Starting phenix.real_space_refine on Sat May 17 18:51:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wbe_37422/05_2025/8wbe_37422_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbe_37422/05_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_37422/05_2025/8wbe_37422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbe_37422/05_2025/8wbe_37422.map" model { file = "/net/cci-nas-00/data/ceres_data/8wbe_37422/05_2025/8wbe_37422_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbe_37422/05_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.31, per 1000 atoms: 0.64 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: 4.04 Conformation dependent library (CDL) restraints added in 2.1 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: 1.89 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: 5.19 Time building geometry restraints manager: 4.77 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: 1.720 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: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 37.520 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.900 ------------------------------------------------------------------------------- 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 : 1.602 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: 1.2858 time to fit residues: 493.7834 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 : 1.735 ------------------------------------------------------------------------------- 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 = 71)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.131339 restraints weight = 16390.999| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.86 r_work: 0.3208 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 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 1.30616 ( 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 : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7590 (tt0) cc_final: 0.7068 (tt0) REVERT: A 102 ARG cc_start: 0.7873 (mmm-85) cc_final: 0.7393 (mmt90) REVERT: A 309 THR cc_start: 0.8600 (m) cc_final: 0.8296 (p) REVERT: A 314 ARG cc_start: 0.7097 (ttp-170) cc_final: 0.6896 (ttm-80) REVERT: B 31 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7241 (mm-40) REVERT: B 35 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7558 (mm110) REVERT: B 59 SER cc_start: 0.8849 (m) cc_final: 0.8602 (p) REVERT: B 70 GLN cc_start: 0.7284 (mt0) cc_final: 0.6980 (mp10) REVERT: B 76 ASN cc_start: 0.6178 (m-40) cc_final: 0.5908 (m110) REVERT: B 89 VAL cc_start: 0.7103 (t) cc_final: 0.6572 (m) REVERT: B 142 GLU cc_start: 0.6265 (pt0) cc_final: 0.5789 (tm-30) REVERT: B 154 GLU cc_start: 0.7886 (pt0) cc_final: 0.7351 (pt0) REVERT: B 168 TRP cc_start: 0.7962 (m100) cc_final: 0.7525 (m100) REVERT: B 274 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7751 (tp30) REVERT: C 12 GLU cc_start: 0.7174 (tt0) cc_final: 0.6834 (tt0) REVERT: C 14 LYS cc_start: 0.8315 (tptm) cc_final: 0.8077 (tptp) REVERT: C 23 ASP cc_start: 0.8187 (t0) cc_final: 0.7972 (t0) REVERT: C 74 GLU cc_start: 0.6645 (mt-10) cc_final: 0.6208 (mp0) REVERT: C 101 LYS cc_start: 0.7208 (mptt) cc_final: 0.6914 (mppt) REVERT: C 177 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7067 (tt0) REVERT: C 214 LYS cc_start: 0.7595 (ptmm) cc_final: 0.7238 (pptt) REVERT: C 274 GLU cc_start: 0.7371 (tp30) cc_final: 0.7159 (tp30) REVERT: a 30 GLU cc_start: 0.8141 (tt0) cc_final: 0.7635 (tt0) REVERT: a 74 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6600 (mp0) REVERT: a 214 LYS cc_start: 0.8603 (mtmt) cc_final: 0.8310 (mtpp) REVERT: a 240 GLN cc_start: 0.8809 (mm110) cc_final: 0.8414 (mm110) REVERT: a 287 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8044 (mm) REVERT: a 314 ARG cc_start: 0.7046 (ttm170) cc_final: 0.6774 (ttm170) REVERT: b 48 ASN cc_start: 0.7677 (m-40) cc_final: 0.7462 (m110) REVERT: b 147 ARG cc_start: 0.6855 (ptm160) cc_final: 0.6524 (ptm160) REVERT: b 157 ASP cc_start: 0.8120 (p0) cc_final: 0.7756 (t0) REVERT: b 345 MET cc_start: 0.5856 (OUTLIER) cc_final: 0.5488 (ptm) REVERT: c 41 ARG cc_start: 0.7299 (ttt90) cc_final: 0.7053 (tpt90) REVERT: c 99 LYS cc_start: 0.7158 (ttmt) cc_final: 0.6896 (ttpp) REVERT: c 154 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6991 (mt-10) REVERT: c 168 TRP cc_start: 0.7187 (m100) cc_final: 0.6886 (m100) REVERT: c 197 ASP cc_start: 0.8330 (p0) cc_final: 0.8006 (p0) REVERT: c 318 MET cc_start: 0.7757 (mpp) cc_final: 0.7514 (mpm) REVERT: c 340 GLU cc_start: 0.4967 (tp30) cc_final: 0.4727 (tp30) outliers start: 44 outliers final: 19 residues processed: 282 average time/residue: 1.2541 time to fit residues: 391.3865 Evaluate side-chains 258 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 235 time to evaluate : 1.680 ------------------------------------------------------------------------------- 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: 10.0000 chunk 74 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 200 optimal weight: 0.0040 chunk 88 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 197 optimal weight: 0.5980 chunk 182 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 34 optimal weight: 0.4980 chunk 65 optimal weight: 7.