Starting phenix.real_space_refine on Thu Jun 4 06:59:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w1z_65560/06_2026/9w1z_65560.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w1z_65560/06_2026/9w1z_65560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w1z_65560/06_2026/9w1z_65560.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w1z_65560/06_2026/9w1z_65560.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w1z_65560/06_2026/9w1z_65560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w1z_65560/06_2026/9w1z_65560.map" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 80 5.16 5 C 6944 2.51 5 N 1902 2.21 5 O 2062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10988 Number of models: 1 Model: "" Number of chains: 4 Chain: "a" Number of atoms: 2807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2807 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "b" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2687 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "B" Number of atoms: 2807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2807 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "A" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2687 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Time building chain proxies: 2.41, per 1000 atoms: 0.22 Number of scatterers: 10988 At special positions: 0 Unit cell: (104.676, 123.464, 87.901, 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 80 16.00 O 2062 8.00 N 1902 7.00 C 6944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, 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 291 " - pdb=" SG CYS a 312 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " 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 291 " - pdb=" SG CYS b 312 " 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 291 " - pdb=" SG CYS B 312 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " 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 291 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 472.7 milliseconds 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2560 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 21 sheets defined 19.3% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'a' and resid 27 through 31 Processing helix chain 'a' and resid 38 through 53 removed outlier: 3.684A pdb=" N ALA a 43 " --> pdb=" O PRO a 39 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER a 44 " --> pdb=" O SER a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 61 through 82 Proline residue: a 73 - end of helix 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 226 through 230 Processing helix chain 'a' and resid 244 through 248 Processing helix chain 'a' and resid 252 through 256 removed outlier: 3.828A pdb=" N TYR a 256 " --> pdb=" O GLN a 253 " (cutoff:3.500A) Processing helix chain 'a' and resid 341 through 345 removed outlier: 3.506A pdb=" N ASN a 344 " --> pdb=" O LYS a 341 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU a 345 " --> pdb=" O GLU a 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 341 through 345' Processing helix chain 'b' and resid 38 through 52 Processing helix chain 'b' and resid 61 through 82 removed outlier: 3.704A pdb=" N ASN b 65 " --> pdb=" O THR b 61 " (cutoff:3.500A) Proline residue: b 73 - end of helix 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 226 through 230 removed outlier: 3.573A pdb=" N HIS b 229 " --> pdb=" O PRO b 226 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR b 230 " --> pdb=" O LYS b 227 " (cutoff:3.500A) No H-bonds generated for '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 'b' and resid 252 through 256 removed outlier: 3.678A pdb=" N TYR b 256 " --> pdb=" O GLN b 253 " (cutoff:3.500A) Processing helix chain 'b' and resid 266 through 271 removed outlier: 4.402A pdb=" N HIS b 269 " --> pdb=" O GLY b 266 " (cutoff:3.500A) Processing helix chain 'b' and resid 341 through 345 removed outlier: 3.542A pdb=" N ASN b 344 " --> pdb=" O LYS b 341 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU b 345 " --> pdb=" O GLU b 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 341 through 345' Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 38 through 53 Processing helix chain 'B' and resid 61 through 82 removed outlier: 3.543A pdb=" N ASN B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) Proline residue: B 73 - end of helix 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 226 through 230 Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.529A pdb=" N ASN B 255 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR B 256 " --> pdb=" O GLN B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 256' Processing helix chain 'B' and resid 267 through 271 removed outlier: 3.503A pdb=" N GLY B 271 " --> pdb=" O TRP B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 345 removed outlier: 3.559A pdb=" N ASN B 344 " --> pdb=" O LYS B 341 