Starting phenix.real_space_refine on Fri Mar 6 13:30:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t0z_25585/03_2026/7t0z_25585_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t0z_25585/03_2026/7t0z_25585.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/7t0z_25585/03_2026/7t0z_25585_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t0z_25585/03_2026/7t0z_25585_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t0z_25585/03_2026/7t0z_25585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t0z_25585/03_2026/7t0z_25585.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 86 5.16 5 C 10215 2.51 5 N 2568 2.21 5 O 2912 1.98 5 H 15348 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s 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: 31129 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 5471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5471 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 5448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5448 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 5470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5470 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 5447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5447 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 5447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5447 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 319} Chain: "H" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1862 Classifications: {'peptide': 125} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "L" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1664 Classifications: {'peptide': 109} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 100} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.38, per 1000 atoms: 0.17 Number of scatterers: 31129 At special positions: 0 Unit cell: (145.665, 114.374, 132.717, 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 86 16.00 O 2912 8.00 N 2568 7.00 C 10215 6.00 H 15348 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, 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=2.04 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 M 4 " - " MAN M 5 " " MAN M 5 " - " MAN M 6 " " MAN M 8 " - " MAN M 9 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " ALPHA1-6 " BMA M 3 " - " MAN M 7 " " MAN M 7 " - " MAN M 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 K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " NAG-ASN " NAG D 401 " - " ASN D 111 " Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 875.2 milliseconds 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3636 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 14 sheets defined 36.5% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 218 through 239 removed outlier: 4.854A pdb=" N MET A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix removed outlier: 3.846A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 246 through 272 Processing helix chain 'A' and resid 279 through 307 removed outlier: 4.330A pdb=" N PHE A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) 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 Processing helix 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 246 removed outlier: 5.086A pdb=" N LEU B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix removed outlier: 4.000A pdb=" N PHE B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 277 removed outlier: 3.550A pdb=" N ASN B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 311 Processing helix chain 'B' and resid 314 through 345 Proline residue: B 330 - end of helix Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 90 Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 218 through 239 removed outlier: 5.404A pdb=" N MET C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix removed outlier: 3.796A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 272 removed outlier: 4.289A pdb=" N GLU C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 307 removed outlier: 4.650A pdb=" N PHE C 307 " --> pdb=" O ASN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 339 removed outlier: 3.553A pdb=" N ALA C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 12 through 23 removed outlier: 4.052A pdb=" N LEU D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 230 through 244 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: 4.147A pdb=" N ARG D 347 " --> pdb=" O THR D 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 35 Processing helix chain 'E' and resid 85 through 88 removed outlier: 4.003A 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 233 through 256 removed outlier: 3.505A pdb=" N THR E 237 " --> pdb=" O MET E 233 " (cutoff:3.500A) Proline residue: E 243 - end of helix removed outlier: 3.750A pdb=" N SER E 251 " --> pdb=" O ILE E 247 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP E 252 " --> pdb=" O VAL E 248 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP E 256 " --> pdb=" O TRP E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 283 removed outlier: 3.838A pdb=" N THR E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA E 283 " --> pdb=" O LEU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 321 Processing helix chain 'E' and resid 324 through 357 removed outlier: 3.608A pdb=" N LYS E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) Proline