Starting phenix.real_space_refine on Sat Jun 14 09:42:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wbe_37422/06_2025/8wbe_37422_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbe_37422/06_2025/8wbe_37422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wbe_37422/06_2025/8wbe_37422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbe_37422/06_2025/8wbe_37422.map" model { file = "/net/cci-nas-00/data/ceres_data/8wbe_37422/06_2025/8wbe_37422_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbe_37422/06_2025/8wbe_37422_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.148 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: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 10161 2.51 5 N 2769 2.21 5 O 3038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16094 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2782 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "B" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2596 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 314} Chain breaks: 1 Chain: "C" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2576 Classifications: {'peptide': 327} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 311} Chain breaks: 1 Chain: "a" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2782 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "b" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2782 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "c" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2576 Classifications: {'peptide': 327} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 311} Chain breaks: 1 Time building chain proxies: 11.40, per 1000 atoms: 0.71 Number of scatterers: 16094 At special positions: 0 Unit cell: (124.1, 125.8, 121.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 3038 8.00 N 2769 7.00 C 10161 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 15 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 15 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 223 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 316 " distance=2.06 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS b 4 " - pdb=" SG CYS b 15 " distance=2.03 Simple disulfide: pdb=" SG CYS b 55 " - pdb=" SG CYS b 143 " distance=2.03 Simple disulfide: pdb=" SG CYS b 179 " - pdb=" SG CYS b 223 " distance=2.03 Simple disulfide: pdb=" SG CYS b 280 " - pdb=" SG CYS b 329 " distance=2.03 Simple disulfide: pdb=" SG CYS b 313 " - pdb=" SG CYS b 316 " distance=2.03 Simple disulfide: pdb=" SG CYS c 4 " - pdb=" SG CYS c 15 " distance=2.03 Simple disulfide: pdb=" SG CYS c 55 " - pdb=" SG CYS c 143 " distance=2.03 Simple disulfide: pdb=" SG CYS c 179 " - pdb=" SG CYS c 223 " distance=2.03 Simple disulfide: pdb=" SG CYS c 280 " - pdb=" SG CYS c 329 " distance=2.03 Simple disulfide: pdb=" SG CYS c 313 " - pdb=" SG CYS c 316 " distance=2.02 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 Time building additional restraints: 4.03 Conformation dependent library (CDL) restraints added in 2.2 seconds 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3738 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 25 sheets defined 18.1% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 Processing helix chain 'A' and resid 61 through 82 removed outlier: 5.581A pdb=" N ASN A 73 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLU A 74 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 82 " --> pdb=" O VAL A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 180 through 183 removed outlier: 3.524A pdb=" N LEU A 183 " --> pdb=" O ASP A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.528A pdb=" N THR A 230 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.718A pdb=" N ALA A 248 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'B' and resid 38 through 52 removed outlier: 3.685A pdb=" N LEU B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 43 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B 52 " --> pdb=" O ASN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 72 removed outlier: 3.546A pdb=" N ILE B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 removed outlier: 3.594A pdb=" N TYR B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL B 78 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 180 through 183 removed outlier: 3.689A pdb=" N LEU B 183 " --> pdb=" O ASP B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 183' Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.634A pdb=" N THR B 230 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 removed outlier: 3.600A pdb=" N ALA B 248 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 271 removed outlier: 3.541A pdb=" N LEU B 270 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 345 Processing helix chain 'C' and resid 40 through 53 removed outlier: 3.913A pdb=" N ILE C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 82 removed outlier: 5.170A pdb=" N ASN C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLU C 74 " --> pdb=" O GLN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 148 Processing helix chain 'C' and resid 180 through 183 removed outlier: 3.747A pdb=" N LEU C 183 " --> pdb=" O ASP C 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 183' Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.612A pdb=" N THR C 230 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 248 removed outlier: 3.678A pdb=" N ALA C 248 " --> pdb=" O LYS C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 271 removed outlier: 3.814A pdb=" N GLY C 271 " --> pdb=" O TRP C 268 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 53 Processing helix chain 'a' and resid 61 through 82 removed outlier: 3.642A pdb=" N ASN a 65 " --> pdb=" O THR a 61 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE a 66 " --> pdb=" O ARG a 62 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET a 67 " --> pdb=" O LEU a 63 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASN a 73 " --> pdb=" O LYS a 69 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLU a 74 " --> pdb=" O GLN a 70 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 180 through 183 removed outlier: 3.709A pdb=" N LEU a 183 " --> pdb=" O ASP a 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 180 through 183' Processing helix chain 'a' and resid 226 through 230 removed outlier: 3.821A pdb=" N THR a 230 " --> pdb=" O LYS a 227 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 248 removed outlier: 3.590A pdb=" N ALA a 248 " --> pdb=" O LYS a 245 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 271 removed outlier: 3.602A pdb=" N GLY a 271 " --> pdb=" O TRP a 268 " (cutoff:3.500A) Processing helix chain 'a' and resid 341 through 345 Processing helix chain 'b' and resid 38 through 51 Processing helix chain 'b' and resid 61 through 72 removed outlier: 3.578A pdb=" N ASN b 65 " --> pdb=" O THR b 61 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE b 66 " --> pdb=" O ARG b 62 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET b 67 " --> pdb=" O LEU b 63 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 83 removed outlier: 3.853A pdb=" N GLY b 83 " --> pdb=" O LEU b 79 " (cutoff:3.500A) Processing helix chain 'b' and resid 144 through 148 removed outlier: 3.733A pdb=" N ARG b 148 " --> pdb=" O ASN b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 180 through 183 Processing helix chain 'b' and resid 226 through 230 Processing helix chain 'b' and resid 244 through 248 removed outlier: 3.516A pdb=" N ALA b 248 " --> pdb=" O LYS b 245 " (cutoff:3.500A) Processing helix chain 'c' and resid 38 through 53 removed outlier: 3.801A pdb=" N ALA c 43 " --> pdb=" O PRO c 39 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 82 removed outlier: 3.671A pdb=" N ILE c 66 " --> pdb=" O ARG c 62 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N MET c 67 " --> pdb=" O LEU c 63 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASN c 73 " --> pdb=" O LYS c 69 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLU c 74 " --> pdb=" O GLN c 70 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY c 82 " --> pdb=" O VAL c 