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 345 " --> pdb=" O GLU B 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 341 through 345' Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.726A pdb=" N ALA A 43 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 82 removed outlier: 3.655A pdb=" N ASN A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) Proline residue: A 73 - end of helix 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 226 through 230 removed outlier: 3.608A pdb=" N HIS A 229 " --> pdb=" O PRO A 226 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 230 " --> pdb=" O LYS A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 230' Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.736A pdb=" N ALA A 248 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.716A pdb=" N TYR A 256 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.757A pdb=" N LEU A 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'a' and resid 20 through 22 removed outlier: 4.340A pdb=" N ILE b 19 " --> pdb=" O GLU b 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 32 through 36 removed outlier: 3.512A pdb=" N ILE a 167 " --> pdb=" O LYS a 33 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU a 169 " --> pdb=" O GLN a 35 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN a 166 " --> pdb=" O TYR a 158 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR a 158 " --> pdb=" O ASN a 166 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TRP a 168 " --> pdb=" O GLU a 156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 87 through 90 removed outlier: 6.618A pdb=" N THR a 87 " --> pdb=" O PHE a 133 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ILE a 135 " --> pdb=" O THR a 87 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N MET a 89 " --> pdb=" O ILE a 135 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 329 through 331 removed outlier: 3.503A pdb=" N LEU a 273 " --> pdb=" O PHE a 217 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE a 277 " --> pdb=" O GLU a 213 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N GLU a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLU a 203 " --> pdb=" O GLU a 213 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA a 215 " --> pdb=" O TRP a 201 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TRP a 201 " --> pdb=" O ALA a 215 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA a 193 " --> pdb=" O SER a 204 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER a 185 " --> pdb=" O ALA a 196 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 186 " --> pdb=" O ILE a 188 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TRP A 201 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA A 215 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLU A 203 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N GLU A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE A 277 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR A 323 " --> pdb=" O TRP A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 284 through 287 Processing sheet with id=AA7, first strand: chain 'b' and resid 32 through 36 removed outlier: 6.243A pdb=" N LYS b 33 " --> pdb=" O ILE b 167 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU b 169 " --> pdb=" O LYS b 33 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLN b 35 " --> pdb=" O LEU b 169 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N LEU b 171 " --> pdb=" O GLN b 35 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP b 157 " --> pdb=" O TRP b 168 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LYS b 170 " --> pdb=" O VAL b 155 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N VAL b 155 " --> pdb=" O LYS b 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 56 through 58 removed outlier: 6.875A pdb=" N GLY b 56 " --> pdb=" O ALA b 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'b' and resid 87 through 90 removed outlier: 6.400A pdb=" N THR b 87 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE b 135 " --> pdb=" O THR b 87 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N MET b 89 " --> pdb=" O ILE b 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'b' and resid 274 through 276 removed outlier: 3.549A pdb=" N LYS b 211 " --> pdb=" O ALA b 205 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLU b 203 " --> pdb=" O GLU b 213 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA b 215 " --> pdb=" O TRP b 201 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TRP b 201 " --> pdb=" O ALA b 215 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER B 185 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 193 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TRP B 201 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA B 215 " --> pdb=" O TRP B 201 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLU B 203 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N