residue: E 340 - end of helix Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.727A pdb=" N THR H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.656A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.875A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 51 removed outlier: 8.346A pdb=" N VAL A 38 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N ARG A 68 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N MET A 40 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ALA A 66 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE A 42 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N GLN A 64 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE A 44 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR A 62 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR A 58 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL A 50 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP A 56 " --> pdb=" O VAL A 50 " (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: 3.950A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.882A 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 54 removed outlier: 6.441A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) 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 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 99 through 101 current: chain 'B' and resid 209 through 221 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 36 through 47 removed outlier: 6.469A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (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: 3.618A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY C 203 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 39 through 49 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 39 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 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 99 through 101 current: chain 'D' and resid 208 through 221 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 51 through 66 removed outlier: 6.418A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLU E 71 " --> pdb=" O PRO E 64 " (cutoff:3.500A) 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 Processing sheet with id=AB1, first strand: chain 'E' and resid 111 through 113 removed outlier: 3.571A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'H' and resid 33 through 39 removed outlier: 6.973A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 60 current: chain 'H' and resid 113 through 114 Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 13 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 99 602 hydrogen bonds defined for protein. 1731 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: 6.45 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14880 1.03 - 1.23: 1305 1.23 - 1.43: 6255 1.43 - 1.63: 8942 1.63 - 1.83: 149 Bond restraints: 31531 Sorted by residual: bond pdb=" N TYR A 205 " pdb=" H TYR A 205 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.87e+01 bond pdb=" N ARG L 91 " pdb=" H ARG L 91 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" N TYR L 97 " pdb=" H TYR L 97 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" N THR B 130 " pdb=" H THR B 130 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.82e+01 bond pdb=" N PHE B 65 " pdb=" H PHE B 65 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.82e+01 ... (remaining 31526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 55952 2.09 - 4.19: 614 4.19 - 6.28: 61 6.28 - 8.37: 15 8.37 - 10.46: 3 Bond angle restraints: 56645 Sorted by residual: angle pdb=" N THR C 202 " pdb=" CA THR C 202 " pdb=" CB THR C 202 " ideal model delta sigma weight residual 110.65 102.42 8.23 1.47e+00 4.63e-01 3.13e+01 angle pdb=" C THR C 202 " pdb=" CA THR C 202 " pdb=" CB THR C 202 " ideal model delta sigma weight residual 109.55 118.14 -8.59 1.68e+00 3.54e-01 2.61e+01 angle pdb=" CA VAL H 104 " pdb=" C VAL H 104 " pdb=" O VAL H 104 " ideal model delta sigma weight residual 121.92 116.93 4.99 1.17e+00 7.31e-01 1.82e+01 angle pdb=" CA PRO C 206 " pdb=" C PRO C 206 " pdb=" O PRO C 206 " ideal model delta sigma weight residual 121.98 116.78 5.20 1.23e+00 6.61e-01 1.79e+01 angle pdb=" CA GLU C 155 " pdb=" C GLU C 155 " pdb=" O GLU C 155 " ideal model delta sigma weight residual 121.58 116.87 4.71 1.16e+00 7.43e-01 1.65e+01 ... (remaining 56640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 14394 21.62 - 43.24: 690 43.24 - 64.86: 156 64.86 - 86.48: 36 86.48 - 108.10: 14 Dihedral angle restraints: 15290 sinusoidal: 8338 harmonic: 6952 Sorted by residual: dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 165 " pdb=" CB CYS E 165 " ideal model delta sinusoidal sigma weight residual -86.00 -30.53 -55.47 1 1.00e+01 1.00e-02 4.16e+01 dihedral pdb=" CA CYS E 165 " pdb=" C CYS E 165 " pdb=" N PRO E 166 " pdb=" CA PRO E 166 " ideal model delta harmonic sigma weight residual 180.00 -154.25 -25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ARG D 37 " pdb=" C ARG D 37 " pdb=" N VAL D 38 " pdb=" CA VAL D 38 " ideal model delta harmonic sigma weight residual 180.00 156.92 23.08 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 15287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2049 0.056 - 0.113: 432 0.113 - 0.169: 62 0.169 - 0.225: 4 0.225 - 0.281: 3 Chirality restraints: 2550 Sorted by residual: 