78 " (cutoff:3.500A) Processing helix chain 'c' and resid 144 through 148 removed outlier: 3.562A pdb=" N ARG c 148 " --> pdb=" O ASN c 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 180 through 183 removed outlier: 3.889A pdb=" N LEU c 183 " --> pdb=" O ASP c 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 180 through 183' Processing helix chain 'c' and resid 226 through 230 Processing helix chain 'c' and resid 244 through 248 removed outlier: 3.514A pdb=" N ALA c 248 " --> pdb=" O LYS c 245 " (cutoff:3.500A) Processing helix chain 'c' and resid 267 through 271 removed outlier: 3.725A pdb=" N LEU c 270 " --> pdb=" O PRO c 267 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY c 271 " --> pdb=" O TRP c 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 267 through 271' Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.227A pdb=" N LYS A 33 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N MET A 169 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLN A 35 " --> pdb=" O MET A 169 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N PHE A 171 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASN A 166 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TYR A 158 " --> pdb=" O ASN A 166 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TRP A 168 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.821A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL A 89 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 331 removed outlier: 3.529A pdb=" N GLU A 274 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N PHE A 277 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N GLU A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU A 203 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA A 215 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP A 201 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP a 201 " --> pdb=" O ALA a 215 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA a 215 " --> pdb=" O TRP a 201 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLU a 203 " --> pdb=" O GLU a 213 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N GLU a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE a 277 " --> pdb=" O GLU a 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 287 removed outlier: 5.952A pdb=" N THR A 284 " --> pdb=" O TRP A 311 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N CYS A 313 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N THR A 286 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 13 through 16 Processing sheet with id=AA7, first strand: chain 'B' and resid 34 through 35 removed outlier: 6.515A pdb=" N ASN B 166 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR B 158 " --> pdb=" O ASN B 166 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TRP B 168 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.903A pdb=" N GLY B 56 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 328 through 331 removed outlier: 3.881A pdb=" N GLY B 328 " --> pdb=" O GLY B 325 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 274 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE B 277 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N GLU B 213 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLU B 203 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA B 215 " --> pdb=" O TRP B 201 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP B 201 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N SER b 205 " --> pdb=" O ILE b 212 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE b 212 " --> pdb=" O SER b 205 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N GLU b 213 " --> pdb=" O PHE b 277 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N PHE b 277 " --> pdb=" O GLU b 213 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU b 274 " --> pdb=" O LEU b 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 284 through 287 removed outlier: 6.250A pdb=" N THR B 284 " --> pdb=" O TRP B 311 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N CYS B 313 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR B 286 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 16 Processing sheet with id=AB3, first strand: chain 'C' and resid 32 through 35 removed outlier: 6.743A pdb=" N ASN C 166 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR C 158 " --> pdb=" O ASN C 166 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TRP C 168 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 89 through 90 removed outlier: 6.221A pdb=" N VAL C 89 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE C 57 " --> pdb=" O LEU C 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 210 through 214 removed outlier: 6.942A pdb=" N GLU C 203 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 196 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP c 201 " --> pdb=" O ALA c 215 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA c 215 " --> pdb=" O TRP c 201 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLU c 203 " --> pdb=" O GLU c 213 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N GLU c 213 " --> pdb=" O PHE c 277 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE c 277 " --> pdb=" O GLU c 213 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 274 through 277 Processing sheet with id=AB7, first strand: chain 'C' and resid 285 through 287 removed outlier: 6.155A pdb=" N THR C 286 " --> pdb=" O CYS C 313 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'a' and resid 33 through 35 removed outlier: 6.542A pdb=" N ASN a 166 " --> pdb=" O TYR a 158 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N TYR a 158 " --> pdb=" O ASN a 166 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TRP a 168 " --> pdb=" O GLU a 156 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'a' and resid 87 through 90 removed outlier: 6.871A pdb=" N THR a 87 " --> pdb=" O PHE a 133 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE a 135 " --> pdb=" O THR a 87 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL a 89 " --> pdb=" O ILE a 135 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'a' and resid 284 through 287 removed outlier: 6.163A pdb=" N THR a 284 " --> pdb=" O TRP a 311 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N CYS a 313 " --> pdb=" O THR a 284 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR a 286 " --> pdb=" O CYS a 313 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 32 through 35 removed outlier: 6.323A pdb=" N LYS b 33 " --> pdb=" O ILE b 167 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N MET b 169 " --> pdb=" O LYS b 33 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN b 35 " --> pdb=" O MET b 169 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N PHE b 171 " --> pdb=" O GLN b 35 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN b 166 " --> pdb=" O TYR b 158 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TYR b 158 " --> pdb=" O ASN b 166 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TRP b 168 " --> pdb=" O GLU b 156 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'b' and resid 87 through 90 removed outlier: 7.243A pdb=" N THR b 87 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE b 135 " --> pdb=" O THR b 87 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL b 89 " --> pdb=" O ILE b 135 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'b' and resid 284 through 287 removed outlier: 6.521A pdb=" N THR b 284 " --> pdb=" O TRP b 311 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N CYS b 313 " --> pdb=" O THR b 284 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR b 286 " --> pdb=" O CYS b 313 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'c' and resid 33 through 35 removed outlier: 7.023A pdb=" N TRP c 168 " --> pdb=" O GLU c 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 89 through 90 removed outlier: 6.478A pdb=" N VAL c 89 " --> pdb=" O ILE c 135 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'c' and resid 284 through 287 423 hydrogen bonds defined for protein. 1086 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: 4.95 Time building geometry restraints manager: 4.