALPHA1-6 : bond 0.00472 ( 2) link_ALPHA1-6 : angle 2.19026 ( 6) link_BETA1-4 : bond 0.00303 ( 10) link_BETA1-4 : angle 1.76046 ( 30) link_NAG-ASN : bond 0.00393 ( 7) link_NAG-ASN : angle 2.63415 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9094 (mpt) cc_final: 0.8225 (mpt) REVERT: A 138 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7895 (mtt) REVERT: A 185 GLN cc_start: 0.7992 (tt0) cc_final: 0.7776 (tt0) REVERT: A 241 TRP cc_start: 0.6632 (m-10) cc_final: 0.6063 (m-10) REVERT: A 269 ARG cc_start: 0.7006 (mmm160) cc_final: 0.6751 (mmm-85) REVERT: A 286 MET cc_start: 0.7505 (tpp) cc_final: 0.7252 (tpp) REVERT: B 21 ARG cc_start: 0.7727 (mmp80) cc_final: 0.7319 (mmp-170) REVERT: B 58 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8543 (mtt) REVERT: B 73 GLU cc_start: 0.8266 (mp0) cc_final: 0.8057 (mp0) REVERT: B 124 ASP cc_start: 0.8322 (t0) cc_final: 0.7871 (t0) REVERT: B 279 LYS cc_start: 0.8096 (mptt) cc_final: 0.7814 (mptt) REVERT: B 282 TYR cc_start: 0.8020 (p90) cc_final: 0.7223 (p90) REVERT: C 40 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8714 (mtt) REVERT: C 283 MET cc_start: 0.8358 (mmm) cc_final: 0.7726 (mmm) REVERT: C 297 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7664 (mp) REVERT: D 36 GLU cc_start: 0.8365 (mp0) cc_final: 0.8083 (mp0) REVERT: D 83 VAL cc_start: 0.9402 (OUTLIER) cc_final: 0.9164 (t) REVERT: E 152 GLN cc_start: 0.7145 (mm-40) cc_final: 0.6831 (mm-40) REVERT: E 258 ASN cc_start: 0.7799 (t0) cc_final: 0.7336 (t0) REVERT: E 297 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.6800 (t0) REVERT: E 313 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6637 (tp30) REVERT: L2 86 ASP cc_start: 0.8460 (m-30) cc_final: 0.7946 (m-30) REVERT: H 62 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7629 (tm-30) REVERT: H 80 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.6061 (p90) REVERT: H 90 ASP cc_start: 0.7983 (m-30) cc_final: 0.7697 (m-30) REVERT: H2 10 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: H2 33 ASP cc_start: 0.8268 (p0) cc_final: 0.7763 (p0) REVERT: H2 80 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.5805 (p90) REVERT: L 84 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8206 (tm-30) outliers start: 22 outliers final: 13 residues processed: 249 average time/residue: 1.1717 time to fit residues: 332.7272 Evaluate side-chains 259 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain L2 residue 57 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H2 residue 10 GLU Chi-restraints excluded: chain H2 residue 80 TYR Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 37 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 303 ASN B 56 HIS L2 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.115462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.084671 restraints weight = 77073.003| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.39 r_work: 0.2953 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17891 Z= 0.176 Angle : 0.566 9.613 24382 Z= 0.286 Chirality : 0.042 0.209 2817 Planarity : 0.005 0.065 2998 Dihedral : 5.924 55.923 2859 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.27 % Allowed : 14.06 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.19), residues: 2121 helix: 1.89 (0.21), residues: 614 sheet: -1.41 (0.19), residues: 644 loop : -0.84 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 17 TYR 0.029 0.001 TYR A 244 PHE 0.016 0.001 PHE D 329 TRP 0.025 0.001 TRP A 319 HIS 0.009 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00407 (17859) covalent geometry : angle 0.55495 (24294) SS BOND : bond 0.00299 ( 8) SS BOND : angle 1.23270 ( 16) hydrogen bonds : bond 0.03239 ( 650) hydrogen bonds : angle 4.38924 ( 1842) link_ALPHA1-2 : bond 0.00179 ( 3) link_ALPHA1-2 : angle 2.01196 ( 9) link_ALPHA1-3 : bond 0.00588 ( 2) link_ALPHA1-3 : angle 1.80179 ( 6) link_ALPHA1-6 : bond 0.00370 ( 2) link_ALPHA1-6 : angle 2.09006 ( 6) link_BETA1-4 : bond 0.00274 ( 10) link_BETA1-4 : angle 1.67813 ( 30) link_NAG-ASN : bond 0.00390 ( 7) link_NAG-ASN : angle 2.57406 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 