Starting phenix.real_space_refine on Sun Aug 24 09:44:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bqh_44799/08_2025/9bqh_44799_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bqh_44799/08_2025/9bqh_44799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bqh_44799/08_2025/9bqh_44799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bqh_44799/08_2025/9bqh_44799.map" model { file = "/net/cci-nas-00/data/ceres_data/9bqh_44799/08_2025/9bqh_44799_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bqh_44799/08_2025/9bqh_44799_trim.cif" } resolution = 2.27 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= 0.007 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 66 5.16 5 C 6027 2.51 5 N 1521 2.21 5 O 2205 1.98 5 H 8664 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18483 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5824 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 374, 5799 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Conformer: "B" Number of residues, atoms: 374, 5799 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 bond proxies already assigned to first conformer: 5838 Chain: "B" Number of atoms: 5824 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 374, 5799 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Conformer: "B" Number of residues, atoms: 374, 5799 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 bond proxies already assigned to first conformer: 5838 Chain: "C" Number of atoms: 5824 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 374, 5799 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Conformer: "B" Number of residues, atoms: 374, 5799 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 bond proxies already assigned to first conformer: 5838 Chain: "D" 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: "E" 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 147 Unusual residues: {'LMT': 3, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 112 Unusual residues: {'LMT': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Unusual residues: {'LMT': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG A 19 " occ=0.57 ... (46 atoms not shown) pdb="HH22BARG A 19 " occ=0.43 residue: pdb=" N AARG B 19 " occ=0.57 ... (46 atoms not shown) pdb="HH22BARG B 19 " occ=0.43 residue: pdb=" N AARG C 19 " occ=0.57 ... (46 atoms not shown) pdb="HH22BARG C 19 " occ=0.43 Time building chain proxies: 5.53, per 1000 atoms: 0.30 Number of scatterers: 18483 At special positions: 0 Unit cell: (91.368, 86.184, 132.84, 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 66 16.00 O 2205 8.00 N 1521 7.00 C 6027 6.00 H 8664 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 227 " distance=2.04 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 227 " distance=2.04 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 227 " distance=2.04 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 270 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 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 L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A 401 " - " ASN A 110 " " NAG A 402 " - " ASN A 153 " " NAG A 403 " - " ASN A 199 " " NAG B 402 " - " ASN B 110 " " NAG B 403 " - " ASN B 153 " " NAG B 404 " - " ASN B 199 " " NAG C 402 " - " ASN C 110 " " NAG C 403 " - " ASN C 153 " " NAG C 404 " - " ASN C 199 " " NAG D 1 " - " ASN A 75 " " NAG E 1 " - " ASN A 184 " " NAG F 1 " - " ASN A 208 " " NAG G 1 " - " ASN B 75 " " NAG H 1 " - " ASN B 184 " " NAG I 1 " - " ASN B 208 " " NAG J 1 " - " ASN C 75 " " NAG K 1 " - " ASN C 184 " " NAG L 1 " - " ASN C 208 " Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 815.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 21 sheets defined 29.5% alpha, 50.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 25 through 46 Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.832A pdb=" N VAL A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 331 through 346 removed outlier: 3.645A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 removed outlier: 4.299A pdb=" N THR A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'B' and resid 4 through 13 Processing helix chain 'B' and resid 25 through 46 Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 210 through 215 Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.833A pdb=" N VAL B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 331 through 346 removed outlier: 3.646A pdb=" N THR B 335 " --> pdb=" O ASP B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 360 removed outlier: 4.299A pdb=" N THR B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 371 Processing helix chain 'C' and resid 4 through 13 Processing helix chain 'C' and resid 25 through 46 Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 210 through 215 Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.832A pdb=" N VAL C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 Processing helix chain 'C' and resid 331 through 346 removed outlier: 3.646A pdb=" N THR C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 360 removed outlier: 