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5216 1.34 - 1.46: 3962 1.46 - 1.58: 7156 1.58 - 1.71: 0 1.71 - 1.83: 180 Bond restraints: 16514 Sorted by residual: bond pdb=" N TRP B 80 " pdb=" CA TRP B 80 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.32e-02 5.74e+03 7.15e+00 bond pdb=" N ASN B 76 " pdb=" CA ASN B 76 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.25e-02 6.40e+03 6.42e+00 bond pdb=" N LEU B 75 " pdb=" CA LEU B 75 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.32e-02 5.74e+03 6.31e+00 bond pdb=" N VAL B 78 " pdb=" CA VAL B 78 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.17e-02 7.31e+03 6.23e+00 bond pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.30e-02 5.92e+03 5.80e+00 ... (remaining 16509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 21575 1.23 - 2.47: 658 2.47 - 3.70: 147 3.70 - 4.94: 13 4.94 - 6.17: 9 Bond angle restraints: 22402 Sorted by residual: angle pdb=" N LEU B 75 " pdb=" CA LEU B 75 " pdb=" C LEU B 75 " ideal model delta sigma weight residual 113.20 108.63 4.57 1.21e+00 6.83e-01 1.43e+01 angle pdb=" N THR C 317 " pdb=" CA THR C 317 " pdb=" C THR C 317 " ideal model delta sigma weight residual 109.40 103.40 6.00 1.63e+00 3.76e-01 1.35e+01 angle pdb=" CA THR C 317 " pdb=" C THR C 317 " pdb=" O THR C 317 " ideal model delta sigma weight residual 120.70 117.12 3.58 1.08e+00 8.57e-01 1.10e+01 angle pdb=" CA GLU B 81 " pdb=" C GLU B 81 " pdb=" O GLU B 81 " ideal model delta sigma weight residual 120.51 115.87 4.64 1.43e+00 4.89e-01 1.05e+01 angle pdb=" C THR a 27 " pdb=" N TRP a 28 " pdb=" CA TRP a 28 " ideal model delta sigma weight residual 121.54 127.63 -6.09 1.91e+00 2.74e-01 1.02e+01 ... (remaining 22397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 8851 17.38 - 34.75: 783 34.75 - 52.13: 132 52.13 - 69.50: 28 69.50 - 86.88: 13 Dihedral angle restraints: 9807 sinusoidal: 3987 harmonic: 5820 Sorted by residual: dihedral pdb=" CB CYS A 313 " pdb=" SG CYS A 313 " pdb=" SG CYS A 316 " pdb=" CB CYS A 316 " ideal model delta sinusoidal sigma weight residual 93.00 173.67 -80.67 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CB CYS a 55 " pdb=" SG CYS a 55 " pdb=" SG CYS a 143 " pdb=" CB CYS a 143 " ideal model delta sinusoidal sigma weight residual -86.00 -141.86 55.86 1 1.00e+01 1.00e-02 4.21e+01 dihedral pdb=" CA TYR B 158 " pdb=" C TYR B 158 " pdb=" N GLY B 159 " pdb=" CA GLY B 159 " ideal model delta harmonic sigma weight residual 180.00 152.36 27.64 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 9804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1613 0.037 - 0.074: 554 0.074 - 0.111: 171 0.111 - 0.148: 45 0.148 - 0.184: 4 Chirality restraints: 2387 Sorted by residual: chirality pdb=" CA THR C 317 " pdb=" N THR C 317 " pdb=" C THR C 317 " pdb=" CB THR C 317 " both_signs ideal model delta sigma weight residual False 2.53 2.71 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CA LEU C 321 " pdb=" N LEU C 321 " pdb=" C LEU C 321 " pdb=" CB LEU C 321 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.32e-01 chirality pdb=" CB ILE C 287 " pdb=" CA ILE C 287 " pdb=" CG1 ILE C 287 " pdb=" CG2 ILE C 287 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 2384 not shown) Planarity restraints: 2862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 75 " 0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C LEU B 75 " -0.073 2.00e-02 2.50e+03 pdb=" O LEU B 75 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN B 76 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 74 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.76e+00 pdb=" C GLU B 74 " 0.045 2.00e-02 2.50e+03 pdb=" O GLU B 74 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU B 75 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 81 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C GLU B 81 " -0.040 2.00e-02 2.50e+03 pdb=" O GLU B 81 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY B 82 " 0.014 2.00e-02 2.50e+03 ... (remaining 2859 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1094 2.74 - 3.28: 14705 3.28 - 3.82: 24684 3.82 - 4.36: 31902 4.36 - 4.90: 55270 Nonbonded interactions: 127655 Sorted by model distance: nonbonded pdb=" OD2 ASP A 197 " pdb=" NZ LYS A 221 " model vdw 2.196 3.120 nonbonded pdb=" O THR B 262 " pdb=" NH2 ARG B 294 " model vdw 2.198 3.120 nonbonded pdb=" O ASP b 23 " pdb=" OG1 THR b 27 " model vdw 2.203 3.040 nonbonded pdb=" O THR c 262 " pdb=" NH2 ARG c 294 " model vdw 2.217 3.120 nonbonded pdb=" OD2 ASP a 197 " pdb=" NZ LYS a 221 " model vdw 2.226 3.120 ... (remaining 127650 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 1 through 107 or resid 133 through 352)) selection = (chain 'B' and (resid 1 through 107 or resid 133 through 352)) selection = chain 'C' selection = (chain 'a' and (resid 1 through 107 or resid 133 through 352)) selection = (chain 'b' and (resid 1 through 107 or resid 133 through 352)) selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.300 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 40.310 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.002 0.038 16544 Z= 0.128 Angle : 0.543 6.172 22462 Z= 0.310 Chirality : 0.042 0.184 2387 Planarity : 0.003 0.053 2862 Dihedral : 13.421 86.876 5979 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.04 % Favored : 94.91 % Rotamer: Outliers : 0.23 % Allowed : 0.23 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.18), residues: 2022 helix: 0.97 (0.37), residues: 224 sheet: -2.23 (0.22), residues: 513 loop : -1.10 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 80 HIS 0.003 0.001 HIS A 229 PHE 0.024 0.001 PHE b 20 TYR 0.017 0.001 TYR B 158 ARG 0.002 0.000 ARG C 148 Details of bonding type rmsd hydrogen bonds : bond 0.25579 ( 423) hydrogen bonds : angle 9.07223 ( 1086) SS BOND : bond 0.00513 ( 30) SS BOND : angle 1.33211 ( 60) covalent geometry : bond 0.00231 (16514) covalent geometry : angle 0.53953 (22402) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 343 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7032 (m-90) cc_final: 0.6587 (p-90) REVERT: A 70 GLN cc_start: 0.7309 (tt0) cc_final: 0.6819 (tt0) REVERT: A 272 LYS cc_start: 0.8809 (mttp) cc_final: 0.8367 (mtpm) REVERT: A 309 THR cc_start: 0.8395 (m) cc_final: 0.8146 (p) REVERT: B 17 SER cc_start: 0.9000 (p) cc_final: 0.8765 (t) REVERT: B 30 GLU cc_start: 0.8491 (pt0) cc_final: 0.7735 (mm-30) REVERT: B 35 GLN cc_start: 0.7239 (mm-40) cc_final: 0.7011 (mm110) REVERT: B 59 SER cc_start: 0.8840 (m) cc_final: 0.8434 (p) REVERT: B 70 GLN cc_start: 0.6983 (mt0) cc_final: 0.6736 (mp10) REVERT: B 166 ASN cc_start: 0.8086 (m-40) cc_final: 0.7784 (m-40) REVERT: B 168 TRP cc_start: 0.7647 (m100) cc_final: 0.7236 (m100) REVERT: B 214 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7971 (mtpp) REVERT: B 274 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7631 (tp30) REVERT: B 340 GLU cc_start: 0.5594 (tm-30) cc_final: 0.5182 (tm-30) REVERT: C 12 GLU cc_start: 0.7039 (tt0) cc_final: 0.6637 (tt0) REVERT: C 14 LYS cc_start: 0.8682 (tptm) cc_final: 0.8342 (tptp) REVERT: C 23 ASP cc_start: 0.8182 (t0) cc_final: 0.7809 (t70) REVERT: C 35 GLN cc_start: 0.7382 (tp40) cc_final: 0.7138 (tp40) REVERT: C 74 GLU cc_start: 0.6436 (mt-10) cc_final: 0.6067 (mp0) REVERT: C 177 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6957 (tt0) REVERT: C 274 GLU cc_start: 0.7513 (tp30) cc_final: 0.7217 (tp30) REVERT: a 55 CYS cc_start: 0.6994 (t) cc_final: 0.6739 (p) REVERT: a 74 GLU cc_start: 0.6553 (mt-10) cc_final: 0.6192 (mp0) REVERT: a 214 LYS cc_start: 0.8342 (mtmt) cc_final: 0.7862 (mtpp) REVERT: a 240 GLN cc_start: 0.8768 (mm110) cc_final: 0.8370 (mm110) REVERT: a 314 ARG cc_start: 0.6720 (ttm170) cc_final: 0.6409 (ttm170) REVERT: a 344 ASN cc_start: 0.7197 (t0) cc_final: 0.6960 (m110) REVERT: b 14 LYS cc_start: 0.8325 (tptt) cc_final: 0.8074 (tptp) REVERT: b 92 ASP cc_start: 0.6581 (p0) cc_final: 0.6126 (p0) REVERT: b 99 LYS cc_start: 0.8149 (ttpp) cc_final: 0.7704 (tttp) REVERT: b 324 LEU cc_start: 0.8554 (mp) cc_final: 0.8343 (mt) REVERT: c 99 LYS cc_start: 0.7025 (ttmt) cc_final: 