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 ASN 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 = 0.4310 r_free = 0.4310 target = 0.208754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.140606 restraints weight = 16352.165| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.84 r_work: 0.3362 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16544 Z= 0.094 Angle : 0.482 5.769 22462 Z= 0.256 Chirality : 0.041 0.147 2387 Planarity : 0.003 0.030 2862 Dihedral : 4.417 27.124 2168 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.29 % Allowed : 12.86 % Favored : 84.85 % 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: -1.30 (0.19), residues: 2022 helix: 1.50 (0.37), residues: 225 sheet: -1.60 (0.22), residues: 556 loop : -0.93 (0.17), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 80 HIS 0.005 0.001 HIS b 293 PHE 0.014 0.001 PHE b 20 TYR 0.017 0.001 TYR c 256 ARG 0.004 0.000 ARG b 336 Details of bonding type rmsd hydrogen bonds : bond 0.03285 ( 423) hydrogen bonds : angle 5.46785 ( 1086) SS BOND : bond 0.00174 ( 30) SS BOND : angle 0.99044 ( 60) covalent geometry : bond 0.00215 (16514) covalent geometry : angle 0.47969 (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 296 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 256 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7394 (tt0) cc_final: 0.6883 (tt0) REVERT: B 59 SER cc_start: 0.8826 (m) cc_final: 0.8614 (p) REVERT: B 70 GLN cc_start: 0.7105 (mt0) cc_final: 0.6807 (mp10) REVERT: B 76 ASN cc_start: 0.6105 (m-40) cc_final: 0.5792 (m110) REVERT: B 89 VAL cc_start: 0.6904 (t) cc_final: 0.6373 (m) REVERT: B 142 GLU cc_start: 0.6451 (pt0) cc_final: 0.5818 (tm-30) REVERT: B 154 GLU cc_start: 0.7800 (pt0) cc_final: 0.7374 (pt0) REVERT: B 168 TRP cc_start: 0.7765 (m100) cc_final: 0.7323 (m100) REVERT: B 274 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7545 (tp30) REVERT: C 12 GLU cc_start: 0.7086 (tt0) cc_final: 0.6853 (tt0) REVERT: C 23 ASP cc_start: 0.8080 (t0) cc_final: 0.7714 (t0) REVERT: C 74 GLU cc_start: 0.6433 (mt-10) cc_final: 0.5957 (mp0) REVERT: C 101 LYS cc_start: 0.6983 (mptt) cc_final: 0.6720 (mppt) REVERT: C 177 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6928 (tt0) REVERT: C 214 LYS cc_start: 0.7501 (ptmm) cc_final: 0.6979 (pptt) REVERT: C 240 GLN cc_start: 0.7194 (mm-40) cc_final: 0.6948 (mm110) REVERT: C 258 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.6783 (tm-30) REVERT: C 274 GLU cc_start: 0.7307 (tp30) cc_final: 0.7091 (tp30) REVERT: a 30 GLU cc_start: 0.8238 (tt0) cc_final: 0.7677 (tt0) REVERT: a 74 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6278 (mp0) REVERT: a 214 LYS cc_start: 0.8601 (mtmt) cc_final: 0.8260 (mtpp) REVERT: a 240 GLN cc_start: 0.8688 (mm110) cc_final: 0.8245 (mm110) REVERT: a 287 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8030 (mm) REVERT: a 314 ARG cc_start: 0.7029 (ttm170) cc_final: 0.6752 (ttm170) REVERT: b 48 ASN cc_start: 0.7631 (m-40) cc_final: 0.7398 (m110) REVERT: b 99 LYS cc_start: 0.8342 (ttpp) cc_final: 0.7855 (tttp) REVERT: b 147 ARG cc_start: 0.6613 (ptm160) cc_final: 0.6231 (ptm160) REVERT: b 157 ASP cc_start: 0.8092 (p0) cc_final: 0.7585 (t0) REVERT: c 99 LYS cc_start: 0.6987 (ttmt) cc_final: 0.6692 (ttpp) REVERT: c 154 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6847 (mt-10) REVERT: c 168 TRP cc_start: 0.6917 (m100) cc_final: 0.6606 (m100) REVERT: c 197 ASP cc_start: 0.8091 (p0) cc_final: 0.7834 (p0) REVERT: c 276 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7317 (m-30) REVERT: c 318 MET cc_start: 0.7619 (mpp) cc_final: 0.7347 (mpm) REVERT: c 340 GLU cc_start: 0.4867 (tp30) cc_final: 0.4508 (tp30) outliers start: 40 outliers final: 16 residues processed: 274 average time/residue: 1.1920 time to fit residues: 363.4554 Evaluate side-chains 255 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 235 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 345 MET 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 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 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: 10.0000 chunk 124 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 46 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 154 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN B 48 ASN B 207 ASN B 208 GLN a 48 ASN a 65 ASN b 76 ASN c 166 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.202212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.133559 restraints weight = 16270.606| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.79 r_work: 0.3322 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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 : 0.005 0.050 16544 Z= 0.202 Angle : 0.573 7.620 22462 Z= 0.301 Chirality : 0.044 0.137 2387 Planarity : 0.004 0.030 2862 Dihedral : 4.716 27.465 2166 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.37 % Allowed : 14.35 % Favored : 82.28 % 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: -1.39 (0.19), residues: 2022 helix: 1.47 (0.36), residues: 225 sheet: -1.76 (0.23), residues: 497 loop : -1.00 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 330 HIS 0.004 0.001 HIS A 84 PHE 0.018 0.002 PHE b 20 TYR 0.016 0.002 TYR A 256 ARG 0.005 0.001 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.04280 ( 423) hydrogen bonds : angle 5.49895 ( 1086) SS BOND : bond 0.00215 ( 30) SS BOND : angle 1.46244 ( 60) covalent geometry : bond 0.00497 (16514) covalent geometry : angle 0.56854 (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 296 