4.298A pdb=" N THR C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 18 removed outlier: 4.795A pdb=" N ARG B 24 " --> pdb=" O VAL C 375 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 372 through 375 removed outlier: 4.795A pdb=" N ARG A 24 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 59 Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 69 Processing sheet with id=AA5, first strand: chain 'A' and resid 61 through 69 Processing sheet with id=AA6, first strand: chain 'A' and resid 72 through 76 Processing sheet with id=AA7, first strand: chain 'A' and resid 144 through 151 removed outlier: 9.224A pdb=" N VAL A 144 " --> pdb=" O TRP A 164 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N TRP A 164 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR A 146 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ALA A 162 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ARG A 148 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR A 315 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL A 105 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS A 313 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU A 107 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A 311 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N MET A 109 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ARG A 309 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN A 111 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU A 307 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 144 through 151 removed outlier: 9.224A pdb=" N VAL A 144 " --> pdb=" O TRP A 164 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N TRP A 164 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR A 146 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ALA A 162 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ARG A 148 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR A 315 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL A 105 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS A 313 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU A 107 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A 311 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N MET A 109 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ARG A 309 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN A 111 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU A 307 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 372 through 375 removed outlier: 6.525A pdb=" N LYS A 373 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ARG C 24 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N VAL A 375 " --> pdb=" O ARG C 24 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 55 through 59 Processing sheet with id=AB2, first strand: chain 'B' and resid 61 through 69 Processing sheet with id=AB3, first strand: chain 'B' and resid 61 through 69 Processing sheet with id=AB4, first strand: chain 'B' and resid 72 through 76 Processing sheet with id=AB5, first strand: chain 'B' and resid 144 through 151 removed outlier: 9.223A pdb=" N VAL B 144 " --> pdb=" O TRP B 164 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N TRP B 164 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR B 146 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ALA B 162 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ARG B 148 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR B 315 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL B 105 " --> pdb=" O LYS B 313 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS B 313 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU B 107 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 311 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N MET B 109 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ARG B 309 " --> pdb=" O MET B 109 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN B 111 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU B 307 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 144 through 151 removed outlier: 9.223A pdb=" N VAL B 144 " --> pdb=" O TRP B 164 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N TRP B 164 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR B 146 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ALA B 162 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ARG B 148 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR B 315 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL B 105 " --> pdb=" O LYS B 313 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS B 313 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU B 107 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 311 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N MET B 109 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ARG B 309 " --> pdb=" O MET B 109 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN B 111 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU B 307 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 55 through 59 Processing sheet with id=AB8, first strand: chain 'C' and