1.020 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: A 40 MET cc_start: 0.9081 (mpt) cc_final: 0.8266 (mpt) REVERT: A 138 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7910 (mtt) REVERT: A 185 GLN cc_start: 0.7981 (tt0) cc_final: 0.7771 (tt0) REVERT: A 241 TRP cc_start: 0.6642 (m-10) cc_final: 0.6041 (m-10) REVERT: A 269 ARG cc_start: 0.7027 (mmm160) cc_final: 0.6775 (mmm-85) REVERT: A 286 MET cc_start: 0.7497 (tpp) cc_final: 0.7258 (tpp) REVERT: B 21 ARG cc_start: 0.7764 (mmp80) cc_final: 0.7357 (mmp-170) REVERT: B 58 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8524 (mtt) REVERT: B 73 GLU cc_start: 0.8289 (mp0) cc_final: 0.8082 (mp0) REVERT: B 124 ASP cc_start: 0.8317 (t0) cc_final: 0.7862 (t0) REVERT: B 279 LYS cc_start: 0.8100 (mptt) cc_final: 0.7850 (mptt) REVERT: C 40 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8726 (mtt) REVERT: C 270 GLU cc_start: 0.7017 (mp0) cc_final: 0.6811 (mp0) REVERT: D 36 GLU cc_start: 0.8374 (mp0) cc_final: 0.8088 (mp0) REVERT: D 83 VAL cc_start: 0.9404 (OUTLIER) cc_final: 0.9165 (t) REVERT: E 152 GLN cc_start: 0.7163 (mm-40) cc_final: 0.6855 (mm-40) REVERT: E 258 ASN cc_start: 0.7782 (t0) cc_final: 0.7291 (t0) REVERT: E 297 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6889 (t0) REVERT: E 313 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6741 (tp30) REVERT: L2 86 ASP cc_start: 0.8475 (m-30) cc_final: 0.7971 (m-30) REVERT: H 62 GLN cc_start: 0.7904 (tm-30) cc_final: 0.7635 (tm-30) REVERT: H 80 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.5961 (p90) REVERT: H 90 ASP cc_start: 0.7976 (m-30) cc_final: 0.7698 (m-30) REVERT: H2 10 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: H2 33 ASP cc_start: 0.8264 (p0) cc_final: 0.7725 (p0) REVERT: H2 80 TYR cc_start: 0.7295 (OUTLIER) cc_final: 0.5790 (p90) REVERT: H2 100 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8206 (mt-10) REVERT: L 84 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8238 (tm-30) outliers start: 24 outliers final: 16 residues processed: 252 average time/residue: 1.1537 time to fit residues: 331.9237 Evaluate side-chains 261 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 237 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain L2 residue 57 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H2 residue 10 GLU Chi-restraints excluded: chain H2 residue 80 TYR Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 203 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 31 optimal weight: 0.2980 chunk 85 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 HIS C 224 GLN E 135 ASN L2 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.116090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.085170 restraints weight = 76999.568| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.45 r_work: 0.2957 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17891 Z= 0.126 Angle : 0.552 11.469 24382 Z= 0.278 Chirality : 0.041 0.200 2817 Planarity : 0.004 0.063 2998 Dihedral : 5.779 54.785 2859 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.33 % Allowed : 14.48 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.19), residues: 2121 helix: 1.97 (0.21), residues: 615 sheet: -1.38 (0.20), residues: 644 loop : -0.81 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGL2 17 TYR 0.020 0.001 TYR A 299 PHE 0.013 0.001 PHE D 304 TRP 0.025 0.001 TRP A 319 HIS 0.033 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00290 (17859) covalent geometry : angle 0.54188 (24294) SS BOND : bond 0.00249 ( 8) SS BOND : angle 1.09526 ( 16) hydrogen bonds : bond 0.03127 ( 650) hydrogen bonds : angle 4.33466 ( 1842) link_ALPHA1-2 : bond 0.00143 ( 3) link_ALPHA1-2 : angle 1.92386 ( 9) link_ALPHA1-3 : bond 0.00760 ( 2) link_ALPHA1-3 : angle 1.70913 ( 6) link_ALPHA1-6 : bond 0.00276 ( 2) link_ALPHA1-6 : angle 1.95228 ( 6) link_BETA1-4 : bond 0.00261 ( 10) link_BETA1-4 : angle 1.60826 ( 30) link_NAG-ASN : bond 0.00377 ( 7) link_NAG-ASN : angle 2.47804 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11776.84 seconds wall clock time: 199 minutes 49.35 seconds (11989.35 seconds total)