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 237 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7410 (tt0) cc_final: 0.6886 (tt0) REVERT: A 102 ARG cc_start: 0.7696 (mmm-85) cc_final: 0.7276 (mmt90) REVERT: A 272 LYS cc_start: 0.8800 (mttp) cc_final: 0.8279 (mtpm) REVERT: A 283 THR cc_start: 0.7942 (p) cc_final: 0.7612 (p) REVERT: A 314 ARG cc_start: 0.7131 (ttp-170) cc_final: 0.6810 (ttm-80) REVERT: B 31 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7349 (mm-40) REVERT: B 59 SER cc_start: 0.8865 (m) cc_final: 0.8624 (p) REVERT: B 70 GLN cc_start: 0.7165 (mt0) cc_final: 0.6801 (mp10) REVERT: B 76 ASN cc_start: 0.6181 (m-40) cc_final: 0.5863 (m110) REVERT: B 89 VAL cc_start: 0.7035 (t) cc_final: 0.6503 (m) REVERT: B 142 GLU cc_start: 0.6510 (pt0) cc_final: 0.5900 (tm-30) REVERT: B 154 GLU cc_start: 0.7747 (pt0) cc_final: 0.7434 (pt0) REVERT: B 168 TRP cc_start: 0.7690 (m100) cc_final: 0.7468 (m100) REVERT: B 238 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7768 (mm-30) REVERT: B 274 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7559 (tp30) REVERT: C 12 GLU cc_start: 0.7082 (tt0) cc_final: 0.6844 (tt0) REVERT: C 23 ASP cc_start: 0.8106 (t0) cc_final: 0.7840 (t0) REVERT: C 62 ARG cc_start: 0.7187 (ppt170) cc_final: 0.6852 (ttp80) REVERT: C 74 GLU cc_start: 0.6527 (mt-10) cc_final: 0.6008 (mp0) REVERT: C 101 LYS cc_start: 0.7115 (mptt) cc_final: 0.6817 (mppt) REVERT: C 177 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6788 (tt0) REVERT: C 214 LYS cc_start: 0.7518 (ptmm) cc_final: 0.7108 (pptt) REVERT: C 240 GLN cc_start: 0.7295 (mm-40) cc_final: 0.7069 (mm110) REVERT: C 274 GLU cc_start: 0.7416 (tp30) cc_final: 0.7179 (tp30) REVERT: a 30 GLU cc_start: 0.8268 (tt0) cc_final: 0.7649 (tt0) REVERT: a 47 LEU cc_start: 0.7462 (tp) cc_final: 0.7256 (tp) REVERT: a 74 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6365 (mp0) REVERT: a 214 LYS cc_start: 0.8672 (mtmt) cc_final: 0.8310 (mtpp) REVERT: a 287 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.7996 (mm) REVERT: a 314 ARG cc_start: 0.6945 (ttm170) cc_final: 0.6452 (ttm170) REVERT: b 48 ASN cc_start: 0.7592 (m-40) cc_final: 0.7350 (m110) REVERT: b 147 ARG cc_start: 0.6697 (ptm160) cc_final: 0.6375 (ptt90) REVERT: b 157 ASP cc_start: 0.8107 (p0) cc_final: 0.7628 (t0) REVERT: c 148 ARG cc_start: 0.4803 (OUTLIER) cc_final: 0.3493 (tpp80) REVERT: c 154 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6957 (mt-10) REVERT: c 168 TRP cc_start: 0.6915 (m100) cc_final: 0.6677 (m100) REVERT: c 276 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7243 (m-30) REVERT: c 318 MET cc_start: 0.7615 (mpp) cc_final: 0.7322 (mpm) REVERT: c 340 GLU cc_start: 0.4914 (tp30) cc_final: 0.4578 (tp30) outliers start: 59 outliers final: 33 residues processed: 270 average time/residue: 1.2238 time to fit residues: 366.3039 Evaluate side-chains 263 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 225 time to evaluate : 1.922 ------------------------------------------------------------------------------- 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 156 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 185 SER 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 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 241 MET Chi-restraints excluded: chain C residue 345 MET 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 307 LEU 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 148 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 89 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 70 optimal weight: 0.0770 chunk 102 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.3744 ------------------------------------------------------------------------------- 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 76 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 = 0.4243 r_free = 0.4243 target = 0.202598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.135014 restraints weight = 16524.293| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.96 r_work: 0.3283 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16544 Z= 0.167 Angle : 0.543 7.284 22462 Z= 0.285 Chirality : 0.043 0.137 2387 Planarity : 0.003 0.032 2862 Dihedral : 4.651 27.178 2166 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.66 % Allowed : 15.44 % Favored : 80.90 % 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: -1.35 (0.19), residues: 2022 helix: 1.57 (0.36), residues: 223 sheet: -1.75 (0.23), residues: 503 loop : -0.97 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 80 HIS 0.004 0.001 HIS c 195 PHE 0.015 0.001 PHE b 20 TYR 0.018 0.001 TYR c 256 ARG 0.004 0.000 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.03843 ( 423) hydrogen bonds : angle 5.36709 ( 1086) SS BOND : bond 0.00226 ( 30) SS BOND : angle 1.16025 ( 60) covalent geometry : bond 0.00406 (16514) covalent geometry : angle 0.54034 (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 296 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 232 time to evaluate : 1.925 Fit side-chains revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7351 (tt0) cc_final: 0.6845 (tt0) REVERT: A 81 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6752 (tt0) REVERT: A 102 ARG cc_start: 0.7633 (mmm-85) cc_final: 0.7204 (mmt90) REVERT: A 283 THR cc_start: 0.7865 (p) cc_final: 0.7537 (p) REVERT: A 314 ARG cc_start: 0.7202 (ttp-170) cc_final: 0.6848 (ttm-80) REVERT: B 31 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7344 (mm-40) REVERT: B 59 SER cc_start: 0.8863 (m) cc_final: 0.8624 (p) REVERT: B 70 GLN cc_start: 0.7143 (mt0) cc_final: 0.6740 (mp10) REVERT: B 76 ASN cc_start: 0.6173 (m-40) cc_final: 0.5835 (m110) REVERT: B 89 VAL cc_start: 0.7003 (t) cc_final: 0.6439 (m) REVERT: B 142 GLU cc_start: 0.6560 (pt0) cc_final: 0.5928 (tm-30) REVERT: B 147 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7549 (mtp85) REVERT: B 154 GLU cc_start: 0.7802 (pt0) cc_final: 0.7463 (pt0) REVERT: B 168 TRP cc_start: 0.7653 (m100) cc_final: 0.7363 (m100) REVERT: B 238 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7722 (mm-30) REVERT: B 274 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7519 (tp30) REVERT: C 12 GLU cc_start: 0.7022 (tt0) cc_final: 0.6408 (pm20) REVERT: C 14 LYS cc_start: 0.8133 (tptm) cc_final: 0.7822 (tptp) REVERT: C 23 ASP cc_start: 0.8151 (t0) cc_final: 0.7873 (t0) REVERT: C 62 ARG cc_start: 0.7156 (ppt170) cc_final: 0.6623 (ttp-110) REVERT: C 74 GLU cc_start: 0.6512 (mt-10) cc_final: 0.5965 (mp0) REVERT: C 101 LYS cc_start: 0.7077 (mptt) cc_final: 0.6427 (mppt) REVERT: C 177 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6755 (tt0) REVERT: C 214 LYS cc_start: 0.7546 (ptmm) cc_final: 0.7124 (pptt) REVERT: C 258 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6411 (tm-30) REVERT: C 274 GLU cc_start: 0.7406 (tp30) cc_final: 0.7167 (tp30) REVERT: a 30 GLU cc_start: 0.8255 (tt0) cc_final: 0.7629 (tt0) REVERT: a 74 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6343 (mp0) REVERT: a 101 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.7692 (mttt) REVERT: a 214 LYS cc_start: 0.8651 (mtmt) cc_final: 0.8260 (mtpp) REVERT: a 287 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.7981 (mm) REVERT: a 314 ARG cc_start: 0.6872 (ttm170) cc_final: 0.6397 (ttm170) REVERT: b 48 ASN cc_start: 0.7527 (m-40) cc_final: 0.7264 (m110) REVERT: b 147 ARG cc_start: 0.6502 (ptm160) cc_final: 0.6296 (mtm110) REVERT: b 157 ASP cc_start: 0.8110 (p0) cc_final: 0.7620 (t0) REVERT: c 154 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6861 (mt-10) REVERT: c 168 TRP cc_start: 0.6871 (m100) cc_final: 0.6655 (m100) REVERT: c 197 ASP cc_start: 0.8302 (p0) cc_final: 0.7951 (p0) REVERT: c 276 ASP cc_start: 0.7936 (m-30) cc_final: 0.7260 (m-30) REVERT: c 318 MET cc_start: 0.7618 (mpp) cc_final: 0.7339 (mpm) REVERT: c 340 GLU cc_start: 0.4790 (tp30) cc_final: 0.4497 (tp30) outliers start: 64 outliers final: 35 residues processed: 270 average time/residue: 1.2317 time to fit residues: 368.9568 Evaluate side-chains 271 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 230 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 185 SER 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 93 VAL 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 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 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 89 VAL 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 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 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: 8.9990 chunk 32 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 145 optimal weight: 0.8980 chunk 177 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN B 208 GLN C 254 HIS 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 = 0.4206 r_free = 0.4206 target = 0.198471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.131100 restraints weight = 16367.321| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.96 r_work: 0.3268 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 16544 Z= 0.297 Angle : 0.659 8.164 22462 Z= 0.345 Chirality : 0.047 0.191 2387 Planarity : 0.004 0.046 2862 Dihedral : 5.165 30.750 2166 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.27 % Favored : 92.68 % Rotamer: Outliers : 4.12 % Allowed : 16.70 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.18), residues: 2022 helix: 1.23 (0.35), residues: 225 sheet: -2.03 (0.22), residues: 508 loop : -1.17 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 330 HIS 0.005 0.002 HIS A 84 PHE 0.020 0.002 PHE b 20 TYR 0.021 0.002 TYR A 256 ARG 0.008 0.001 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.05191 ( 423) hydrogen bonds : angle 5.62336 ( 1086) SS BOND : bond 0.00259 ( 30) SS BOND : angle 1.29839 ( 60) covalent geometry : bond 0.00729 (16514) covalent geometry : angle 0.65667 (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 298 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 226 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7324 (tt0) cc_final: 0.6779 (tt0) REVERT: A 102 ARG cc_start: 0.7727 (mmm-85) cc_final: 0.7245 (mmt90) REVERT: A 283 THR cc_start: 0.7824 (p) cc_final: 0.7550 (p) REVERT: A 309 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8205 (p) REVERT: A 314 ARG cc_start: 0.7192 (ttp-170) cc_final: 0.6911 (ttm-80) REVERT: B 31 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7415 (mm-40) REVERT: B 59 SER cc_start: 0.8864 (m) cc_final: 0.8633 (p) REVERT: B 60 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8610 (p) REVERT: B 70 GLN cc_start: 0.7227 (mt0) cc_final: 0.6851 (mp10) REVERT: B 142 GLU cc_start: 0.6627 (pt0) cc_final: 0.6013 (tm-30) REVERT: B 146 GLU cc_start: 0.7317 (mp0) cc_final: 0.7090 (pm20) REVERT: B 147 ARG cc_start: 0.7810 (mtp85) cc_final: 0.7486 (mtp85) REVERT: B 154 GLU cc_start: 0.7816 (pt0) cc_final: 0.7533 (pt0) REVERT: B 274 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7636 (tp30) REVERT: C 12 GLU cc_start: 0.7014 (tt0) cc_final: 0.6262 (pm20) REVERT: C 14 LYS cc_start: 0.8264 (tptm) cc_final: 0.7952 (tptp) REVERT: C 62 ARG cc_start: 0.7293 (ppt170) cc_final: 0.6887 (ttp80) REVERT: C 74 GLU cc_start: 0.6572 (mt-10) cc_final: 0.6068 (mp0) REVERT: C 177 GLU cc_start: 0.7507 (mt-10) cc_final: 0.6677 (tt0) REVERT: C 190 ASP cc_start: 0.7961 (t0) cc_final: 0.7642 (t70) REVERT: C 214 LYS cc_start: 0.7532 (ptmm) cc_final: 0.7119 (pptt) REVERT: C 258 GLN cc_start: 0.7147 (OUTLIER) cc_final: 0.6222 (tm-30) REVERT: C 274 GLU cc_start: 0.7470 (tp30) cc_final: 0.7226 (tp30) REVERT: a 74 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6479 (mp0) REVERT: a 101 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.7684 (mttt) REVERT: a 314 ARG cc_start: 0.6771 (ttm170) cc_final: 0.6290 (ttm170) REVERT: b 147 ARG cc_start: 0.6484 (ptm160) cc_final: 0.5945 (mtm-85) REVERT: b 156 GLU cc_start: 0.7928 (tt0) cc_final: 0.7727 (tt0) REVERT: b 157 ASP cc_start: 0.8214 (p0) cc_final: 0.7629 (t0) REVERT: c 156 GLU cc_start: 0.8090 (pt0) cc_final: 0.7392 (tt0) REVERT: c 168 TRP cc_start: 0.6956 (m100) cc_final: 0.6752 (m100) REVERT: c 276 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7255 (m-30) REVERT: c 318 MET cc_start: 0.7660 (mpp) cc_final: 0.7386 (mpm) REVERT: c 340 GLU cc_start: 0.4874 (tp30) cc_final: 0.4561 (tp30) outliers start: 72 outliers final: 42 residues processed: 269 average time/residue: 1.2212 time to fit residues: 365.8174 Evaluate side-chains 266 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL 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 185 SER 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 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 60 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 93 VAL 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 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 a residue 60 THR Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 101 LYS Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 89 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 173 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 179 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.203695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.135647 restraints weight = 16446.284| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.02 r_work: 0.3297 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16544 Z= 0.100 Angle : 0.509 6.582 22462 Z= 0.269 Chirality : 0.042 0.131 2387 Planarity : 0.003 0.032 2862 Dihedral : 4.553 26.545 2166 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.75 % Favored : 95.20 % Rotamer: Outliers : 2.40 % Allowed : 18.98 % Favored : 78.62 % 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: -1.33 (0.19), residues: 2022 helix: 1.54 (0.36), residues: 224 sheet: -1.94 (0.23), residues: 497 loop : -0.86 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 150 HIS 0.005 0.001 HIS b 293 PHE 0.013 0.001 PHE a 277 TYR 0.019 0.001 TYR c 256 ARG 0.004 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03120 ( 423) hydrogen bonds : angle 5.20948 ( 1086) SS BOND : bond 0.00173 ( 30) SS BOND : angle 1.07962 ( 60) covalent geometry : bond 0.00230 (16514) covalent geometry : angle 0.50636 (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 277 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 235 time to evaluate : 1.680 Fit side-chains revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7725 (tt0) cc_final: 0.7151 (tt0) REVERT: A 146 GLU cc_start: 0.8009 (mp0) cc_final: 0.7464 (mp0) REVERT: A 272 LYS cc_start: 0.8851 (mttp) cc_final: 0.8424 (mtpm) REVERT: A 283 THR cc_start: 0.7982 (p) cc_final: 0.7658 (p) REVERT: A 347 LYS cc_start: 0.8711 (ptpp) cc_final: 0.8064 (pttt) REVERT: B 31 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7526 (mm-40) REVERT: B 70 GLN cc_start: 0.7346 (mt0) cc_final: 0.7048 (mp10) REVERT: B 89 VAL cc_start: 0.7172 (t) cc_final: 0.6594 (m) REVERT: B 142 GLU cc_start: 0.6624 (pt0) cc_final: 0.5985 (tm-30) REVERT: B 147 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7743 (mtp85) REVERT: B 154 GLU cc_start: 0.8021 (pt0) cc_final: 0.7760 (pt0) REVERT: B 274 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7789 (tp30) REVERT: C 12 GLU cc_start: 0.7140 (tt0) cc_final: 0.6505 (pm20) REVERT: C 14 LYS cc_start: 0.8253 (tptm) cc_final: 0.7890 (tptp) REVERT: C 23 ASP cc_start: 0.8196 (t0) cc_final: 0.7864 (t70) REVERT: C 62 ARG cc_start: 0.7479 (ppt170) cc_final: 0.6941 (ttp-110) REVERT: C 74 GLU cc_start: 0.6622 (mt-10) cc_final: 0.6053 (mp0) REVERT: C 101 LYS cc_start: 0.7167 (mptt) cc_final: 0.6539 (mppt) REVERT: C 177 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7055 (tt0) REVERT: C 214 LYS cc_start: 0.7741 (ptmm) cc_final: 0.7439 (pptt) REVERT: C 258 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6346 (tm-30) REVERT: C 274 GLU cc_start: 0.7549 (tp30) cc_final: 0.7303 (tp30) REVERT: a 74 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6550 (mp0) REVERT: a 214 LYS cc_start: 0.8657 (mtmt) cc_final: 0.8372 (mtpp) REVERT: a 314 ARG cc_start: 0.7032 (ttm170) cc_final: 0.6602 (ttm170) REVERT: b 147 ARG cc_start: 0.6821 (ptm160) cc_final: 0.6220 (mtm-85) REVERT: b 157 ASP cc_start: 