resid 61 through 69 Processing sheet with id=AB9, first strand: chain 'C' and resid 61 through 69 Processing sheet with id=AC1, first strand: chain 'C' and resid 72 through 76 Processing sheet with id=AC2, first strand: chain 'C' and resid 144 through 151 removed outlier: 9.224A pdb=" N VAL C 144 " --> pdb=" O TRP C 164 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N TRP C 164 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR C 146 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ALA C 162 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ARG C 148 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR C 315 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL C 105 " --> pdb=" O LYS C 313 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS C 313 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU C 107 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU C 311 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N MET C 109 " --> pdb=" O ARG C 309 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ARG C 309 " --> pdb=" O MET C 109 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN C 111 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU C 307 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 144 through 151 removed outlier: 9.224A pdb=" N VAL C 144 " --> pdb=" O TRP C 164 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N TRP C 164 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR C 146 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ALA C 162 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ARG C 148 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR C 315 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL C 105 " --> pdb=" O LYS C 313 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS C 313 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU C 107 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU C 311 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N MET C 109 " --> pdb=" O ARG C 309 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ARG C 309 " --> pdb=" O MET C 109 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN C 111 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU C 307 " --> pdb=" O GLN C 111 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1299 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: 3.42 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 8649 1.02 - 1.22: 15 1.22 - 1.42: 3900 1.42 - 1.62: 5643 1.62 - 1.82: 90 Bond restraints: 18297 Sorted by residual: bond pdb=" ND2 ASN C 142 " pdb="HD22 ASN C 142 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN A 142 " pdb="HD22 ASN A 142 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN C 142 " pdb="HD21 ASN C 142 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" ND2 ASN B 142 " pdb="HD22 ASN B 142 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" ND2 ASN A 142 " pdb="HD21 ASN A 142 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.57e+01 ... (remaining 18292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 32399 2.21 - 4.43: 265 4.43 - 6.64: 24 6.64 - 8.85: 18 8.85 - 11.06: 6 Bond angle restraints: 32712 Sorted by residual: angle pdb=" C2 LMT B 405 " pdb=" C3 LMT B 405 " pdb=" C4 LMT B 405 " ideal model delta sigma weight residual 117.09 106.03 11.06 3.00e+00 1.11e-01 1.36e+01 angle pdb=" C2 LMT A 404 " pdb=" C3 LMT A 404 " pdb=" C4 LMT A 404 " ideal model delta sigma weight residual 117.09 106.04 11.05 3.00e+00 1.11e-01 1.36e+01 angle pdb=" C2 LMT A 405 " pdb=" C3 LMT A 405 " pdb=" C4 LMT A 405 " ideal model delta sigma weight residual 117.09 106.08 11.01 3.00e+00 1.11e-01 1.35e+01 angle pdb=" N ASN B 142 " pdb=" CA ASN B 142 " pdb=" C ASN B 142 " ideal model delta sigma weight residual 113.23 109.07 4.16 1.24e+00 6.50e-01 1.12e+01 angle pdb=" N ASN C 142 " pdb=" CA ASN C 142 " pdb=" C ASN C 142 " ideal model delta sigma weight residual 113.23 109.08 4.15 1.24e+00 6.50e-01 1.12e+01 ... (remaining 32707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.31: 8640 21.31 - 42.63: 516 42.63 - 63.94: 177 63.94 - 85.25: 33 85.25 - 106.57: 12 Dihedral angle restraints: 9378 sinusoidal: 5469 harmonic: 3909 Sorted by residual: dihedral pdb=" O4 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C5 BMA L 3 " pdb=" O5 BMA L 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.86 106.57 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.85 106.56 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" O4 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C5 BMA I 3 " pdb=" O5 BMA I 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.84 106.55 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 9375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1300 0.057 - 0.114: 217 0.114 - 0.171: 73 0.171 - 0.228: 0 0.228 - 0.285: 9 Chirality restraints: 1599 Sorted by residual: chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1596 not shown) Planarity restraints: 2679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 142 " -0.042 2.00e-02 2.50e+03 4.08e-02 2.50e+01 pdb=" CG ASN C 142 " 