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 -2.56 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.65e+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 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 2547 not shown) Planarity restraints: 4529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 303 " 0.170 2.00e-02 2.50e+03 4.99e-01 3.74e+03 pdb=" CG ASN A 303 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 303 " -0.167 2.00e-02 2.50e+03 pdb=" ND2 ASN A 303 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 303 " -0.842 2.00e-02 2.50e+03 pdb="HD22 ASN A 303 " 0.854 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 238 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C ILE E 238 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE E 238 " -0.019 2.00e-02 2.50e+03 pdb=" N GLN E 239 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 155 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C GLU C 155 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU C 155 " -0.016 2.00e-02 2.50e+03 pdb=" N SER C 156 " -0.015 2.00e-02 2.50e+03 ... (remaining 4526 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 1040 2.15 - 2.76: 58938 2.76 - 3.37: 87142 3.37 - 3.99: 117843 3.99 - 4.60: 182369 Nonbonded interactions: 447332 Sorted by model distance: nonbonded pdb=" O ASP B 145 " pdb=" H MET B 148 " model vdw 1.533 2.450 nonbonded pdb=" O SER B 92 " pdb="HH12 ARG C 86 " model vdw 1.559 2.450 nonbonded pdb=" HH TYR B 60 " pdb=" O PRO B 154 " model vdw 1.580 2.450 nonbonded pdb=" OD1 ASP A 101 " pdb="HH22 ARG B 132 " model vdw 1.582 2.450 nonbonded pdb=" OE1 GLU D 59 " pdb=" HZ2 LYS D 105 " model vdw 1.583 2.450 ... (remaining 447327 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD22)) or resid 150 through 340)) selection = (chain 'C' and resid 7 through 340) } ncs_group { reference = (chain 'B' and (resid 10 through 110 or (resid 111 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD21)) or resid 112 through 347)) selection = (chain 'D' and resid 10 through 347) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.640 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 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:7.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 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 : 0.006 0.087 16206 Z= 0.300 Angle : 0.753 10.463 22076 Z= 0.413 Chirality : 0.048 0.281 2550 Planarity : 0.005 0.049 2705 Dihedral : 14.331 108.098 6183 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: -0.22 (0.19), residues: 1898 helix: 1.48 (0.20), residues: 621 sheet: -0.78 (0.22), residues: 540 loop : -0.97 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 326 TYR 0.029 0.002 TYR C 299 PHE 0.022 0.002 PHE D 258 TRP 0.038 0.002 TRP B 246 HIS 0.005 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00612 (16183) covalent geometry : angle 0.74276 (22014) SS BOND : bond 0.00693 ( 7) SS BOND : angle 1.64571 ( 14) hydrogen bonds : bond 0.11599 ( 602) hydrogen bonds : angle 5.78797 ( 1731) link_ALPHA1-2 : bond 0.00287 ( 3) link_ALPHA1-2 : angle 2.35633 ( 9) link_ALPHA1-3 : bond 0.00384 ( 1) link_ALPHA1-3 : angle 4.20107 ( 3) link_ALPHA1-6 : bond 0.00438 ( 2) link_ALPHA1-6 : angle 2.45114 ( 6) link_BETA1-4 : bond 0.00319 ( 9) link_BETA1-4 : angle 2.14799 ( 27) link_NAG-ASN : bond 0.00188 ( 1) link_NAG-ASN : angle 4.26201 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 THR cc_start: 0.8798 (t) cc_final: 0.7758 (t) REVERT: D 20 ASP cc_start: 0.8115 (m-30) cc_final: 0.7853 (m-30) REVERT: D 131 MET cc_start: 0.8553 (mtp) cc_final: 0.8222 (mtp) REVERT: D 190 GLN cc_start: 0.8162 (pt0) cc_final: 0.7306 (pm20) REVERT: E 99 ASN cc_start: 0.8120 (m110) cc_final: 0.7819 (m-40) REVERT: E 162 GLU cc_start: 0.6620 (tm-30) cc_final: 0.6175 (tm-30) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 1.3382 time to fit residues: 485.8830 Evaluate side-chains 254 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 GLN H 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.097402 restraints weight = 59327.051| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.86 r_work: 0.2889 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16206 Z= 0.152 Angle : 0.582 8.283 22076 Z= 0.302 Chirality : 0.042 0.154 2550 Planarity : 0.005 0.060 2705 Dihedral : 8.786 77.278 2619 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.71 % Allowed : 9.47 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.19), residues: 1898 helix: 1.66 (0.20), residues: 626 sheet: -0.53 (0.22), residues: 514 loop : -0.86 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 321 TYR 0.029 0.001 TYR C 299 PHE 0.015 0.001 PHE A 31 TRP 0.014 0.001 TRP B 246 HIS 0.003 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00345 (16183) covalent geometry : angle 0.57388 (22014) SS BOND : bond 0.00669 ( 7) SS BOND : angle 1.28322 ( 14) hydrogen bonds : bond 0.04595 ( 602) hydrogen bonds : angle 4.92110 ( 1731) link_ALPHA1-2 : bond 0.00272 ( 3) link_ALPHA1-2 : angle 1.69158 ( 9) link_ALPHA1-3 : bond 0.00217 ( 1) link_ALPHA1-3 : angle 1.74999 ( 3) link_ALPHA1-6 : bond 0.00199 ( 2) link_ALPHA1-6 : angle 1.99162 ( 6) link_BETA1-4 : bond 0.00259 ( 9) link_BETA1-4 : angle 1.93182 ( 27) link_NAG-ASN : bond 0.00422 ( 1) link_NAG-ASN : angle 3.65705 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 267 