0.8328 (p0) cc_final: 0.7845 (t0) REVERT: c 156 GLU cc_start: 0.8145 (pt0) cc_final: 0.7574 (tt0) REVERT: c 197 ASP cc_start: 0.8244 (p0) cc_final: 0.7955 (p0) REVERT: c 276 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7506 (m-30) REVERT: c 318 MET cc_start: 0.7672 (mpp) cc_final: 0.7407 (mpm) outliers start: 42 outliers final: 26 residues processed: 260 average time/residue: 1.2676 time to fit residues: 365.1750 Evaluate side-chains 247 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 1.680 ------------------------------------------------------------------------------- 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 185 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 276 ASP 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 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain a residue 70 GLN 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 348 SER Chi-restraints excluded: chain c residue 17 SER Chi-restraints excluded: chain c residue 65 ASN 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: 10.0000 chunk 30 optimal weight: 10.0000 chunk 200 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 184 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 142 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 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 = 0.4216 r_free = 0.4216 target = 0.199488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.130058 restraints weight = 16308.626| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.87 r_work: 0.3282 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16544 Z= 0.250 Angle : 0.622 7.710 22462 Z= 0.325 Chirality : 0.046 0.148 2387 Planarity : 0.004 0.038 2862 Dihedral : 4.919 29.637 2166 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.82 % Favored : 93.13 % Rotamer: Outliers : 3.66 % Allowed : 18.41 % Favored : 77.93 % 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: -1.57 (0.18), residues: 2022 helix: 1.28 (0.36), residues: 228 sheet: -1.97 (0.23), residues: 481 loop : -1.09 (0.17), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 168 HIS 0.006 0.001 HIS b 293 PHE 0.014 0.002 PHE c 277 TYR 0.019 0.002 TYR A 256 ARG 0.009 0.001 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.04621 ( 423) hydrogen bonds : angle 5.45349 ( 1086) SS BOND : bond 0.00247 ( 30) SS BOND : angle 1.17403 ( 60) covalent geometry : bond 0.00613 (16514) covalent geometry : angle 0.61961 (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 285 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 221 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7325 (tt0) cc_final: 0.6795 (tt0) REVERT: A 102 ARG cc_start: 0.7666 (mmm-85) cc_final: 0.7183 (mmt90) REVERT: A 146 GLU cc_start: 0.7945 (mp0) cc_final: 0.7321 (mp0) REVERT: A 283 THR cc_start: 0.7792 (p) cc_final: 0.7508 (p) REVERT: A 309 THR cc_start: 0.8416 (m) cc_final: 0.8116 (p) REVERT: A 314 ARG cc_start: 0.7226 (ttp-170) cc_final: 0.6854 (ttm-80) REVERT: A 347 LYS cc_start: 0.8642 (ptpp) cc_final: 0.7938 (pttt) REVERT: B 31 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7426 (mm-40) REVERT: B 70 GLN cc_start: 0.7302 (mt0) cc_final: 0.6918 (mp10) REVERT: B 142 GLU cc_start: 0.6686 (pt0) cc_final: 0.6036 (tm-30) REVERT: B 146 GLU cc_start: 0.7388 (mp0) cc_final: 0.7150 (pm20) REVERT: B 147 ARG cc_start: 0.7892 (mtp85) cc_final: 0.7554 (mtp85) REVERT: B 154 GLU cc_start: 0.7788 (pt0) cc_final: 0.7509 (pt0) REVERT: B 274 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7534 (tp30) REVERT: C 12 GLU cc_start: 0.6985 (tt0) cc_final: 0.6295 (pm20) REVERT: C 14 LYS cc_start: 0.8164 (tptm) cc_final: 0.7852 (tptp) REVERT: C 62 ARG cc_start: 0.7258 (ppt170) cc_final: 0.6633 (ttp-110) REVERT: C 74 GLU cc_start: 0.6546 (mt-10) cc_final: 0.5988 (mp0) REVERT: C 101 LYS cc_start: 0.7091 (mptt) cc_final: 0.6747 (mppt) REVERT: C 177 GLU cc_start: 0.7496 (mt-10) cc_final: 0.6727 (tt0) REVERT: C 190 ASP cc_start: 0.7913 (t0) cc_final: 0.7584 (t70) REVERT: C 214 LYS cc_start: 0.7534 (ptmm) cc_final: 0.7115 (pptt) REVERT: C 258 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.6118 (tm-30) REVERT: a 74 GLU cc_start: 0.6811 (mt-10) cc_final: 0.6365 (mp0) REVERT: a 214 LYS cc_start: 0.8686 (mtmt) cc_final: 0.7739 (mmmt) REVERT: a 314 ARG cc_start: 0.6780 (ttm170) cc_final: 0.6328 (ttm170) REVERT: b 96 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.7970 (t) REVERT: b 147 ARG cc_start: 0.6596 (ptm160) cc_final: 0.6052 (mtm-85) REVERT: b 156 GLU cc_start: 0.7923 (tt0) cc_final: 0.7678 (tt0) REVERT: b 157 ASP cc_start: 0.8151 (p0) cc_final: 0.7624 (t0) REVERT: c 156 GLU cc_start: 0.8067 (pt0) cc_final: 0.7471 (tt0) REVERT: c 276 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7239 (m-30) REVERT: c 318 MET cc_start: 0.7626 (mpp) cc_final: 0.7349 (mpm) outliers start: 64 outliers final: 41 residues processed: 261 average time/residue: 1.1964 time to fit residues: 347.8341 Evaluate side-chains 256 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 1.650 ------------------------------------------------------------------------------- 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 84 HIS Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 185 SER 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 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 93 VAL 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 93 VAL 