0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN C 142 " 0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN C 142 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 142 " 0.057 2.00e-02 2.50e+03 pdb="HD22 ASN C 142 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 142 " 0.042 2.00e-02 2.50e+03 4.07e-02 2.49e+01 pdb=" CG ASN B 142 " -0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN B 142 " -0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN B 142 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 142 " -0.057 2.00e-02 2.50e+03 pdb="HD22 ASN B 142 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 142 " 0.042 2.00e-02 2.50e+03 4.07e-02 2.49e+01 pdb=" CG ASN A 142 " -0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN A 142 " -0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN A 142 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 142 " -0.057 2.00e-02 2.50e+03 pdb="HD22 ASN A 142 " 0.058 2.00e-02 2.50e+03 ... (remaining 2676 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1005 2.20 - 2.80: 36055 2.80 - 3.40: 48106 3.40 - 4.00: 70815 4.00 - 4.60: 104617 Nonbonded interactions: 260598 Sorted by model distance: nonbonded pdb="HH22 ARG A 301 " pdb=" OE1 GLN C 308 " model vdw 1.601 2.450 nonbonded pdb=" OE1 GLN B 308 " pdb="HH22 ARG C 301 " model vdw 1.601 2.450 nonbonded pdb=" OE1 GLN A 308 " pdb="HH22 ARG B 301 " model vdw 1.602 2.450 nonbonded pdb=" HH TYR A 300 " pdb=" O HOH A 501 " model vdw 1.606 2.450 nonbonded pdb=" O HIS A 286 " pdb="HH22 ARG C 203 " model vdw 1.625 2.450 ... (remaining 260593 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 3 through 18 or resid 20 through 253 or resid 255 through \ 376 or resid 402 through 403)) selection = (chain 'B' and (resid 3 through 18 or resid 20 through 253 or resid 255 through \ 376 or resid 402 through 403)) selection = (chain 'C' and (resid 3 through 18 or resid 20 through 253 or resid 255 through \ 376 or resid 402 through 403)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' } 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=0.43 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: 12.990 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 19.170 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 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 0.049 9675 Z= 0.281 Angle : 0.842 11.064 13188 Z= 0.381 Chirality : 0.053 0.285 1599 Planarity : 0.004 0.036 1581 Dihedral : 16.674 106.566 4233 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.24), residues: 1125 helix: 0.18 (0.30), residues: 321 sheet: 0.12 (0.27), residues: 357 loop : -0.99 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 277 TYR 0.009 0.001 TYR B 299 PHE 0.011 0.001 PHE B 276 TRP 0.009 0.002 TRP B 164 HIS 0.001 0.000 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00575 ( 9633) covalent geometry : angle 0.78434 (13074) SS BOND : bond 0.00322 ( 12) SS BOND : angle 1.18796 ( 24) hydrogen bonds : bond 0.17922 ( 406) hydrogen bonds : angle 7.36474 ( 1299) link_BETA1-4 : bond 0.00441 ( 12) link_BETA1-4 : angle 2.43063 ( 36) link_NAG-ASN : bond 0.00461 ( 18) link_NAG-ASN : angle 4.44346 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8452 (mtmt) cc_final: 0.7901 (mppt) REVERT: A 148 ARG cc_start: 0.7696 (mtm110) cc_final: 0.7016 (mtm-85) REVERT: A 157 LYS cc_start: 0.8029 (mtmm) cc_final: 0.7767 (mtmt) REVERT: A 326 LYS cc_start: 0.8424 (mttt) cc_final: 0.8152 (mmmt) REVERT: B 69 LYS cc_start: 0.8443 (mtmt) cc_final: 0.7868 (mppt) REVERT: B 109 MET cc_start: 0.7929 (mmm) cc_final: 0.7716 (mmm) REVERT: B 148 ARG cc_start: 0.7706 (mtm110) cc_final: 0.7050 (mtm-85) REVERT: B 197 LYS cc_start: 0.8418 (tttt) cc_final: 0.8181 (tttt) REVERT: B 326 LYS cc_start: 0.8427 (mttt) cc_final: 0.8188 (mmmt) REVERT: C 148 ARG cc_start: 0.7686 (mtm110) cc_final: 0.6990 (mtm-85) REVERT: C 326 LYS cc_start: 0.8425 (mttt) cc_final: 0.8168 (mmmt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 1.3784 time to fit residues: 160.5289 Evaluate side-chains 101 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.151477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.106484 restraints weight = 34882.841| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.24 r_work: 0.3085 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9675 Z= 0.153 Angle : 0.633 5.224 13188 Z= 0.327 Chirality : 0.047 0.207 1599 Planarity : 0.004 0.034 1581 Dihedral : 11.032 57.297 2226 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.05 % Allowed : 11.67 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.24), residues: 1125 helix: 0.74 (0.30), residues: 309 sheet: 0.31 (0.28), residues: 330 loop : -0.52 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 273 TYR 0.010 0.002 TYR A 89 PHE 0.016 0.002 PHE B 276 TRP 0.010 0.002 TRP B 259 HIS 0.004 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9633) covalent geometry : angle 0.60962 (13074) SS BOND : bond 0.00513 ( 12) SS BOND : angle 1.46184 ( 24) hydrogen bonds : bond 0.04873 ( 406) hydrogen bonds : angle 5.67363 ( 1299) link_BETA1-4 : bond 0.00234 ( 12) link_BETA1-4 : angle 1.94353 ( 36) link_NAG-ASN : bond 0.00355 ( 18) link_NAG-ASN : angle 2.11902 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8911 (mtmt) cc_final: 0.7853 (mppt) REVERT: A 148 ARG cc_start: 0.7447 (mtm110) cc_final: 0.6408 (mtm-85) REVERT: A 157 LYS cc_start: 0.7573 (mtmm) cc_final: 0.7272 (mtmt) REVERT: A 326 LYS cc_start: 0.8623 (mttt) cc_final: 0.8164 (mmmt) REVERT: B 148 ARG cc_start: 0.7434 (mtm110) cc_final: 0.6402 (mtm-85) REVERT: B 197 LYS cc_start: 0.8457 (tttt) cc_final: 0.8173 (tttt) REVERT: B 326 LYS cc_start: 0.8595 (mttt) cc_final: 0.8071 (mmmt) REVERT: C 38 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7340 (tp) REVERT: C 148 ARG cc_start: 0.7385 (mtm110) cc_final: 0.6303 (mtm-85) REVERT: C 326 LYS cc_start: 0.8613 (mttt) cc_final: 0.8037 (mmmt) outliers start: 10 outliers final: 3 residues processed: 97 average time/residue: 1.3459 time to fit residues: 138.2013 Evaluate side-chains 92 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 361 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.150659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.105591 restraints weight = 36159.946| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.27 r_work: 0.3072 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9675 Z= 0.148 Angle : 0.586 4.692 13188 Z= 0.309 Chirality : 0.046 0.199 1599 Planarity : 0.004 0.037 1581 Dihedral : 9.261 56.141 2226 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.16 % Allowed : 11.67 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.25), residues: 1125 helix: 0.84 (0.30), residues: 309 sheet: -0.02 (0.26), residues: 360 loop : -0.47 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 309 TYR 0.010 0.002 TYR B 89 PHE 0.017 0.002 PHE A 276 TRP 0.010 0.002 TRP B 259 HIS 0.003 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9633) covalent geometry : angle 0.56080 (13074) SS BOND : bond 0.00526 ( 12) SS BOND : angle 1.31207 ( 24) hydrogen bonds : bond 0.04810 ( 406) hydrogen bonds : angle 5.47603 ( 1299) link_BETA1-4 : bond 0.00246 ( 12) link_BETA1-4 : angle 1.93475 ( 36) link_NAG-ASN : bond 0.00357 ( 18) link_NAG-ASN : angle 2.08934 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7475 (tp) REVERT: A 56 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6976 (pt0) REVERT: A 69 LYS cc_start: 0.8914 (mtmt) cc_final: 0.7876 (mppt) REVERT: A 140 HIS cc_start: 0.5703 (m-70) cc_final: 0.5427 (m-70) REVERT: A 148 ARG cc_start: 0.7408 (mtm110) cc_final: 0.6377 (mtm-85) REVERT: A 157 LYS cc_start: 0.7552 (mtmm) cc_final: 0.7234 (mtmt) REVERT: A 197 LYS cc_start: 0.8501 (tttt) cc_final: 0.8139 (tttt) REVERT: A 326 LYS cc_start: 0.8598 (mttt) cc_final: 0.8156 (mttt) REVERT: B 38 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7540 (tp) REVERT: B 148 ARG cc_start: 0.7406 (mtm110) cc_final: 0.6340 (mtm-85) REVERT: B 197 LYS cc_start: 0.8477 (tttt) cc_final: 0.8168 (tttt) REVERT: B 326 LYS cc_start: 0.8582 (mttt) cc_final: 0.8058 (mmmt) REVERT: C 56 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6931 (pt0) REVERT: C 197 LYS cc_start: 0.8533 (tttt) cc_final: 0.8159 (tttt) REVERT: C 326 LYS cc_start: 0.8603 (mttt) cc_final: 0.8116 (mttt) outliers start: 11 outliers final: 3 residues processed: 97 average time/residue: 1.2454 time to fit residues: 127.9412 Evaluate side-chains 95 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 361 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.150841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.105842 restraints weight = 36503.043| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.27 r_work: 0.3075 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9675 Z= 0.139 Angle : 0.570 4.283 13188 Z= 0.301 Chirality : 0.045 0.196 1599 Planarity : 0.004 0.032 1581 Dihedral : 8.893 59.831 2226 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.16 % Allowed : 11.67 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.25), residues: 1125 helix: 0.90 (0.30), residues: 309 sheet: -0.07 (0.27), residues: 360 loop : -0.45 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 203 TYR 0.011 0.002 TYR B 89 PHE 0.016 0.001 PHE B 276 TRP 0.009 0.002 TRP B 259 HIS 0.003 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9633) covalent geometry : angle 0.54764 (13074) SS BOND : bond 0.00504 ( 12) SS BOND : angle 1.35071 ( 24) hydrogen bonds : bond 0.04377 ( 406) hydrogen bonds : angle 5.34351 ( 1299) link_BETA1-4 : bond 0.00143 ( 12) link_BETA1-4 : angle 1.93354 ( 36) link_NAG-ASN : bond 0.00330 ( 18) link_NAG-ASN : angle 1.84751 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.338 Fit side-chains REVERT: A 38 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7470 (tp) REVERT: A 56 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6967 (pt0) REVERT: A 69 LYS cc_start: 0.8919 (mtmt) cc_final: 0.7874 (mppt) REVERT: A 148 ARG cc_start: 0.7426 (mtm110) cc_final: 0.6405 (mtm-85) REVERT: A 157 LYS cc_start: 0.7574 (mtmm) cc_final: 0.7250 (mtmt) REVERT: A 197 LYS cc_start: 0.8505 (tttt) cc_final: 0.8150 (tttt) REVERT: A 326 LYS cc_start: 0.8607 (mttt) cc_final: 0.8147 (mttt) REVERT: B 140 