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8003 (mp0) cc_final: 0.7639 (mp0) REVERT: B 332 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6135 (mp) REVERT: C 294 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7404 (mpt) REVERT: C 305 ILE cc_start: 0.8275 (tp) cc_final: 0.7964 (mt) REVERT: D 17 ARG cc_start: 0.7647 (mtm110) cc_final: 0.7264 (mtm110) REVERT: D 20 ASP cc_start: 0.8404 (m-30) cc_final: 0.8065 (m-30) REVERT: D 78 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6710 (tmmt) REVERT: D 112 MET cc_start: 0.8391 (ttp) cc_final: 0.8159 (ttp) REVERT: D 131 MET cc_start: 0.8763 (mtp) cc_final: 0.8511 (mtp) REVERT: D 190 GLN cc_start: 0.8548 (pt0) cc_final: 0.7765 (pm20) REVERT: E 214 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8527 (mtmm) REVERT: H 76 LYS cc_start: 0.8204 (mttt) cc_final: 0.7439 (mmtm) outliers start: 29 outliers final: 14 residues processed: 279 average time/residue: 1.2374 time to fit residues: 384.5872 Evaluate side-chains 263 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 245 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 345 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 61 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 166 optimal weight: 0.2980 chunk 113 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 ASN C 309 GLN E 60 ASN L 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.130204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.097878 restraints weight = 59111.137| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.85 r_work: 0.2937 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16206 Z= 0.128 Angle : 0.537 6.763 22076 Z= 0.278 Chirality : 0.041 0.151 2550 Planarity : 0.004 0.051 2705 Dihedral : 7.052 65.466 2619 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.71 % Allowed : 11.06 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: 0.22 (0.19), residues: 1898 helix: 1.88 (0.20), residues: 626 sheet: -0.38 (0.22), residues: 513 loop : -0.90 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 321 TYR 0.029 0.001 TYR C 299 PHE 0.013 0.001 PHE H 106 TRP 0.009 0.001 TRP B 246 HIS 0.004 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00290 (16183) covalent geometry : angle 0.52936 (22014) SS BOND : bond 0.00589 ( 7) SS BOND : angle 1.12542 ( 14) hydrogen bonds : bond 0.04116 ( 602) hydrogen bonds : angle 4.63937 ( 1731) link_ALPHA1-2 : bond 0.00148 ( 3) link_ALPHA1-2 : angle 1.72723 ( 9) link_ALPHA1-3 : bond 0.00543 ( 1) link_ALPHA1-3 : angle 1.50609 ( 3) link_ALPHA1-6 : bond 0.00018 ( 2) link_ALPHA1-6 : angle 1.94119 ( 6) link_BETA1-4 : bond 0.00312 ( 9) link_BETA1-4 : angle 1.76064 ( 27) link_NAG-ASN : bond 0.00375 ( 1) link_NAG-ASN : angle 3.20535 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 259 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7973 (mp0) cc_final: 0.7639 (mp0) REVERT: B 312 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6837 (tptm) REVERT: B 332 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.6190 (mp) REVERT: C 207 ARG cc_start: 0.8720 (ttm-80) cc_final: 0.8495 (ttm-80) REVERT: C 294 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7434 (mpt) REVERT: C 305 ILE cc_start: 0.8232 (tp) cc_final: 0.7911 (mt) REVERT: D 17 ARG cc_start: 0.7685 (mtm110) cc_final: 0.7302 (mtm110) REVERT: D 20 ASP cc_start: 0.8373 (m-30) cc_final: 0.8049 (m-30) REVERT: D 131 MET cc_start: 0.8751 (mtp) cc_final: 0.8523 (mtp) REVERT: D 190 GLN cc_start: 0.8553 (pt0) cc_final: 0.7762 (pm20) REVERT: D 294 TYR cc_start: 0.7782 (t80) cc_final: 0.7371 (t80) REVERT: E 162 GLU cc_start: 0.6607 (tm-30) cc_final: 0.6321 (tm-30) REVERT: H 3 GLN cc_start: 0.8332 (mm-40) cc_final: 0.8094 (mm110) outliers start: 29 outliers final: 16 residues processed: 272 average time/residue: 1.1517 time to fit residues: 351.5658 Evaluate side-chains 259 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 240 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 345 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 182 optimal weight: 0.5980 chunk 158 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 60 ASN E 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.128711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.096424 restraints weight = 59160.408| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.95 r_work: 0.2906 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16206 Z= 0.154 Angle : 0.542 6.696 22076 Z= 0.280 Chirality : 0.041 0.180 2550 Planarity : 0.004 0.053 2705 Dihedral : 6.489 58.426 2619 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.82 % Allowed : 11.94 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: 0.28 (0.19), residues: 1898 helix: 1.98 (0.20), residues: 626 sheet: -0.35 (0.23), residues: 509 loop : -0.91 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 265 TYR 0.029 0.001 TYR C 299 PHE 0.013 0.001 PHE B 336 TRP 0.009 0.001 TRP C 241 HIS 0.004 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00353 (16183) covalent geometry : angle 0.53453 (22014) SS BOND : bond 0.00599 ( 7) SS BOND : angle 1.24976 ( 14) hydrogen bonds : bond 0.04017 ( 602) hydrogen bonds : angle 4.53001 ( 1731) link_ALPHA1-2 : bond 0.00157 ( 3) link_ALPHA1-2 : angle 1.80200 ( 9) link_ALPHA1-3 : bond 0.00472 ( 1) link_ALPHA1-3 : angle 1.47164 ( 3) link_ALPHA1-6 : bond 0.00230 ( 2) link_ALPHA1-6 : angle 2.12955 ( 6) link_BETA1-4 : bond 