0.6630 (ttpp) REVERT: c 168 TRP cc_start: 0.6784 (m100) cc_final: 0.6472 (m100) outliers start: 4 outliers final: 3 residues processed: 347 average time/residue: 1.4078 time to fit residues: 540.4409 Evaluate side-chains 244 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 241 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 218 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 96 optimal weight: 30.0000 chunk 117 optimal weight: 5.9990 chunk 183 optimal weight: 0.1980 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 48 ASN b 48 ASN b 76 ASN b 84 HIS c 166 ASN c 181 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.202639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.132692 restraints weight = 16390.795| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.90 r_work: 0.3219 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16544 Z= 0.205 Angle : 0.591 7.953 22462 Z= 0.313 Chirality : 0.044 0.138 2387 Planarity : 0.004 0.037 2862 Dihedral : 4.974 44.556 2172 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.52 % Allowed : 9.95 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.18), residues: 2022 helix: 1.33 (0.37), residues: 225 sheet: -1.79 (0.22), residues: 535 loop : -1.16 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP b 330 HIS 0.007 0.001 HIS a 50 PHE 0.029 0.002 PHE b 20 TYR 0.016 0.001 TYR c 256 ARG 0.006 0.001 ARG C 148 Details of bonding type rmsd hydrogen bonds : bond 0.04886 ( 423) hydrogen bonds : angle 6.06105 ( 1086) SS BOND : bond 0.00237 ( 30) SS BOND : angle 1.30617 ( 60) covalent geometry : bond 0.00498 (16514) covalent geometry : angle 0.58756 (22402) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 256 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7588 (tt0) cc_final: 0.7077 (tt0) REVERT: A 102 ARG cc_start: 0.7885 (mmm-85) cc_final: 0.7407 (mmt90) REVERT: A 309 THR cc_start: 0.8597 (m) cc_final: 0.8294 (p) REVERT: B 31 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7242 (mm-40) REVERT: B 35 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7557 (mm110) REVERT: B 59 SER cc_start: 0.8848 (m) cc_final: 0.8603 (p) REVERT: B 70 GLN cc_start: 0.7301 (mt0) cc_final: 0.7004 (mp10) REVERT: B 76 ASN cc_start: 0.6211 (m-40) cc_final: 0.5935 (m110) REVERT: B 89 VAL cc_start: 0.7141 (t) cc_final: 0.6611 (m) REVERT: B 142 GLU cc_start: 0.6260 (pt0) cc_final: 0.5808 (tm-30) REVERT: B 154 GLU cc_start: 0.7890 (pt0) cc_final: 0.7359 (pt0) REVERT: B 166 ASN cc_start: 0.8330 (m-40) cc_final: 0.8126 (m-40) REVERT: B 168 TRP cc_start: 0.7958 (m100) cc_final: 0.7521 (m100) REVERT: B 274 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7754 (tp30) REVERT: C 12 GLU cc_start: 0.7161 (tt0) cc_final: 0.6817 (tt0) REVERT: C 14 LYS cc_start: 0.8308 (tptm) cc_final: 0.8067 (tptp) REVERT: C 23 ASP cc_start: 0.8183 (t0) cc_final: 0.7971 (t0) REVERT: C 74 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6225 (mp0) REVERT: C 101 LYS cc_start: 0.7240 (mptt) cc_final: 0.6951 (mppt) REVERT: C 177 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7072 (tt0) REVERT: C 214 LYS cc_start: 0.7593 (ptmm) cc_final: 0.7239 (pptt) REVERT: C 274 GLU cc_start: 0.7377 (tp30) cc_final: 0.7165 (tp30) REVERT: a 30 GLU cc_start: 0.8110 (tt0) cc_final: 0.7605 (tt0) REVERT: a 74 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6602 (mp0) REVERT: a 214 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8310 (mtpp) REVERT: a 240 GLN cc_start: 0.8814 (mm110) cc_final: 0.8421 (mm110) REVERT: a 287 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8044 (mm) REVERT: a 314 ARG cc_start: 0.7048 (ttm170) cc_final: 0.6776 (ttm170) REVERT: b 48 ASN cc_start: 0.7708 (m-40) cc_final: 0.7494 (m110) REVERT: b 147 ARG cc_start: 0.6874 (ptm160) cc_final: 0.6540 (ptm160) REVERT: b 157 ASP cc_start: 0.8105 (p0) cc_final: 0.7761 (t0) REVERT: b 345 MET cc_start: 0.5874 (OUTLIER) cc_final: 0.5505 (ptm) REVERT: c 41 ARG cc_start: 0.7307 (ttt90) cc_final: 0.7066 (tpt90) REVERT: c 99 LYS cc_start: 0.7173 (ttmt) cc_final: 0.6917 (ttpp) REVERT: c 154 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7036 (mt-10) REVERT: c 168 TRP cc_start: 0.7224 (m100) cc_final: 0.6927 (m100) REVERT: c 197 ASP cc_start: 0.8322 (p0) cc_final: 0.8000 (p0) REVERT: c 318 MET cc_start: 0.7767 (mpp) cc_final: 0.7526 (mpm) REVERT: c 340 GLU cc_start: 0.5008 (tp30) cc_final: 0.4766 (tp30) outliers start: 44 outliers final: 19 residues processed: 282 average time/residue: 1.3337 time to fit residues: 415.7857 Evaluate side-chains 257 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 234 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 177 GLU Chi-restraints excluded: chain b residue 345 MET Chi-restraints excluded: chain b residue 348 SER Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 324 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 176 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 197 optimal weight: 0.2980 chunk 182 optimal weight: 8.9990 chunk 166 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 ASN C 254 HIS a 48 ASN a 65 ASN b 293 HIS c 166 ASN c 310 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.200301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.132060 restraints weight = 16427.070| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.98 r_work: 0.3254 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16544 Z= 0.255 Angle : 0.622 6.739 22462 Z= 0.328 Chirality : 0.046 0.177 2387 Planarity : 0.004 0.037 2862 Dihedral : 5.123 38.095 2168 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.87 % Favored : 93.08 % Rotamer: Outliers : 3.72 % Allowed : 13.49 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.18), residues: 2022 helix: 1.35 (0.36), residues: 222 sheet: -1.94 (0.23), residues: 497 loop : -1.17 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 330 HIS 0.007 0.001 HIS a 50 PHE 0.025 0.002 PHE b 20 TYR 0.018 0.002 TYR A 256 ARG 0.005 0.001 ARG C 148 Details of bonding type rmsd hydrogen bonds : bond 0.05082 ( 423) hydrogen bonds : angle 5.76610 ( 1086) SS BOND : bond 0.00248 ( 30) SS BOND : angle 1.25329 ( 60) covalent geometry : bond 0.00625 (16514) covalent geometry : angle 0.61950 (22402) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 239 time to evaluate : 1.871 Fit side-chains revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7298 (tt0) cc_final: 0.6767 (tt0) REVERT: A 309 THR cc_start: 0.8433 (m) cc_final: 0.8047 (p) REVERT: B 31 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7337 (mm-40) REVERT: B 59 SER cc_start: 0.8875 (m) cc_final: 0.8648 (p) REVERT: B 70 GLN cc_start: 0.7142 (mt0) cc_final: 0.6728 (mp10) REVERT: B 76 ASN cc_start: 0.6144 (m-40) cc_final: 0.5785 (m110) REVERT: B 89 VAL cc_start: 0.6878 (t) cc_final: 0.6327 (m) REVERT: B 142 GLU cc_start: 0.6491 (pt0) cc_final: 0.5865 (tm-30) REVERT: B 154 GLU cc_start: 0.7825 (pt0) cc_final: 0.7262 (pt0) REVERT: B 168 TRP cc_start: 0.7739 (m100) cc_final: 0.7492 (m100) REVERT: B 274 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7586 (tp30) REVERT: C 12 GLU cc_start: 0.7013 (tt0) cc_final: 0.6660 (tt0) REVERT: C 14 LYS cc_start: 0.8184 (tptm) cc_final: 0.7914 (tptp) REVERT: C 62 ARG cc_start: 0.7191 (ppt170) cc_final: 0.6852 (ttp80) REVERT: C 74 GLU cc_start: 0.6547 (mt-10) cc_final: 0.6088 (mp0) REVERT: C 101 LYS cc_start: 0.7116 (mptt) cc_final: 0.6785 (mppt) REVERT: C 177 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6677 (tt0) REVERT: C 214 LYS cc_start: 0.7513 (ptmm) cc_final: 0.7066 (pptt) REVERT: C 258 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.6441 (tm-30) REVERT: C 274 GLU cc_start: 0.7428 (tp30) cc_final: 0.7174 (tp30) REVERT: a 30 GLU cc_start: 0.8282 (tt0) cc_final: 0.7658 (tt0) REVERT: a 74 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6450 (mp0) REVERT: a 101 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.7702 (mttt) REVERT: a 214 LYS cc_start: 0.8692 (mtmt) cc_final: 0.8303 (mtpp) REVERT: a 287 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7859 (mm) REVERT: a 314 ARG cc_start: 0.6786 (ttm170) cc_final: 0.6475 (ttm170) REVERT: b 48 ASN cc_start: 0.7509 (m-40) cc_final: 