HIS cc_start: 0.5558 (m-70) cc_final: 0.5352 (m-70) REVERT: B 197 LYS cc_start: 0.8488 (tttt) cc_final: 0.8228 (tttt) REVERT: B 326 LYS cc_start: 0.8578 (mttt) cc_final: 0.8153 (mttt) REVERT: C 38 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7371 (tp) REVERT: C 56 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6930 (pt0) REVERT: C 197 LYS cc_start: 0.8540 (tttt) cc_final: 0.8171 (tttt) REVERT: C 326 LYS cc_start: 0.8601 (mttt) cc_final: 0.8075 (mmmt) outliers start: 11 outliers final: 4 residues processed: 90 average time/residue: 1.2939 time to fit residues: 123.4885 Evaluate side-chains 93 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 361 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.150317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.105779 restraints weight = 33850.126| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.22 r_work: 0.3073 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9675 Z= 0.148 Angle : 0.578 4.292 13188 Z= 0.306 Chirality : 0.045 0.200 1599 Planarity : 0.004 0.034 1581 Dihedral : 8.888 58.927 2226 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.37 % Allowed : 11.99 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.25), residues: 1125 helix: 0.94 (0.30), residues: 306 sheet: -0.07 (0.27), residues: 360 loop : -0.50 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 277 TYR 0.011 0.002 TYR B 299 PHE 0.017 0.002 PHE B 276 TRP 0.010 0.002 TRP B 259 HIS 0.003 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9633) covalent geometry : angle 0.55486 (13074) SS BOND : bond 0.00511 ( 12) SS BOND : angle 1.36061 ( 24) hydrogen bonds : bond 0.04543 ( 406) hydrogen bonds : angle 5.34256 ( 1299) link_BETA1-4 : bond 0.00153 ( 12) link_BETA1-4 : angle 1.98277 ( 36) link_NAG-ASN : bond 0.00315 ( 18) link_NAG-ASN : angle 1.90173 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.512 Fit side-chains REVERT: A 38 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7487 (tp) REVERT: A 56 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6952 (pt0) REVERT: A 69 LYS cc_start: 0.8919 (mtmt) cc_final: 0.7870 (mppt) REVERT: A 148 ARG cc_start: 0.7389 (mtm110) cc_final: 0.6353 (mtm-85) REVERT: A 157 LYS cc_start: 0.7533 (mtmm) cc_final: 0.7203 (mtmt) REVERT: A 197 LYS cc_start: 0.8493 (tttt) cc_final: 0.8142 (tttt) REVERT: A 326 LYS cc_start: 0.8603 (mttt) cc_final: 0.8139 (mttt) REVERT: B 197 LYS cc_start: 0.8472 (tttt) cc_final: 0.8162 (tttt) REVERT: B 326 LYS cc_start: 0.8560 (mttt) cc_final: 0.8118 (mttt) REVERT: C 38 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7359 (tp) REVERT: C 56 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6938 (pt0) REVERT: C 197 LYS cc_start: 0.8526 (tttt) cc_final: 0.8163 (tttt) REVERT: C 260 ASP cc_start: 0.8084 (m-30) cc_final: 0.7869 (m-30) REVERT: C 326 LYS cc_start: 0.8606 (mttt) cc_final: 0.8109 (mttt) outliers start: 13 outliers final: 3 residues processed: 92 average time/residue: 1.6876 time to fit residues: 164.3476 Evaluate side-chains 94 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 361 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 98 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.150695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.106348 restraints weight = 33395.422| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.19 r_work: 0.3082 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9675 Z= 0.134 Angle : 0.554 4.262 13188 Z= 0.294 Chirality : 0.045 0.190 1599 Planarity : 0.004 0.033 1581 Dihedral : 8.730 56.844 2226 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.05 % Allowed : 11.99 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.25), residues: 1125 helix: 1.00 (0.30), residues: 306 sheet: -0.07 (0.27), residues: 360 loop : -0.48 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 277 TYR 0.010 0.002 TYR A 299 PHE 0.015 0.001 PHE B 276 TRP 0.009 0.002 TRP B 259 HIS 0.002 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9633) covalent geometry : angle 0.53256 (13074) SS BOND : bond 0.00468 ( 12) SS BOND : angle 1.30045 ( 24) hydrogen bonds : bond 0.04304 ( 406) hydrogen bonds : angle 5.26394 ( 1299) link_BETA1-4 : bond 0.00168 ( 12) link_BETA1-4 : angle 1.88860 ( 36) link_NAG-ASN : bond 0.00296 ( 18) link_NAG-ASN : angle 1.77448 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.412 Fit side-chains REVERT: A 38 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7467 (tp) REVERT: A 56 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6942 (pt0) REVERT: A 148 ARG cc_start: 0.7386 (mtm110) cc_final: 0.6384 (mtm-85) REVERT: A 157 LYS cc_start: 0.7529 (mtmm) cc_final: 0.7185 (mtmt) REVERT: A 197 LYS cc_start: 0.8459 (tttt) cc_final: 0.8119 (tttt) REVERT: A 326 LYS cc_start: 0.8598 (mttt) cc_final: 0.8136 (mttt) REVERT: B 197 LYS cc_start: 0.8481 (tttt) cc_final: 0.8176 (tttt) REVERT: B 326 LYS cc_start: 0.8557 (mttt) cc_final: 0.8120 (mttt) REVERT: C 38 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7304 (tp) REVERT: C 56 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6913 (pt0) REVERT: C 197 LYS