0.00264 ( 9) link_BETA1-4 : angle 1.76688 ( 27) link_NAG-ASN : bond 0.00350 ( 1) link_NAG-ASN : angle 3.50467 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 257 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7332 (mtt-85) REVERT: B 279 LYS cc_start: 0.7433 (mmmt) cc_final: 0.7017 (mptp) REVERT: B 332 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6214 (mp) REVERT: C 294 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7442 (mpt) REVERT: C 298 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8148 (tm-30) REVERT: C 305 ILE cc_start: 0.8226 (tp) cc_final: 0.7921 (mt) REVERT: D 17 ARG cc_start: 0.7724 (mtm110) cc_final: 0.7326 (mtm110) REVERT: D 20 ASP cc_start: 0.8331 (m-30) cc_final: 0.7957 (m-30) REVERT: D 131 MET cc_start: 0.8771 (mtp) cc_final: 0.8550 (mtp) REVERT: D 190 GLN cc_start: 0.8585 (pt0) cc_final: 0.7786 (pm20) REVERT: D 294 TYR cc_start: 0.7713 (t80) cc_final: 0.7235 (t80) REVERT: H 3 GLN cc_start: 0.8327 (mm-40) cc_final: 0.8107 (mm110) outliers start: 31 outliers final: 19 residues processed: 270 average time/residue: 1.2278 time to fit residues: 371.5899 Evaluate side-chains 262 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 240 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 71 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 154 GLN L 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.128880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.096256 restraints weight = 59335.152| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.83 r_work: 0.2924 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16206 Z= 0.163 Angle : 0.544 6.510 22076 Z= 0.280 Chirality : 0.041 0.193 2550 Planarity : 0.004 0.053 2705 Dihedral : 6.206 54.719 2619 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.29 % Allowed : 12.41 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: 0.31 (0.19), residues: 1898 helix: 2.03 (0.20), residues: 626 sheet: -0.34 (0.23), residues: 509 loop : -0.90 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 207 TYR 0.028 0.001 TYR C 299 PHE 0.013 0.001 PHE H 106 TRP 0.006 0.001 TRP B 246 HIS 0.004 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00377 (16183) covalent geometry : angle 0.53606 (22014) SS BOND : bond 0.00619 ( 7) SS BOND : angle 1.33874 ( 14) hydrogen bonds : bond 0.04029 ( 602) hydrogen bonds : angle 4.47813 ( 1731) link_ALPHA1-2 : bond 0.00142 ( 3) link_ALPHA1-2 : angle 1.82768 ( 9) link_ALPHA1-3 : bond 0.00425 ( 1) link_ALPHA1-3 : angle 1.46710 ( 3) link_ALPHA1-6 : bond 0.00239 ( 2) link_ALPHA1-6 : angle 2.11077 ( 6) link_BETA1-4 : bond 0.00270 ( 9) link_BETA1-4 : angle 1.73696 ( 27) link_NAG-ASN : bond 0.00335 ( 1) link_NAG-ASN : angle 3.57125 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 248 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7951 (mp0) cc_final: 0.7612 (mp0) REVERT: B 17 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7357 (mtt-85) REVERT: B 279 LYS cc_start: 0.7506 (mmmt) cc_final: 0.7076 (mptp) REVERT: B 332 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6229 (mp) REVERT: C 17 ASP cc_start: 0.7964 (m-30) cc_final: 0.7474 (m-30) REVERT: C 274 LYS cc_start: 0.7759 (mmtm) cc_final: 0.7236 (mmtt) REVERT: C 294 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7459 (mpt) REVERT: C 298 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8374 (tm-30) REVERT: C 305 ILE cc_start: 0.8245 (tp) cc_final: 0.7970 (mt) REVERT: D 16 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.7974 (t) REVERT: D 17 ARG cc_start: 0.7724 (mtm110) cc_final: 0.7388 (mtm110) REVERT: D 20 ASP cc_start: 0.8318 (m-30) cc_final: 0.7919 (m-30) REVERT: D 78 LYS cc_start: 0.7228 (OUTLIER) cc_final: 0.6795 (tmmt) REVERT: D 131 MET cc_start: 0.8768 (mtp) cc_final: 0.8545 (mtp) REVERT: D 190 GLN cc_start: 0.8595 (pt0) cc_final: 0.7773 (pm20) REVERT: H 3 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8120 (mm110) REVERT: H 11 LEU cc_start: 0.8028 (mm) cc_final: 0.7721 (tp) REVERT: H 76 LYS cc_start: 0.8153 (mttt) cc_final: 0.7433 (mmtt) outliers start: 39 outliers final: 23 residues processed: 266 average time/residue: 1.2670 time to fit residues: 376.4348 Evaluate side-chains 269 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 241 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 345 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 153 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN L 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.096653 restraints weight = 58917.100| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.84 r_work: 0.2825 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16206 Z= 0.192 Angle : 0.565 6.522 22076 Z= 0.290 Chirality : 0.042 0.201 2550 Planarity : 0.004 0.054 2705 Dihedral : 6.137 52.581 2619 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.53 % Allowed : 12.59 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: 0.28 (0.19), residues: 1898 helix: 2.01 (0.20), residues: 626 sheet: -0.45 (0.22), residues: 512 loop : -0.86 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 67 TYR 0.029 0.002 TYR C 299 PHE 0.014 0.002 PHE H 106 TRP 0.009 0.001 TRP D 246 HIS 0.004 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00447 (16183) covalent geometry : angle 0.55565 (22014) SS BOND : bond 0.00650 ( 7) SS BOND : angle 1.49671 ( 14) hydrogen bonds : bond 0.04107 ( 602) hydrogen