0.7244 (m110) REVERT: b 157 ASP cc_start: 0.8143 (p0) cc_final: 0.7577 (t0) REVERT: b 180 ASP cc_start: 0.8404 (t0) cc_final: 0.8170 (t0) REVERT: c 148 ARG cc_start: 0.4724 (OUTLIER) cc_final: 0.3455 (tpp80) REVERT: c 154 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6863 (mt-10) REVERT: c 168 TRP cc_start: 0.6912 (m100) cc_final: 0.6698 (m100) REVERT: c 276 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7206 (m-30) REVERT: c 318 MET cc_start: 0.7687 (mpp) cc_final: 0.7426 (mpm) REVERT: c 340 GLU cc_start: 0.4856 (tp30) cc_final: 0.4506 (tp30) outliers start: 65 outliers final: 32 residues processed: 273 average time/residue: 1.4962 time to fit residues: 451.6951 Evaluate side-chains 253 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 101 LYS Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 177 GLU Chi-restraints excluded: chain b residue 293 HIS Chi-restraints excluded: chain b residue 307 LEU Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain b residue 348 SER Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 98 SER Chi-restraints excluded: chain c residue 148 ARG Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 185 SER Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 276 ASP Chi-restraints excluded: chain c residue 324 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 30 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 46 optimal weight: 0.0980 chunk 104 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN B 207 ASN a 48 ASN c 166 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.204458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.134922 restraints weight = 16277.267| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.68 r_work: 0.3314 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16544 Z= 0.098 Angle : 0.503 7.302 22462 Z= 0.267 Chirality : 0.042 0.132 2387 Planarity : 0.003 0.030 2862 Dihedral : 4.636 36.685 2168 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.69 % Allowed : 15.49 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.19), residues: 2022 helix: 1.53 (0.37), residues: 225 sheet: -1.67 (0.22), residues: 526 loop : -0.97 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 80 HIS 0.009 0.001 HIS b 293 PHE 0.013 0.001 PHE a 277 TYR 0.017 0.001 TYR c 256 ARG 0.003 0.000 ARG b 336 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 423) hydrogen bonds : angle 5.34242 ( 1086) SS BOND : bond 0.00188 ( 30) SS BOND : angle 0.99066 ( 60) covalent geometry : bond 0.00224 (16514) covalent geometry : angle 0.50137 (22402) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 236 time to evaluate : 1.618 Fit side-chains revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7741 (tt0) cc_final: 0.7245 (tt0) REVERT: A 272 LYS cc_start: 0.8882 (mttp) cc_final: 0.8465 (mtpm) REVERT: B 31 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7478 (mm-40) REVERT: B 70 GLN cc_start: 0.7338 (mt0) cc_final: 0.7015 (mp10) REVERT: B 76 ASN cc_start: 0.6264 (m-40) cc_final: 0.5916 (m110) REVERT: B 89 VAL cc_start: 0.7299 (t) cc_final: 0.6747 (m) REVERT: B 142 GLU cc_start: 0.6581 (pt0) cc_final: 0.6001 (tm-30) REVERT: B 147 ARG cc_start: 0.8023 (mtp85) cc_final: 0.7744 (mtp85) REVERT: B 154 GLU cc_start: 0.7999 (pt0) cc_final: 0.7761 (pt0) REVERT: B 168 TRP cc_start: 0.7959 (m100) cc_final: 0.7686 (m100) REVERT: B 238 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7926 (mm-30) REVERT: B 274 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7840 (tp30) REVERT: C 12 GLU cc_start: 0.7187 (tt0) cc_final: 0.6594 (pm20) REVERT: C 14 LYS cc_start: 0.8255 (tptm) cc_final: 0.7963 (tptp) REVERT: C 62 ARG cc_start: 0.7353 (ppt170) cc_final: 0.6906 (ttp-110) REVERT: C 74 GLU cc_start: 0.6614 (mt-10) cc_final: 0.6045 (mp0) REVERT: C 101 LYS cc_start: 0.7220 (mptt) cc_final: 0.6589 (mppt) REVERT: C 177 GLU cc_start: 0.7640 (mt-10) cc_final: 0.6973 (tt0) REVERT: C 214 LYS cc_start: 0.7741 (ptmm) cc_final: 0.7422 (pptt) REVERT: a 30 GLU cc_start: 0.8321 (tt0) cc_final: 0.7773 (tt0) REVERT: a 74 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6574 (mp0) REVERT: a 214 LYS cc_start: 0.8609 (mtmt) cc_final: 0.7876 (mmmt) REVERT: a 287 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8063 (mm) REVERT: a 314 ARG cc_start: 0.7044 (ttm170) cc_final: 0.6597 (ttm170) REVERT: b 48 ASN cc_start: 0.7693 (m-40) cc_final: 0.7419 (m110) REVERT: b 157 ASP cc_start: 0.8318 (p0) cc_final: 0.7874 (t0) REVERT: c 154 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7116 (mt-10) REVERT: c 168 TRP cc_start: 0.7193 (m100) cc_final: 0.6977 (m100) REVERT: c 276 ASP cc_start: 0.8104 (m-30) cc_final: 0.7499 (m-30) REVERT: c 318 MET cc_start: 0.7712 (mpp) cc_final: 0.7445 (mpm) REVERT: c 340 GLU cc_start: 0.4923 (tp30) cc_final: 0.4603 (tp30) outliers start: 47 outliers final: 25 residues processed: 264 average time/residue: 1.3102 time to fit residues: 383.9522 Evaluate side-chains 244 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 208 GLN Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 344 ASN Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 177 GLU Chi-restraints excluded: chain b residue 307 LEU Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 324 LEU Chi-restraints excluded: chain c residue 345 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 89 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 48 ASN b 208 GLN b 293 HIS c 166 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.204414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.135288 restraints weight = 16517.801| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.97 r_work: 0.3315 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16544 Z= 0.145 Angle : 0.530 8.163 22462 Z= 0.279 Chirality : 0.043 0.141 2387 Planarity : 0.003 0.030 2862 Dihedral : 4.661 36.392 2168 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.43 % Allowed : 16.47 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.19), residues: 2022 helix: 1.64 (0.37), residues: 223 sheet: -1.92 (0.23), residues: 491 loop : -0.93 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 80 HIS 0.004 0.001 HIS c 195 PHE 0.013 0.001 PHE B 277 TYR 0.017 0.001 TYR c 256 ARG 0.003 0.000 ARG b 314 Details of bonding type rmsd hydrogen bonds : bond 0.03631 ( 423) hydrogen bonds : angle 5.25508 ( 1086) SS BOND : bond 0.00211 ( 30) SS BOND : angle 1.47467 ( 60) covalent geometry : bond 0.00352 (16514) covalent geometry : angle 0.52515 (22402) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 223 time to evaluate : 3.049 Fit side-chains revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7328 (tt0) cc_final: 0.6816 (tt0) REVERT: A 272 LYS cc_start: 0.8752 (mttp) cc_final: 0.8239 (mtpm) REVERT: A 283 THR cc_start: 0.7950 (p) cc_final: 0.7599 (p) REVERT: B 31 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7350 (mm-40) REVERT: B 70 GLN cc_start: 0.7137 (mt0) cc_final: 0.6721 (mp10) REVERT: B 76 ASN cc_start: 0.6236 (m-40) cc_final: 0.5895 (m110) REVERT: B 89 VAL cc_start: 0.6909 (t) cc_final: 0.6378 (m) REVERT: B 142 GLU cc_start: 0.6551 (pt0) cc_final: 0.5892 (tm-30) REVERT: B 147 ARG cc_start: 0.7876 (mtp85) cc_final: 0.7560 (mtp85) REVERT: B 154 GLU cc_start: 0.7818 (pt0) cc_final: 0.7506 (pt0) REVERT: B 213 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8078 (pt0) REVERT: B 238 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7795 (mm-30) REVERT: B 274 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7517 (tp30) REVERT: B 310 GLN cc_start: 0.6030 (OUTLIER) cc_final: 0.5738 (mp10) REVERT: C 12 GLU cc_start: 0.7003 (tt0) cc_final: 0.6391 (pm20) REVERT: C 14 LYS cc_start: 0.8106 (tptm) cc_final: 0.7781 (tptp) REVERT: C 62 ARG cc_start: 0.7152 (ppt170) cc_final: 0.6614 (ttp-110) REVERT: C 74 GLU cc_start: 0.6501 (mt-10) cc_final: 0.5953 (mp0) REVERT: C 101 LYS cc_start: 0.7053 (mptt) cc_final: 0.6622 (mppt) REVERT: C 177 GLU cc_start: 0.7452 (mt-10) cc_final: 0.6675 (tt0) REVERT: C 214 LYS cc_start: 0.7558 (ptmm) cc_final: 0.7147 (pptt) REVERT: a 30 GLU cc_start: 0.8267 (tt0) cc_final: 0.7617 (tt0) REVERT: a 74 GLU cc_start: 0.6757 (mt-10) cc_final: 