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 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 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 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 241 MET 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: 0.9990 chunk 130 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 178 optimal weight: 20.0000 chunk 163 optimal weight: 5.9990 chunk 181 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.4250 r_free = 0.4250 target = 0.203402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.134327 restraints weight = 16334.864| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.87 r_work: 0.3324 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16544 Z= 0.107 Angle : 0.522 7.936 22462 Z= 0.275 Chirality : 0.042 0.152 2387 Planarity : 0.003 0.037 2862 Dihedral : 4.494 26.214 2166 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.90 % Favored : 95.05 % Rotamer: Outliers : 2.17 % Allowed : 20.13 % Favored : 77.70 % 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: -1.30 (0.19), residues: 2022 helix: 1.52 (0.37), residues: 225 sheet: -1.89 (0.23), residues: 493 loop : -0.85 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 168 HIS 0.006 0.001 HIS b 293 PHE 0.013 0.001 PHE B 277 TYR 0.019 0.001 TYR c 256 ARG 0.008 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03152 ( 423) hydrogen bonds : angle 5.16532 ( 1086) SS BOND : bond 0.00172 ( 30) SS BOND : angle 0.99916 ( 60) covalent geometry : bond 0.00251 (16514) covalent geometry : angle 0.52009 (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 257 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 219 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7646 (tt0) cc_final: 0.7171 (tt0) REVERT: A 146 GLU cc_start: 0.8018 (mp0) cc_final: 0.7394 (mp0) REVERT: A 272 LYS cc_start: 0.8819 (mttp) cc_final: 0.8365 (mtpm) REVERT: A 283 THR cc_start: 0.7941 (p) cc_final: 0.7617 (p) REVERT: A 347 LYS cc_start: 0.8722 (ptpp) cc_final: 0.8040 (pttt) REVERT: B 31 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7484 (mm-40) REVERT: B 70 GLN cc_start: 0.7325 (mt0) cc_final: 0.7046 (mp10) REVERT: B 89 VAL cc_start: 0.7184 (t) cc_final: 0.6637 (m) REVERT: B 142 GLU cc_start: 0.6662 (pt0) cc_final: 0.6051 (pp20) REVERT: B 146 GLU cc_start: 0.7396 (mp0) cc_final: 0.7178 (pt0) REVERT: B 147 ARG cc_start: 0.8123 (mtp85) cc_final: 0.7814 (mtp85) REVERT: B 154 GLU cc_start: 0.8002 (pt0) cc_final: 0.7751 (pt0) REVERT: B 213 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8090 (pt0) REVERT: B 274 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7696 (tp30) REVERT: C 12 GLU cc_start: 0.7152 (tt0) cc_final: 0.6532 (pm20) REVERT: C 14 LYS cc_start: 0.8201 (tptm) cc_final: 0.7835 (tptp) REVERT: C 74 GLU cc_start: 0.6625 (mt-10) cc_final: 0.6038 (mp0) REVERT: C 101 LYS cc_start: 0.7161 (mptt) cc_final: 0.6748 (mppt) REVERT: C 177 GLU cc_start: 0.7599 (mt-10) cc_final: 0.6896 (tt0) REVERT: C 214 LYS cc_start: 0.7724 (ptmm) cc_final: 0.7403 (pptt) REVERT: C 258 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6240 (tm-30) REVERT: a 74 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6472 (mp0) REVERT: a 214 LYS cc_start: 0.8612 (mtmt) cc_final: 0.8328 (mtpp) REVERT: a 314 ARG cc_start: 0.7019 (ttm170) cc_final: 0.6611 (ttm170) REVERT: b 50 HIS cc_start: 0.7100 (t-90) cc_final: 0.6842 (t-90) REVERT: b 147 ARG cc_start: 0.6804 (ptm160) cc_final: 0.6193 (mtm-85) REVERT: b 157 ASP cc_start: 0.8299 (p0) cc_final: 0.7865 (t0) REVERT: c 156 GLU cc_start: 0.8144 (pt0) cc_final: 0.7625 (tt0) REVERT: c 197 ASP cc_start: 0.8206 (p0) cc_final: 0.7860 (p0) REVERT: c 276 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7448 (m-30) REVERT: c 318 MET cc_start: 0.7658 (mpp) cc_final: 0.7407 (mpm) outliers start: 38 outliers final: 27 residues processed: 241 average time/residue: 1.1954 time to fit residues: 321.0199 Evaluate side-chains 243 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 1.693 ------------------------------------------------------------------------------- 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 185 SER 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 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 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 CYS Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 264 THR 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 346 VAL Chi-restraints excluded: chain c residue 17 SER Chi-restraints excluded: chain c residue 65 ASN 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: 8.9990 chunk 66 optimal weight: 0.0020 chunk 117 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.7394 ------------------------------------------------------------------------------- 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 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 = 0.4244 r_free = 0.4244 target = 0.202703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134424 restraints weight = 16402.478| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.90 r_work: 0.3330 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16544 Z= 0.135 Angle : 0.541 7.775 22462 Z= 0.282 Chirality : 0.043 0.139 2387 Planarity : 0.003 0.034 2862 Dihedral : 4.503 26.439 2166 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.44 % Favored : 94.51 % Rotamer: Outliers : 2.29 % Allowed : 20.18 % Favored : 77.53 % 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: -1.30 (0.19), residues: 2022 helix: 1.54 (0.37), residues: 225 sheet: -1.89 (0.23), residues: 497 loop : -0.85 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 168 HIS 0.007 0.001 HIS b 293 PHE 0.013 0.001 PHE B 277 TYR 0.018 0.001 TYR c 256 ARG 0.009 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 423) hydrogen bonds : angle 5.16702 ( 1086) SS BOND : bond 0.00177 ( 30) SS BOND : angle 1.00913 ( 60) covalent geometry : bond 0.00324 (16514) covalent geometry : angle 0.53900 (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 261 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7328 (tt0) cc_final: 0.6832 (tt0) REVERT: A 102 ARG cc_start: 0.7596 (mmm-85) cc_final: 0.7142 (mmt90) REVERT: A 146 GLU cc_start: 0.7967 (mp0) cc_final: 0.7262 (mp0) REVERT: A 272 LYS cc_start: 0.8738 (mttp) cc_final: 0.8108 (mtpm) REVERT: A 283 THR cc_start: 0.7738 (p) cc_final: 0.7405 (p) REVERT: A 314 ARG cc_start: 0.7257 (ttp-170) cc_final: 0.6948 (ttm-80) REVERT: A 347 LYS cc_start: 0.8610 (ptpp) cc_final: 0.7880 (pttt) REVERT: B 31 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7428 (mm-40) REVERT: B 70 GLN cc_start: 0.7236 (mt0) cc_final: 0.6884 (mp10) REVERT: B 89 VAL cc_start: 0.6928 (t) cc_final: 0.6628 (p) REVERT: B 142 GLU cc_start: 0.6829 (pt0) cc_final: 0.6118 (pp20) REVERT: B 146 GLU cc_start: 0.7359 (mp0) cc_final: 0.7131 (pt0) REVERT: B 147 ARG cc_start: 0.7962 (mtp85) cc_final: 0.7635 (mtp85) REVERT: B 154 GLU cc_start: 0.7820 (pt0) cc_final: 0.7532 (pt0) REVERT: B 274 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7469 (tp30) REVERT: C 12 GLU cc_start: 0.6985 (tt0) cc_final: 0.6326 (pm20) REVERT: C 14 LYS cc_start: 0.8105 (tptm) cc_final: 0.7739 (tptp) REVERT: C 62 ARG cc_start: 0.7246 (ppt170) cc_final: 0.6586 (ttp-110) REVERT: C 74 GLU cc_start: 0.6552 (mt-10) cc_final: 0.5972 (mp0) REVERT: C 101 LYS cc_start: 0.7033 (mptt) cc_final: 0.6619 (mppt) REVERT: C 177 GLU cc_start: 0.7457 (mt-10) cc_final: 0.6709 (tt0) REVERT: C 214 LYS cc_start: 0.7575 (ptmm) cc_final: 0.7164 (pptt) REVERT: C 258 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6077 (tm-30) REVERT: a 74 GLU cc_start: 0.6749 (mt-10) cc_final: 0.6279 (mp0) REVERT: a 214 LYS cc_start: 0.8604 (mtmt) cc_final: 0.8227 (mtpp) REVERT: a 287 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7929 (mm) REVERT: a 314 ARG cc_start: 0.6884 (ttm170) cc_final: 0.6444 (ttm170) REVERT: b 50 HIS cc_start: 0.6993 (t-90) cc_final: 0.6738 (t-90) REVERT: b 147 ARG cc_start: 0.6681 (ptm160) cc_final: 0.6104 (mtm-85) REVERT: b 157 ASP cc_start: 0.8127 (p0) cc_final: 0.7638 (t0) REVERT: c 156 GLU cc_start: 0.8039 (pt0) cc_final: 0.7520 (tt0) REVERT: c 197 ASP cc_start: 0.8228 (p0) cc_final: 0.7851 (p0) REVERT: c 276 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7238 (m-30) REVERT: c 318 MET cc_start: 0.7625 (mpp) cc_final: 0.7353 (mpm) outliers start: 40 outliers final: 32 residues processed: 247 average time/residue: 1.1818 time to fit residues: 323.9622 Evaluate side-chains 249 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 1.645 ------------------------------------------------------------------------------- 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 185 SER 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 324 LEU Chi-restraints excluded: chain A residue 340 GLU 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 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 CYS 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 287 ILE 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 346 VAL Chi-restraints excluded: chain c residue 17 SER Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 65 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 87 optimal weight: 0.0010 chunk 86 optimal weight: 0.6980 chunk 45 optimal weight: 20.0000 chunk 26 optimal weight: 0.5980 chunk 157 optimal weight: 0.9980 chunk 201 optimal weight: 20.0000 chunk 50 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 180 optimal weight: 20.0000 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 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 = 0.4274 r_free = 0.4274 target = 0.205984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.139574 restraints weight = 16407.152| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.00 r_work: 0.3313 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16544 Z= 0.090 Angle : 0.504 7.850 22462 Z= 0.263 Chirality : 0.042 0.144 2387 Planarity : 0.003 0.053 2862 Dihedral : 4.199 23.272 2166 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.90 % Favored : 95.05 % Rotamer: Outliers : 1.89 % Allowed : 20.93 % Favored : 77.19 % 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: -1.09 (0.19), residues: 2022 helix: 1.57 (0.37), residues: 225 sheet: -1.70 (0.23), residues: 533 loop : -0.66 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 28 HIS 0.008 0.001 HIS b 293 PHE 0.013 0.001 PHE a 277 TYR 0.019 0.001 TYR c 256 ARG 0.011 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.02711 ( 423) hydrogen bonds : angle 4.97167 ( 1086) SS BOND : bond 0.00144 ( 30) SS BOND : angle 0.91273 ( 60) covalent geometry : bond 0.00208 (16514) covalent geometry : angle 0.50250 (22402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13461.11 seconds wall clock time: 232 minutes 7.54 seconds (13927.54 seconds total)