bonds : angle 4.47187 ( 1731) link_ALPHA1-2 : bond 0.00153 ( 3) link_ALPHA1-2 : angle 1.91434 ( 9) link_ALPHA1-3 : bond 0.00307 ( 1) link_ALPHA1-3 : angle 1.61977 ( 3) link_ALPHA1-6 : bond 0.00377 ( 2) link_ALPHA1-6 : angle 2.24745 ( 6) link_BETA1-4 : bond 0.00272 ( 9) link_BETA1-4 : angle 1.82628 ( 27) link_NAG-ASN : bond 0.00320 ( 1) link_NAG-ASN : angle 3.92679 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 250 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7935 (mp0) cc_final: 0.7567 (mp0) REVERT: A 153 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: B 17 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7264 (mtt-85) REVERT: B 279 LYS cc_start: 0.7572 (mmmt) cc_final: 0.7098 (mptp) REVERT: B 317 ARG cc_start: 0.5838 (OUTLIER) cc_final: 0.5162 (ttm-80) REVERT: B 332 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6132 (mp) REVERT: C 17 ASP cc_start: 0.7959 (m-30) cc_final: 0.7433 (m-30) REVERT: C 274 LYS cc_start: 0.7623 (mmtm) cc_final: 0.7227 (mmtt) REVERT: C 294 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7374 (mpt) REVERT: C 298 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8337 (tm-30) REVERT: D 16 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.7925 (t) REVERT: D 17 ARG cc_start: 0.7652 (mtm110) cc_final: 0.7304 (mtm110) REVERT: D 20 ASP cc_start: 0.8262 (m-30) cc_final: 0.7815 (m-30) REVERT: D 131 MET cc_start: 0.8877 (mtp) cc_final: 0.8663 (mtp) REVERT: D 190 GLN cc_start: 0.8612 (pt0) cc_final: 0.7694 (pm20) REVERT: E 214 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8528 (mtmm) REVERT: H 11 LEU cc_start: 0.8052 (mm) cc_final: 0.7726 (tp) REVERT: H 76 LYS cc_start: 0.8079 (mttt) cc_final: 0.7305 (mmtt) outliers start: 43 outliers final: 27 residues processed: 269 average time/residue: 1.2278 time to fit residues: 369.7975 Evaluate side-chains 274 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 240 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 317 ARG Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 25 optimal weight: 0.9980 chunk 169 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 60 ASN E 154 GLN L 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.130499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.098912 restraints weight = 59036.275| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.84 r_work: 0.2847 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16206 Z= 0.130 Angle : 0.529 6.453 22076 Z= 0.272 Chirality : 0.041 0.209 2550 Planarity : 0.004 0.054 2705 Dihedral : 5.770 51.350 2619 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.88 % Allowed : 13.12 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: 0.38 (0.19), residues: 1898 helix: 2.12 (0.20), residues: 627 sheet: -0.43 (0.22), residues: 512 loop : -0.80 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 265 TYR 0.028 0.001 TYR C 299 PHE 0.016 0.001 PHE B 336 TRP 0.010 0.001 TRP D 246 HIS 0.003 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00296 (16183) covalent geometry : angle 0.52212 (22014) SS BOND : bond 0.00515 ( 7) SS BOND : angle 1.16256 ( 14) hydrogen bonds : bond 0.03825 ( 602) hydrogen bonds : angle 4.36703 ( 1731) link_ALPHA1-2 : bond 0.00134 ( 3) link_ALPHA1-2 : angle 1.72021 ( 9) link_ALPHA1-3 : bond 0.00635 ( 1) link_ALPHA1-3 : angle 1.19798 ( 3) link_ALPHA1-6 : bond 0.00058 ( 2) link_ALPHA1-6 : angle 1.89729 ( 6) link_BETA1-4 : bond 0.00245 ( 9) link_BETA1-4 : angle 1.67140 ( 27) link_NAG-ASN : bond 0.00408 ( 1) link_NAG-ASN : angle 3.27330 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7948 (mp0) cc_final: 0.7602 (mp0) REVERT: A 137 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7699 (tmm) REVERT: B 279 LYS cc_start: 0.7466 (mmmt) cc_final: 0.7002 (mptp) REVERT: B 317 ARG cc_start: 0.5801 (OUTLIER) cc_final: 0.5067 (ttm-80) REVERT: B 332 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6114 (mp) REVERT: C 17 ASP cc_start: 0.7927 (m-30) cc_final: 0.7405 (m-30) REVERT: C 274 LYS cc_start: 0.7580 (mmtm) cc_final: 0.7194 (mmtt) REVERT: C 294 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7381 (mpt) REVERT: C 298 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8309 (tm-30) REVERT: D 16 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.7932 (t) REVERT: D 17 ARG cc_start: 0.7684 (mtm110) cc_final: 0.7332 (mtm110) REVERT: D 20 ASP cc_start: 0.8279 (m-30) cc_final: 0.7832 (m-30) REVERT: D 131 MET cc_start: 0.8836 (mtp) cc_final: 0.8624 (mtp) REVERT: D 190 GLN cc_start: 0.8583 (pt0) cc_final: 0.7679 (pm20) REVERT: D 246 TRP cc_start: 0.7822 (m100) cc_final: 0.7534 (t-100) REVERT: E 214 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8519 (mtmm) REVERT: H 11 LEU cc_start: 0.8052 (mm) cc_final: 0.7719 (tp) REVERT: H 76 LYS cc_start: 0.8057 (mttt) cc_final: 0.7287 (mmtt) outliers start: 32 outliers final: 20 residues processed: 266 average time/residue: 1.1954 time to fit residues: 355.8453 Evaluate side-chains 267 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 241 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 317 ARG Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 24 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 69 optimal weight: 0.0010 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 60 ASN E 154 GLN L 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.129273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.097211 