0.6304 (mp0) REVERT: a 214 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8227 (mtpp) REVERT: a 276 ASP cc_start: 0.8251 (p0) cc_final: 0.8012 (p0) REVERT: a 287 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.7991 (mm) REVERT: a 314 ARG cc_start: 0.6877 (ttm170) cc_final: 0.6406 (ttm170) REVERT: b 48 ASN cc_start: 0.7537 (m-40) cc_final: 0.7266 (m110) REVERT: b 157 ASP cc_start: 0.8096 (p0) cc_final: 0.7609 (t0) REVERT: b 238 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: c 154 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6890 (mt-10) REVERT: c 168 TRP cc_start: 0.6887 (m100) cc_final: 0.6686 (m100) REVERT: c 276 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7259 (m-30) REVERT: c 318 MET cc_start: 0.7615 (mpp) cc_final: 0.7341 (mpm) REVERT: c 340 GLU cc_start: 0.4785 (tp30) cc_final: 0.4474 (tp30) outliers start: 60 outliers final: 36 residues processed: 255 average time/residue: 1.6189 time to fit residues: 468.1471 Evaluate side-chains 255 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 GLN Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 208 GLN Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 344 ASN Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 307 LEU Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain c residue 17 SER Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 276 ASP Chi-restraints excluded: chain c residue 324 LEU Chi-restraints excluded: chain c residue 345 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 61 optimal weight: 20.0000 chunk 164 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 177 optimal weight: 8.9990 chunk 200 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN a 48 ASN b 293 HIS c 166 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.200998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.132005 restraints weight = 16341.694| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.87 r_work: 0.3308 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16544 Z= 0.204 Angle : 0.578 8.176 22462 Z= 0.303 Chirality : 0.044 0.139 2387 Planarity : 0.004 0.032 2862 Dihedral : 4.861 37.561 2168 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.38 % Favored : 93.57 % Rotamer: Outliers : 3.77 % Allowed : 16.92 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.19), residues: 2022 helix: 1.57 (0.36), residues: 223 sheet: -2.00 (0.23), residues: 491 loop : -0.99 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 330 HIS 0.005 0.001 HIS b 293 PHE 0.014 0.002 PHE b 20 TYR 0.017 0.002 TYR c 256 ARG 0.009 0.001 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 423) hydrogen bonds : angle 5.33547 ( 1086) SS BOND : bond 0.00186 ( 30) SS BOND : angle 1.27182 ( 60) covalent geometry : bond 0.00498 (16514) covalent geometry : angle 0.57526 (22402) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 216 time to evaluate : 1.773 Fit side-chains revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7399 (tt0) cc_final: 0.6871 (tt0) REVERT: A 283 THR cc_start: 0.7912 (p) cc_final: 0.7585 (p) REVERT: B 31 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7414 (mm-40) REVERT: B 70 GLN cc_start: 0.7275 (mt0) cc_final: 0.6933 (mp10) REVERT: B 142 GLU cc_start: 0.6599 (pt0) cc_final: 0.5926 (tm-30) REVERT: B 147 ARG cc_start: 0.7933 (mtp85) cc_final: 0.7562 (mtp85) REVERT: B 213 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8029 (pt0) REVERT: B 238 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7759 (mm-30) REVERT: B 274 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7573 (tp30) REVERT: C 12 GLU cc_start: 0.7033 (tt0) cc_final: 0.6385 (pm20) REVERT: C 14 LYS cc_start: 0.8230 (tptm) cc_final: 0.7914 (tptp) REVERT: C 62 ARG cc_start: 0.7255 (ppt170) cc_final: 0.6695 (ttp-110) REVERT: C 74 GLU cc_start: 0.6559 (mt-10) cc_final: 0.5987 (mp0) REVERT: C 101 LYS cc_start: 0.7166 (mptt) cc_final: 0.6486 (mppt) REVERT: C 177 GLU cc_start: 0.7499 (mt-10) cc_final: 0.6686 (tt0) REVERT: C 214 LYS cc_start: 0.7588 (ptmm) cc_final: 0.7187 (pptt) REVERT: C 258 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6443 (tm-30) REVERT: a 30 GLU cc_start: 0.8227 (tt0) cc_final: 0.7599 (tt0) REVERT: a 74 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6384 (mp0) REVERT: a 214 LYS cc_start: 0.8675 (mtmt) cc_final: 0.7764 (mmmt) REVERT: a 287 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7992 (mm) REVERT: a 314 ARG cc_start: 0.6838 (ttm170) cc_final: 0.6367 (ttm170) REVERT: b 147 ARG cc_start: 0.6709 (mtm110) cc_final: 0.6508 (mtm110) REVERT: b 157 ASP cc_start: 0.8143 (p0) cc_final: 0.7658 (t0) REVERT: b 238 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7679 (mt-10) REVERT: c 154 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6982 (mt-10) REVERT: c 276 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7270 (m-30) REVERT: c 318 MET cc_start: 0.7664 (mpp) cc_final: 0.7387 (mpm) REVERT: c 340 GLU cc_start: 0.4935 (tp30) cc_final: 0.4618 (tp30) outliers start: 66 outliers final: 43 residues processed: 250 average time/residue: 1.3683 time to fit residues: 379.3306 Evaluate side-chains 264 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 213 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 208 GLN Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 324 LEU Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 177 GLU Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain b residue 348 SER Chi-restraints excluded: chain c residue 17 SER Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 228 THR Chi-restraints excluded: chain c residue 276 ASP Chi-restraints excluded: chain c residue 324 LEU Chi-restraints excluded: chain c residue 345 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 173 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 chunk 65 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN B 208 GLN a 48 ASN b 293 HIS c 166 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.201480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.133748 restraints weight = 16490.071| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.96 r_work: 0.3304 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16544 Z= 0.172 Angle : 0.552 6.826 22462 Z= 0.290 Chirality : 0.043 0.138 2387 Planarity : 0.003 0.037 2862 Dihedral : 4.780 37.164 2168 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.08 % Favored : 93.87 % Rotamer: Outliers : 3.72 % Allowed : 18.12 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.19), residues: 2022 helix: 1.56 (0.36), residues: 224 sheet: -1.95 (0.23), residues: 491 loop : -0.97 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP c 168 HIS 0.005 0.001 HIS b 293 PHE 0.012 0.001 PHE B 277 TYR 0.018 0.001 TYR c 256 ARG 0.011 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 423) hydrogen bonds : angle 5.24204 ( 1086) SS BOND : bond 0.00215 ( 30) SS BOND : angle 1.11833 ( 60) covalent geometry : bond 0.00421 (16514) covalent geometry : angle 0.55001 (22402) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 214 time to evaluate : 2.579 Fit side-chains revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7360 (tt0) cc_final: 0.6838 (tt0) REVERT: A 272 LYS cc_start: 0.8764 (mttp) cc_final: 0.8235 (mtpm) REVERT: A 283 THR cc_start: 0.7860 (p) cc_final: 0.7526 (p) REVERT: B 31 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7387 (mm-40) REVERT: B 70 GLN cc_start: 0.7230 (mt0) cc_final: 0.6846 (mp10) REVERT: B 142 GLU cc_start: 0.6659 (pt0) cc_final: 0.6024 (tm-30) REVERT: B 146 GLU cc_start: 0.7371 (mp0) cc_final: 0.7140 (pm20) REVERT: B 147 ARG cc_start: 0.7932 (mtp85) cc_final: 0.7598 (mtp85) REVERT: B 213 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8038 (pt0) REVERT: B 238 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7762 (mm-30) REVERT: B 274 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7477 (tp30) REVERT: C 12 GLU cc_start: 0.6975 (tt0) cc_final: 0.6306 (pm20) REVERT: C 14 LYS cc_start: 0.8160 (tptm) cc_final: 0.7775 (tptp) REVERT: C 62 ARG cc_start: 0.7212 (ppt170) cc_final: 0.6635 (ttp-110) REVERT: C 74 GLU cc_start: 0.6532 (mt-10) cc_final: 0.5983 (mp0) REVERT: C 101 