cc_start: 0.8532 (tttt) cc_final: 0.8173 (tttt) REVERT: C 260 ASP cc_start: 0.8060 (m-30) cc_final: 0.7839 (m-30) REVERT: C 326 LYS cc_start: 0.8590 (mttt) cc_final: 0.8099 (mttt) outliers start: 10 outliers final: 3 residues processed: 89 average time/residue: 1.3815 time to fit residues: 130.5371 Evaluate side-chains 92 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 361 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 105 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 89 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.151464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.106974 restraints weight = 34825.378| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.24 r_work: 0.3090 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9675 Z= 0.118 Angle : 0.528 4.262 13188 Z= 0.282 Chirality : 0.044 0.182 1599 Planarity : 0.004 0.032 1581 Dihedral : 8.474 54.989 2226 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.95 % Allowed : 12.09 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.25), residues: 1125 helix: 1.10 (0.31), residues: 306 sheet: -0.04 (0.27), residues: 360 loop : -0.48 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 148 TYR 0.009 0.001 TYR C 89 PHE 0.014 0.001 PHE B 276 TRP 0.008 0.002 TRP B 259 HIS 0.002 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9633) covalent geometry : angle 0.50861 (13074) SS BOND : bond 0.00427 ( 12) SS BOND : angle 1.24215 ( 24) hydrogen bonds : bond 0.04096 ( 406) hydrogen bonds : angle 5.17466 ( 1299) link_BETA1-4 : bond 0.00201 ( 12) link_BETA1-4 : angle 1.76723 ( 36) link_NAG-ASN : bond 0.00301 ( 18) link_NAG-ASN : angle 1.63146 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7476 (tp) REVERT: A 148 ARG cc_start: 0.7386 (mtm180) cc_final: 0.6382 (mtm-85) REVERT: A 157 LYS cc_start: 0.7516 (mtmm) cc_final: 0.7169 (mtmt) REVERT: A 197 LYS cc_start: 0.8465 (tttt) cc_final: 0.8166 (tttt) REVERT: A 326 LYS cc_start: 0.8594 (mttt) cc_final: 0.8139 (mttt) REVERT: B 38 LEU cc_start: 0.7675 (tp) cc_final: 0.7368 (tp) REVERT: B 197 LYS cc_start: 0.8482 (tttt) cc_final: 0.8179 (tttt) REVERT: B 326 LYS cc_start: 0.8535 (mttt) cc_final: 0.8104 (mttt) REVERT: C 38 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7291 (tp) REVERT: C 260 ASP cc_start: 0.8044 (m-30) cc_final: 0.7824 (m-30) REVERT: C 326 LYS cc_start: 0.8571 (mttt) cc_final: 0.8086 (mttt) outliers start: 9 outliers final: 2 residues processed: 91 average time/residue: 1.4282 time to fit residues: 137.9997 Evaluate side-chains 90 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 361 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 78 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.150481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.106250 restraints weight = 32957.158| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.18 r_work: 0.3081 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9675 Z= 0.144 Angle : 0.566 4.275 13188 Z= 0.300 Chirality : 0.045 0.195 1599 Planarity : 0.004 0.033 1581 Dihedral : 8.637 55.531 2226 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.63 % Allowed : 12.62 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.25), residues: 1125 helix: 1.01 (0.30), residues: 306 sheet: -0.06 (0.27), residues: 360 loop : -0.51 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 277 TYR 0.010 0.002 TYR A 299 PHE 0.017 0.002 PHE B 276 TRP 0.009 0.002 TRP B 259 HIS 0.002 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9633) covalent geometry : angle 0.54396 (13074) SS BOND : bond 0.00496 ( 12) SS BOND : angle 1.35331 ( 24) hydrogen bonds : bond 0.04388 ( 406) hydrogen bonds : angle 5.25308 ( 1299) link_BETA1-4 : bond 0.00094 ( 12) link_BETA1-4 : angle 1.92263 ( 36) link_NAG-ASN : bond 0.00290 ( 18) link_NAG-ASN : angle 1.83656 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7511 (tp) REVERT: A 148 ARG cc_start: 0.7406 (mtm180) cc_final: 0.6411 (mtm-85) REVERT: A 157 LYS cc_start: 0.7554 (mtmm) cc_final: 0.7209 (mtmt) REVERT: A 197 LYS cc_start: 0.8460 (tttt) cc_final: 0.8167 (tttt) REVERT: A 326 LYS cc_start: 0.8618 (mttt) cc_final: 0.8064 (mttt) REVERT: B 38 LEU cc_start: 0.7715 (tp) cc_final: 0.7407 (tp) REVERT: B 197 LYS cc_start: 0.8488 (tttt) cc_final: 0.8192 (tttt) REVERT: B 326 LYS cc_start: 0.8564 (mttt) cc_final: 0.8133 (mttt) REVERT: C 38 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7330 (tp) REVERT: C 260 ASP cc_start: 0.8085 (m-30) cc_final: 0.7864 (m-30) REVERT: C 326 LYS cc_start: 0.8596 (mttt) cc_final: 0.8113 (mttt) outliers start: 6 outliers final: 2 residues processed: 88 average time/residue: 1.3235 time to fit residues: 123.1656 Evaluate side-chains 88 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 361 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.0470 chunk 13 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 chunk 46 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.146879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.104325 restraints weight = 33042.473| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.04 r_work: 0.3059 