restraints weight = 59227.357| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.95 r_work: 0.2925 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16206 Z= 0.147 Angle : 0.540 6.429 22076 Z= 0.276 Chirality : 0.041 0.213 2550 Planarity : 0.004 0.053 2705 Dihedral : 5.639 52.611 2619 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.00 % Allowed : 13.53 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: 0.42 (0.19), residues: 1898 helix: 2.16 (0.20), residues: 627 sheet: -0.42 (0.22), residues: 512 loop : -0.78 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 269 TYR 0.028 0.001 TYR C 299 PHE 0.014 0.001 PHE B 336 TRP 0.006 0.001 TRP D 246 HIS 0.003 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00339 (16183) covalent geometry : angle 0.53309 (22014) SS BOND : bond 0.00537 ( 7) SS BOND : angle 1.23332 ( 14) hydrogen bonds : bond 0.03841 ( 602) hydrogen bonds : angle 4.33633 ( 1731) link_ALPHA1-2 : bond 0.00152 ( 3) link_ALPHA1-2 : angle 1.79716 ( 9) link_ALPHA1-3 : bond 0.00572 ( 1) link_ALPHA1-3 : angle 1.34076 ( 3) link_ALPHA1-6 : bond 0.00153 ( 2) link_ALPHA1-6 : angle 2.05999 ( 6) link_BETA1-4 : bond 0.00255 ( 9) link_BETA1-4 : angle 1.67301 ( 27) link_NAG-ASN : bond 0.00371 ( 1) link_NAG-ASN : angle 3.37783 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 243 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7993 (mp0) cc_final: 0.7681 (mp0) REVERT: A 137 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7774 (tmm) REVERT: B 279 LYS cc_start: 0.7506 (mmmt) cc_final: 0.7103 (mptp) REVERT: B 317 ARG cc_start: 0.5928 (OUTLIER) cc_final: 0.5249 (ttm-80) REVERT: B 332 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6293 (mp) REVERT: C 17 ASP cc_start: 0.7982 (m-30) cc_final: 0.7510 (m-30) REVERT: C 274 LYS cc_start: 0.7591 (mmtm) cc_final: 0.7235 (mmtt) REVERT: C 298 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8358 (tm-30) REVERT: D 16 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.7968 (t) REVERT: D 17 ARG cc_start: 0.7781 (mtm110) cc_final: 0.7448 (mtm110) REVERT: D 20 ASP cc_start: 0.8313 (m-30) cc_final: 0.7890 (m-30) REVERT: D 131 MET cc_start: 0.8763 (mtp) cc_final: 0.8549 (mtp) REVERT: D 190 GLN cc_start: 0.8599 (pt0) cc_final: 0.7798 (pm20) REVERT: D 225 TYR cc_start: 0.8518 (t80) cc_final: 0.8214 (t80) REVERT: D 246 TRP cc_start: 0.7886 (m100) cc_final: 0.7622 (t-100) REVERT: H 11 LEU cc_start: 0.8024 (mm) cc_final: 0.7733 (tp) REVERT: H 76 LYS cc_start: 0.8134 (mttt) cc_final: 0.7399 (mmtt) REVERT: L 81 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7298 (pp20) outliers start: 34 outliers final: 22 residues processed: 258 average time/residue: 1.1907 time to fit residues: 343.8252 Evaluate side-chains 266 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 239 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 317 ARG Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN L 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.129042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.096854 restraints weight = 59077.381| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.82 r_work: 0.2901 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16206 Z= 0.212 Angle : 0.582 6.605 22076 Z= 0.298 Chirality : 0.042 0.220 2550 Planarity : 0.004 0.054 2705 Dihedral : 5.822 53.691 2619 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.94 % Allowed : 13.94 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: 0.32 (0.19), residues: 1898 helix: 2.05 (0.20), residues: 627 sheet: -0.46 (0.22), residues: 513 loop : -0.83 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 269 TYR 0.029 0.002 TYR C 299 PHE 0.014 0.002 PHE H 106 TRP 0.006 0.001 TRP A 319 HIS 0.003 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00494 (16183) covalent geometry : angle 0.57269 (22014) SS BOND : bond 0.00661 ( 7) SS BOND : angle 1.60337 ( 14) hydrogen bonds : bond 0.04135 ( 602) hydrogen bonds : angle 4.41965 ( 1731) link_ALPHA1-2 : bond 0.00193 ( 3) link_ALPHA1-2 : angle 1.99570 ( 9) link_ALPHA1-3 : bond 0.00295 ( 1) link_ALPHA1-3 : angle 1.68315 ( 3) link_ALPHA1-6 : bond 0.00484 ( 2) link_ALPHA1-6 : angle 2.34829 ( 6) link_BETA1-4 : bond 0.00274 ( 9) link_BETA1-4 : angle 1.83753 ( 27) link_NAG-ASN : bond 0.00298 ( 1) link_NAG-ASN : angle 4.17313 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 240 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7984 (mp0) cc_final: 0.7657 (mp0) REVERT: A 137 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7659 (tmm) REVERT: B 17 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7360 (mtt-85) REVERT: B 279 LYS cc_start: 0.7616 (mmmt) cc_final: 0.7224 (mptp) REVERT: B 317 ARG cc_start: 0.5941 (OUTLIER) cc_final: 0.5264 (ttm-80) REVERT: B 332 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6361 (mp) REVERT: C 17 ASP cc_start: 0.7911 (m-30) cc_final: 0.7469 (m-30) REVERT: C 274 LYS cc_start: 0.7634 (mmtm) cc_final: 0.7269 (mmtt) REVERT: C 298 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8475 (tm-30) REVERT: D 16 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8004 (t) REVERT: D 20 ASP cc_start: 0.8251 (m-30) cc_final: 0.7772 (m-30) REVERT: D 131 MET cc_start: 0.8791 (mtp) cc_final: 0.8550 (mtp) REVERT: D 190 GLN cc_start: 0.8613 (pt0) cc_final: 0.7799 (pm20) REVERT: D 228 ILE cc_start: 0.8441 (tp) cc_final: 