LYS cc_start: 0.7057 (mptt) cc_final: 0.6396 (mppt) REVERT: C 177 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6717 (tt0) REVERT: C 214 LYS cc_start: 0.7563 (ptmm) cc_final: 0.7156 (pptt) REVERT: a 30 GLU cc_start: 0.8223 (tt0) cc_final: 0.7572 (tt0) REVERT: a 74 GLU cc_start: 0.6789 (mt-10) cc_final: 0.6335 (mp0) REVERT: a 214 LYS cc_start: 0.8660 (mtmt) cc_final: 0.8265 (mtpp) REVERT: a 276 ASP cc_start: 0.8365 (p0) cc_final: 0.7995 (p0) REVERT: a 287 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8031 (mm) REVERT: a 314 ARG cc_start: 0.6823 (ttm170) cc_final: 0.6364 (ttm170) REVERT: b 147 ARG cc_start: 0.6617 (mtm110) cc_final: 0.6392 (mtm110) REVERT: b 157 ASP cc_start: 0.8129 (p0) cc_final: 0.7640 (t0) REVERT: b 238 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: c 156 GLU cc_start: 0.8020 (pt0) cc_final: 0.7414 (tt0) REVERT: c 276 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7266 (m-30) REVERT: c 318 MET cc_start: 0.7628 (mpp) cc_final: 0.7368 (mpm) outliers start: 65 outliers final: 43 residues processed: 248 average time/residue: 1.5684 time to fit residues: 430.3230 Evaluate side-chains 254 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 205 time to evaluate : 3.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 208 GLN Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 324 LEU Chi-restraints excluded: chain a residue 344 ASN Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 148 ARG Chi-restraints excluded: chain b residue 177 GLU Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain b residue 348 SER Chi-restraints excluded: chain c residue 17 SER Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 276 ASP Chi-restraints excluded: chain c residue 324 LEU Chi-restraints excluded: chain c residue 345 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 201 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN b 293 HIS c 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.201310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.133062 restraints weight = 16274.357| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.85 r_work: 0.3319 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16544 Z= 0.170 Angle : 0.553 6.631 22462 Z= 0.291 Chirality : 0.043 0.137 2387 Planarity : 0.003 0.039 2862 Dihedral : 4.758 36.137 2168 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.38 % Favored : 93.57 % Rotamer: Outliers : 3.37 % Allowed : 18.64 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.19), residues: 2022 helix: 1.59 (0.36), residues: 224 sheet: -1.95 (0.23), residues: 493 loop : -0.96 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 168 HIS 0.006 0.001 HIS b 293 PHE 0.012 0.001 PHE c 277 TYR 0.018 0.001 TYR c 256 ARG 0.016 0.001 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 423) hydrogen bonds : angle 5.21950 ( 1086) SS BOND : bond 0.00164 ( 30) SS BOND : angle 1.06728 ( 60) covalent geometry : bond 0.00413 (16514) covalent geometry : angle 0.55146 (22402) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 214 time to evaluate : 3.936 Fit side-chains revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7361 (tt0) cc_final: 0.6829 (tt0) REVERT: A 272 LYS cc_start: 0.8769 (mttp) cc_final: 0.8228 (mtpm) REVERT: A 283 THR cc_start: 0.7857 (p) cc_final: 0.7525 (p) REVERT: B 31 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7378 (mm-40) REVERT: B 70 GLN cc_start: 0.7232 (mt0) cc_final: 0.6861 (mp10) REVERT: B 89 VAL cc_start: 0.6957 (t) cc_final: 0.6419 (m) REVERT: B 142 GLU cc_start: 0.6715 (pt0) cc_final: 0.6082 (tm-30) REVERT: B 146 GLU cc_start: 0.7341 (mp0) cc_final: 0.7101 (pt0) REVERT: B 147 ARG cc_start: 0.7947 (mtp85) cc_final: 0.7610 (mtp85) REVERT: B 154 GLU cc_start: 0.7791 (pt0) cc_final: 0.7514 (pt0) REVERT: B 213 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8010 (pt0) REVERT: B 238 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.6768 (pm20) REVERT: B 274 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7475 (tp30) REVERT: C 12 GLU cc_start: 0.7002 (tt0) cc_final: 0.6322 (pm20) REVERT: C 14 LYS cc_start: 0.8144 (tptm) cc_final: 0.7759 (tptp) REVERT: C 62 ARG cc_start: 0.7227 (ppt170) cc_final: 0.6634 (ttp-110) REVERT: C 74 GLU cc_start: 0.6536 (mt-10) cc_final: 0.5977 (mp0) REVERT: C 101 LYS cc_start: 0.7081 (mptt) cc_final: 0.6431 (mppt) REVERT: C 177 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6707 (tt0) REVERT: C 190 ASP cc_start: 0.7896 (t0) cc_final: 0.7569 (t70) REVERT: C 214 LYS cc_start: 0.7559 (ptmm) cc_final: 0.7156 (pptt) REVERT: C 258 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.6335 (tm-30) REVERT: a 30 GLU cc_start: 0.8229 (tt0) cc_final: 0.7582 (tt0) REVERT: a 74 GLU cc_start: 0.6775 (mt-10) cc_final: 0.6321 (mp0) REVERT: a 214 LYS cc_start: 0.8647 (mtmt) cc_final: 0.8250 (mtpp) REVERT: a 276 ASP cc_start: 0.8266 (p0) cc_final: 0.8021 (p0) REVERT: a 287 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8042 (mm) REVERT: a 314 ARG cc_start: 0.6842 (ttm170) cc_final: 0.6388 (ttm170) REVERT: b 96 VAL cc_start: 0.8403 (OUTLIER) cc_final: 0.7997 (t) REVERT: b 147 ARG cc_start: 0.6612 (mtm110) cc_final: 0.6349 (mtm110) REVERT: b 157 ASP cc_start: 0.8156 (p0) cc_final: 0.7681 (t0) REVERT: b 238 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7643 (mt-10) REVERT: c 156 GLU cc_start: 0.8003 (pt0) cc_final: 0.7454 (tt0) REVERT: c 276 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7238 (m-30) REVERT: c 318 MET cc_start: 0.7613 (mpp) cc_final: 0.7347 (mpm) outliers start: 59 outliers final: 45 residues processed: 248 average time/residue: 1.6291 time to fit residues: 448.4518 Evaluate side-chains 260 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 207 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 208 GLN Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 324 LEU Chi-restraints excluded: chain a residue 344 ASN Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 302 THR Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain b residue 348 SER Chi-restraints excluded: chain c residue 17 SER Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 276 ASP Chi-restraints excluded: chain c residue 324 LEU Chi-restraints excluded: chain c residue 345 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 20 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 178 optimal weight: 20.0000 chunk 163 optimal weight: 4.9990 chunk 181 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN b 293 HIS c 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.201457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.133429 restraints weight = 16354.436| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.79 r_work: 0.3321 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16544 Z= 0.162 Angle : 0.555 7.205 22462 Z= 0.291 Chirality : 0.043 0.144 2387 Planarity : 0.003 0.045 2862 Dihedral : 4.731 34.651 2168 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.84 % Favored : 94.11 % Rotamer: Outliers : 3.37 % Allowed : 18.81 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.19), residues: 2022 helix: 1.58 (0.36), residues: 224 sheet: -1.91 (0.23), residues: 493 loop : -0.95 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP c 168 HIS 0.007 0.001 HIS b 293 PHE 0.012 0.001 PHE c 277 TYR 0.018 0.001 TYR c 256 ARG 0.015 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 423) hydrogen bonds : angle 5.19927 ( 1086) SS BOND : bond 0.00167 ( 30) SS BOND : angle 1.05031 ( 60) covalent geometry : bond 0.00395 (16514) covalent geometry : angle 0.55320 (22402) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 212 time to evaluate : 2.012 Fit side-chains revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7355 (tt0) cc_final: 0.6824 (tt0) REVERT: A 272 LYS cc_start: 0.8761 (mttp) cc_final: 0.8222 (mtpm) REVERT: A 283 THR cc_start: 0.7845 (p) cc_final: 0.7515 (p) REVERT: B 31 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7369 (mm-40) REVERT: B 70 GLN cc_start: 0.7262 (mt0) cc_final: 0.6930 (mp10) REVERT: B 89 VAL cc_start: 0.7004 (t) cc_final: 0.6469 (m) REVERT: B 142 GLU cc_start: 0.6737 (pt0) cc_final: 0.6097 (pp20) REVERT: B 146 GLU cc_start: 0.7361 (mp0) cc_final: 0.7141 (pt0) REVERT: B 147 ARG cc_start: 0.7961 (mtp85) cc_final: 0.7625 (mtp85) REVERT: B 213 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8011 (pt0) REVERT: B 238 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.6773 (pm20) REVERT: B 274 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7474 (tp30) REVERT: C 12 GLU cc_start: 0.6987 (tt0) cc_final: 0.6301 (pm20) REVERT: C 14 LYS cc_start: 0.8122 (tptm) cc_final: 0.7740 (tptp) REVERT: C 62 ARG cc_start: 0.7230 (ppt170) cc_final: 0.6615 (ttp-110) REVERT: C 74 GLU cc_start: 0.6612 (mt-10) cc_final: 0.6033 (mp0) REVERT: C 101 LYS cc_start: 0.7083 (mptt) cc_final: 0.6433 (mppt) REVERT: C 177 GLU cc_start: 0.7486 (mt-10) cc_final: 0.6725 (tt0) REVERT: C 190 ASP cc_start: 0.7888 (t0) cc_final: 0.7555 (t70) REVERT: C 214 LYS cc_start: 0.7558 (ptmm) cc_final: 0.7152 (pptt) REVERT: C 258 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6303 (tm-30) REVERT: a 30 GLU cc_start: 0.8251 (tt0) cc_final: 0.7583 (tt0) REVERT: a 47 LEU cc_start: 0.7409 (tp) cc_final: 0.7208 (tp) REVERT: a 74 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6338 (mp0) REVERT: a 214 LYS cc_start: 0.8639 (mtmt) cc_final: 0.8240 (mtpp) REVERT: a 287 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8039 (mm) REVERT: a 314 ARG cc_start: 0.6825 (ttm170) cc_final: 0.6375 (ttm170) REVERT: b 50 HIS cc_start: 0.7020 (t-90) cc_final: 0.6769 (t-90) REVERT: b 96 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8003 (t) REVERT: b 147 ARG cc_start: 0.6713 (mtm110) cc_final: 0.6436 (mtm110) REVERT: b 157 ASP cc_start: 0.8153 (p0) cc_final: 0.7695 (t0) REVERT: b 238 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7639 (mt-10) REVERT: c 156 GLU cc_start: 0.8041 (pt0) cc_final: 0.7502 (tt0) REVERT: c 276 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7246 (m-30) REVERT: c 318 MET cc_start: 0.7626 (mpp) cc_final: 0.7357 (mpm) outliers start: 59 outliers final: 44 residues processed: 245 average time/residue: 1.5949 time to fit residues: 436.8592 Evaluate side-chains 257 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 208 GLN Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 324 LEU Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain b residue 148 ARG Chi-restraints excluded: chain b residue 177 GLU Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain c residue 17 SER Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 276 ASP Chi-restraints excluded: chain c residue 324 LEU Chi-restraints excluded: chain c residue 345 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 91 optimal weight: 10.0000 chunk 66 optimal weight: 0.0870 chunk 117 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN a 35 GLN a 48 ASN a 269 HIS b 293 HIS c 166 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.205383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.138128 restraints weight = 16426.523| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.83 r_work: 0.3363 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16544 Z= 0.092 Angle : 0.504 8.975 22462 Z= 0.263 Chirality : 0.042 0.153 2387 Planarity : 0.003 0.055 2862 Dihedral : 4.306 28.230 2168 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.85 % Favored : 95.10 % Rotamer: Outliers : 2.12 % Allowed : 20.41 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.19), residues: 2022 helix: 1.70 (0.37), residues: 224 sheet: -1.71 (0.24), residues: 491 loop : -0.77 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 150 HIS 0.007 0.001 HIS b 293 PHE 0.014 0.001 PHE a 277 TYR 0.019 0.001 TYR c 256 ARG 0.013 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.02757 ( 423) hydrogen bonds : angle 4.94693 ( 1086) SS BOND : bond 0.00138 ( 30) SS BOND : angle 0.93876 ( 60) covalent geometry : bond 0.00210 (16514) covalent geometry : angle 0.50221 (22402) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 1.753 Fit side-chains revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7717 (tt0) cc_final: 0.7243 (tt0) REVERT: A 283 THR cc_start: 0.7909 (p) cc_final: 0.7548 (p) REVERT: A 314 ARG cc_start: 0.7486 (ttm-80) cc_final: 0.7100 (ttt-90) REVERT: B 70 GLN cc_start: 0.7338 (mt0) cc_final: 0.7059 (mp10) REVERT: B 89 VAL cc_start: 0.7270 (t) cc_final: 0.6790 (m) REVERT: B 142 GLU cc_start: 0.6787 (pt0) cc_final: 0.6095 (pp20) REVERT: B 147 ARG cc_start: 0.8153 (mtp85) cc_final: 0.7840 (mtp85) REVERT: B 154 GLU cc_start: 0.7991 (pt0) cc_final: 0.7744 (pt0) REVERT: B 213 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8105 (pt0) REVERT: B 238 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.6899 (pm20) REVERT: B 274 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7760 (tp30) REVERT: C 12 GLU cc_start: 0.7134 (tt0) cc_final: 0.6505 (pm20) REVERT: C 14 LYS cc_start: 0.8171 (tptm) cc_final: 0.7797 (tptp) REVERT: C 74 GLU cc_start: 0.6513 (mt-10) cc_final: 0.6002 (mp0) REVERT: C 101 LYS cc_start: 0.7086 (mptt) cc_final: 0.6705 (mppt) REVERT: C 177 GLU cc_start: 0.7608 (mt-10) cc_final: 0.6930 (tt0) REVERT: C 214 LYS cc_start: 0.7681 (ptmm) cc_final: 0.7281 (pptt) REVERT: C 258 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6356 (tm-30) REVERT: C 314 ARG cc_start: 0.4898 (ttm170) cc_final: 0.4586 (ttm170) REVERT: a 30 GLU cc_start: 0.8277 (tt0) cc_final: 0.7717 (tt0) REVERT: a 74 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6426 (mp0) REVERT: a 169 MET cc_start: 0.9156 (mmm) cc_final: 0.8947 (mmm) REVERT: a 214 LYS cc_start: 0.8559 (mtmt) cc_final: 0.8290 (mtpp) REVERT: a 276 ASP cc_start: 0.8332 (p0) cc_final: 0.8036 (p0) REVERT: a 287 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8141 (mm) REVERT: a 314 ARG cc_start: 0.7085 (ttm170) cc_final: 0.6655 (ttm170) REVERT: b 50 HIS cc_start: 0.7090 (t-90) cc_final: 0.6866 (t-90) REVERT: b 96 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8161 (t) REVERT: b 147 ARG cc_start: 0.7074 (mtm110) cc_final: 0.6779 (mtm110) REVERT: b 157 ASP cc_start: 0.8250 (p0) cc_final: 0.7935 (t0) REVERT: b 238 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7638 (mt-10) REVERT: c 156 GLU cc_start: 0.8049 (pt0) cc_final: 0.7624 (tt0) REVERT: c 276 ASP cc_start: 0.8110 (m-30) cc_final: 0.7448 (m-30) REVERT: c 318 MET cc_start: 0.7637 (mpp) cc_final: 0.7406 (mpm) outliers start: 37 outliers final: 27 residues processed: 242 average time/residue: 1.2064 time to fit residues: 324.7855 Evaluate side-chains 247 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain b residue 148 ARG Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 324 LEU Chi-restraints excluded: chain c residue 345 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 87 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 201 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 180 optimal weight: 0.0870 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN B 208 GLN a 35 GLN a 48 ASN b 293 HIS c 166 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.204590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.136298 restraints weight = 16431.548| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.88 r_work: 0.3351 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16544 Z= 0.104 Angle : 0.515 8.730 22462 Z= 0.269 Chirality : 0.042 0.159 2387 Planarity : 0.003 0.051 2862 Dihedral : 4.277 26.933 2168 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.95 % Favored : 95.00 % Rotamer: Outliers : 2.23 % Allowed : 20.81 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.19), residues: 2022 helix: 1.71 (0.37), residues: 224 sheet: -1.68 (0.24), residues: 493 loop : -0.73 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 168 HIS 0.007 0.001 HIS b 293 PHE 0.013 0.001 PHE c 277 TYR 0.018 0.001 TYR c 256 ARG 0.016 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.02992 ( 423) hydrogen bonds : angle 4.92766 ( 1086) SS BOND : bond 0.00156 ( 30) SS BOND : angle 0.92079 ( 60) covalent geometry : bond 0.00245 (16514) covalent geometry : angle 0.51382 (22402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15401.98 seconds wall clock time: 274 minutes 30.38 seconds (16470.38 seconds total)