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9675 Z= 0.117 Angle : 0.526 4.257 13188 Z= 0.281 Chirality : 0.044 0.178 1599 Planarity : 0.004 0.032 1581 Dihedral : 8.360 59.405 2226 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.63 % Allowed : 12.72 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.25), residues: 1125 helix: 1.15 (0.31), residues: 306 sheet: -0.05 (0.27), residues: 360 loop : -0.49 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 277 TYR 0.009 0.001 TYR B 89 PHE 0.013 0.001 PHE B 276 TRP 0.008 0.002 TRP B 259 HIS 0.002 0.000 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9633) covalent geometry : angle 0.50727 (13074) SS BOND : bond 0.00413 ( 12) SS BOND : angle 1.24208 ( 24) hydrogen bonds : bond 0.04054 ( 406) hydrogen bonds : angle 5.14782 ( 1299) link_BETA1-4 : bond 0.00205 ( 12) link_BETA1-4 : angle 1.74560 ( 36) link_NAG-ASN : bond 0.00300 ( 18) link_NAG-ASN : angle 1.60942 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7501 (mtm180) cc_final: 0.6577 (mtm-85) REVERT: A 157 LYS cc_start: 0.7697 (mtmm) cc_final: 0.7380 (mtmt) REVERT: A 197 LYS cc_start: 0.8592 (tttt) cc_final: 0.8330 (tttt) REVERT: A 326 LYS cc_start: 0.8662 (mttt) cc_final: 0.8179 (mttt) REVERT: B 38 LEU cc_start: 0.7908 (tp) cc_final: 0.7627 (tp) REVERT: B 197 LYS cc_start: 0.8625 (tttt) cc_final: 0.8361 (tttt) REVERT: B 326 LYS cc_start: 0.8621 (mttt) cc_final: 0.8264 (mttt) REVERT: C 38 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7565 (tp) REVERT: C 326 LYS cc_start: 0.8620 (mttt) cc_final: 0.8192 (mttt) outliers start: 6 outliers final: 3 residues processed: 87 average time/residue: 1.3125 time to fit residues: 121.5700 Evaluate side-chains 90 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 361 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.146309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.103094 restraints weight = 35348.242| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.12 r_work: 0.3042 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9675 Z= 0.130 Angle : 0.545 4.262 13188 Z= 0.290 Chirality : 0.044 0.187 1599 Planarity : 0.004 0.032 1581 Dihedral : 8.325 55.981 2226 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.42 % Allowed : 12.83 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.25), residues: 1125 helix: 1.10 (0.30), residues: 306 sheet: -0.06 (0.27), residues: 360 loop : -0.48 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 203 TYR 0.010 0.001 TYR A 299 PHE 0.015 0.001 PHE B 276 TRP 0.009 0.002 TRP B 259 HIS 0.002 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9633) covalent geometry : angle 0.52488 (13074) SS BOND : bond 0.00454 ( 12) SS BOND : angle 1.30148 ( 24) hydrogen bonds : bond 0.04216 ( 406) hydrogen bonds : angle 5.19003 ( 1299) link_BETA1-4 : bond 0.00155 ( 12) link_BETA1-4 : angle 1.82141 ( 36) link_NAG-ASN : bond 0.00294 ( 18) link_NAG-ASN : angle 1.72176 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7499 (mtm180) cc_final: 0.6563 (mtm-85) REVERT: A 157 LYS cc_start: 0.7698 (mtmm) cc_final: 0.7380 (mtmt) REVERT: A 197 LYS cc_start: 0.8599 (tttt) cc_final: 0.8337 (tttt) REVERT: A 326 LYS cc_start: 0.8676 (mttt) cc_final: 0.8183 (mttt) REVERT: B 38 LEU cc_start: 0.7930 (tp) cc_final: 0.7648 (tp) REVERT: B 197 LYS cc_start: 0.8634 (tttt) cc_final: 0.8371 (tttt) REVERT: B 326 LYS cc_start: 0.8638 (mttt) cc_final: 0.8272 (mttt) REVERT: C 38 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7577 (tp) REVERT: C 326 LYS cc_start: 0.8637 (mttt) cc_final: 0.8203 (mttt) outliers start: 4 outliers final: 3 residues processed: 85 average time/residue: 1.3248 time to fit residues: 119.5908 Evaluate side-chains 88 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 361 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 24 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.145942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.102216 restraints weight = 37544.221| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.17 r_work: 0.3030 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9675 Z= 0.140 Angle : 0.563 4.275 13188 Z= 0.298 Chirality : 0.045 0.190 1599 Planarity : 0.004 0.032 1581 Dihedral : 8.393 59.897 2226 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.53 % Allowed : 12.72 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.25), residues: 1125 helix: 1.05 (0.30), residues: 306 sheet: -0.06 (0.27), residues: 360 loop : -0.51 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 203 TYR 0.010 0.002 TYR A 299 PHE 0.016 0.002 PHE A 276 TRP 0.009 0.002 TRP B 259 HIS 0.002 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9633) covalent geometry : angle 0.54164 (13074) SS BOND : bond 0.00486 ( 12) SS BOND : angle 1.34698 ( 24) hydrogen bonds : bond 0.04339 ( 406) hydrogen bonds : angle 5.23318 ( 1299) link_BETA1-4 : bond 0.00146 ( 12) link_BETA1-4 : angle 1.89620 ( 36) link_NAG-ASN : bond 0.00304 ( 18) link_NAG-ASN : angle 1.79323 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7836.34 seconds wall clock time: 133 minutes 18.08 seconds (7998.08 seconds total)