0.8071 (mp) REVERT: H 3 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8247 (mm110) REVERT: H 11 LEU cc_start: 0.8060 (mm) cc_final: 0.7789 (tp) REVERT: H 76 LYS cc_start: 0.8147 (mttt) cc_final: 0.7404 (mmtt) REVERT: L 81 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7391 (pp20) outliers start: 33 outliers final: 26 residues processed: 256 average time/residue: 1.2708 time to fit residues: 364.0361 Evaluate side-chains 270 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 ARG Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 103 optimal weight: 0.0980 chunk 181 optimal weight: 0.9980 chunk 142 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 chunk 63 optimal weight: 0.0670 chunk 38 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 60 ASN E 154 GLN L 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.132338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.099895 restraints weight = 58719.156| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.79 r_work: 0.2936 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 16206 Z= 0.101 Angle : 0.518 6.313 22076 Z= 0.265 Chirality : 0.040 0.213 2550 Planarity : 0.004 0.054 2705 Dihedral : 5.306 54.384 2619 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.47 % Allowed : 14.65 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.19), residues: 1898 helix: 2.26 (0.20), residues: 627 sheet: -0.42 (0.23), residues: 492 loop : -0.70 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 269 TYR 0.029 0.001 TYR C 299 PHE 0.016 0.001 PHE A 289 TRP 0.019 0.001 TRP D 246 HIS 0.003 0.000 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00229 (16183) covalent geometry : angle 0.51238 (22014) SS BOND : bond 0.00421 ( 7) SS BOND : angle 0.86066 ( 14) hydrogen bonds : bond 0.03554 ( 602) hydrogen bonds : angle 4.23425 ( 1731) link_ALPHA1-2 : bond 0.00268 ( 3) link_ALPHA1-2 : angle 1.59096 ( 9) link_ALPHA1-3 : bond 0.01025 ( 1) link_ALPHA1-3 : angle 0.79255 ( 3) link_ALPHA1-6 : bond 0.00259 ( 2) link_ALPHA1-6 : angle 1.60438 ( 6) link_BETA1-4 : bond 0.00269 ( 9) link_BETA1-4 : angle 1.56583 ( 27) link_NAG-ASN : bond 0.00460 ( 1) link_NAG-ASN : angle 2.63290 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 250 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7959 (mp0) cc_final: 0.7650 (mp0) REVERT: A 137 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7652 (tmm) REVERT: B 279 LYS cc_start: 0.7457 (mmmt) cc_final: 0.7094 (mptp) REVERT: B 317 ARG cc_start: 0.5828 (OUTLIER) cc_final: 0.5119 (ttm-80) REVERT: C 17 ASP cc_start: 0.7941 (m-30) cc_final: 0.7480 (m-30) REVERT: C 274 LYS cc_start: 0.7588 (mmtm) cc_final: 0.7219 (mmtt) REVERT: D 16 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8067 (t) REVERT: D 17 ARG cc_start: 0.7708 (mtm110) cc_final: 0.7342 (mtm110) REVERT: D 20 ASP cc_start: 0.8471 (m-30) cc_final: 0.8140 (m-30) REVERT: D 131 MET cc_start: 0.8734 (mtp) cc_final: 0.8533 (mtp) REVERT: D 190 GLN cc_start: 0.8544 (pt0) cc_final: 0.7711 (pm20) REVERT: D 225 TYR cc_start: 0.8460 (t80) cc_final: 0.8197 (t80) REVERT: D 228 ILE cc_start: 0.8390 (tp) cc_final: 0.8003 (mp) REVERT: D 246 TRP cc_start: 0.7684 (m100) cc_final: 0.7479 (t-100) REVERT: E 162 GLU cc_start: 0.6762 (tm-30) cc_final: 0.6531 (tm-30) REVERT: H 3 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8206 (mm110) REVERT: H 11 LEU cc_start: 0.7986 (mm) cc_final: 0.7717 (tp) REVERT: H 76 LYS cc_start: 0.8108 (mttt) cc_final: 0.7367 (mmtt) outliers start: 25 outliers final: 17 residues processed: 261 average time/residue: 1.2288 time to fit residues: 358.1403 Evaluate side-chains 259 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 239 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 331 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 10 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 181 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.129279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.097399 restraints weight = 59304.976| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.88 r_work: 0.2943 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16206 Z= 0.124 Angle : 0.527 6.381 22076 Z= 0.268 Chirality : 0.041 0.205 2550 Planarity : 0.004 0.052 2705 Dihedral : 5.251 55.844 2619 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.29 % Allowed : 14.94 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: 0.57 (0.19), residues: 1898 helix: 2.30 (0.20), residues: 626 sheet: -0.34 (0.23), residues: 504 loop : -0.70 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 207 TYR 0.029 0.001 TYR C 299 PHE 0.019 0.001 PHE B 336 TRP 0.012 0.001 TRP D 246 HIS 0.003 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00287 (16183) covalent geometry : angle 0.52091 (22014) SS BOND : bond 0.00461 ( 7) SS BOND : angle 1.08029 ( 14) hydrogen bonds : bond 0.03595 ( 602) hydrogen bonds : angle 4.21624 ( 1731) link_ALPHA1-2 : bond 0.00178 ( 3) link_ALPHA1-2 : angle 1.73387 ( 9) link_ALPHA1-3 : bond 0.00721 ( 1) link_ALPHA1-3 : angle 1.21060 ( 3) link_ALPHA1-6 : bond 0.00084 ( 2) link_ALPHA1-6 : angle 1.98827 ( 6) link_BETA1-4 : bond 0.00261 ( 9) link_BETA1-4 : angle 1.56849 ( 27) link_NAG-ASN : bond 0.00374 ( 1) link_NAG-ASN : angle 3.02632 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11220.31 seconds wall clock time: 190 minutes 26.49 seconds (11426.49 seconds total)