GLU B 213 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE B 277 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'b' and resid 285 through 287 removed outlier: 6.386A pdb=" N VAL b 286 " --> pdb=" O CYS b 313 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.680A pdb=" N LYS B 14 " --> pdb=" O VAL B 5 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 20 through 22 removed outlier: 3.717A pdb=" N ILE A 19 " --> pdb=" O GLU A 30 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 32 through 35 removed outlier: 3.608A pdb=" N ILE B 167 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN B 166 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N TYR B 158 " --> pdb=" O ASN B 166 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP B 168 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.962A pdb=" N GLY B 56 " --> pdb=" O ALA B 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.636A pdb=" N THR B 87 " --> pdb=" O PHE B 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 284 through 287 removed outlier: 6.470A pdb=" N THR B 284 " --> pdb=" O TRP B 311 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N CYS B 313 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL B 286 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 32 through 36 removed outlier: 3.788A pdb=" N LYS A 33 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP A 157 " --> pdb=" O TRP A 168 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LYS A 170 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL A 155 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 56 through 57 removed outlier: 6.622A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 88 through 90 removed outlier: 6.228A pdb=" N MET A 89 " --> pdb=" O ILE A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 285 through 287 removed outlier: 6.421A pdb=" N VAL A 286 " --> pdb=" O CYS A 313 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 660 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: 1.55 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3570 1.34 - 1.46: 2653 1.46 - 1.58: 4933 1.58 - 1.70: 0 1.70 - 1.82: 116 Bond restraints: 11272 Sorted by residual: bond pdb=" CA ASP a 208 " pdb=" CB ASP a 208 " ideal model delta sigma weight residual 1.530 1.550 -0.020 1.69e-02 3.50e+03 1.36e+00 bond pdb=" CA THR B 72 " pdb=" C THR B 72 " ideal model delta sigma weight residual 1.522 1.534 -0.012 1.26e-02 6.30e+03 9.52e-01 bond pdb=" CA ASP B 208 " pdb=" CB ASP B 208 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 8.12e-01 bond pdb=" C THR B 72 " pdb=" N PRO B 73 " ideal model delta sigma weight residual 1.335 1.347 -0.011 1.36e-02 5.41e+03 7.05e-01 bond pdb=" CA ASP B 208 " pdb=" C ASP B 208 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.34e-02 5.57e+03 6.72e-01 ... (remaining 11267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 15026 1.39 - 2.78: 211 2.78 - 4.17: 42 4.17 - 5.56: 5 5.56 - 6.95: 2 Bond angle restraints: 15286 Sorted by residual: angle pdb=" C LYS B 122 " pdb=" N MET B 123 " pdb=" CA MET B 123 " ideal model delta sigma weight residual 121.54 125.94 -4.40 1.91e+00 2.74e-01 5.30e+00 angle pdb=" CA ASP a 208 " pdb=" CB ASP a 208 " pdb=" CG ASP a 208 " ideal model delta sigma weight residual 112.60 114.90 -2.30 1.00e+00 1.00e+00 5.27e+00 angle pdb=" CA ASP B 208 " pdb=" CB ASP B 208 " pdb=" CG ASP B 208 " ideal model delta sigma weight residual 112.60 114.74 -2.14 1.00e+00 1.00e+00 4.59e+00 angle pdb=" N THR B 72 " pdb=" CA THR B 72 " pdb=" C THR B 72 " ideal model delta sigma weight residual 113.16 116.17 -3.01 1.42e+00 4.96e-01 4.48e+00 angle pdb=" C ASN B 207 " pdb=" N ASP B 208 " pdb=" CA ASP B 208 " ideal model delta sigma weight residual 121.54 125.55 -4.01 1.91e+00 2.74e-01 4.40e+00 ... (remaining 15281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 5609 17.19 - 34.39: 829 34.39 - 51.58: 256 51.58 - 68.78: 53 68.78 - 85.97: 14 Dihedral angle restraints: 6761 sinusoidal: 2797 harmonic: 3964 Sorted by residual: dihedral pdb=" CB CYS a 280 " pdb=" SG CYS a 280 " pdb=" SG CYS a 329 " pdb=" CB CYS a 329 " ideal model delta sinusoidal sigma weight residual -86.00 -169.03 83.03 1 1.00e+01 1.00e-02 8.44e+01 dihedral pdb=" CB CYS A 280 " pdb=" SG CYS A 280 " pdb=" SG CYS A 329 " pdb=" CB CYS A 329 " ideal model delta sinusoidal sigma weight residual -86.00 -166.82 80.82 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 312 " pdb=" CB CYS A 312 " ideal model delta sinusoidal sigma weight residual -86.00 -154.07 68.07 1 1.00e+01 1.00e-02 6.02e+01 ... (remaining 6758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1171 0.039 - 0.077: 343 0.077 - 0.116: 114 0.116 - 0.154: 17 0.154 - 0.193: 1 Chirality restraints: 1646 Sorted by residual: chirality pdb=" CA THR B 72 " pdb=" N THR B 72 " pdb=" C THR B 72 " pdb=" CB THR B 72 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" CA ILE a 243 " pdb=" N ILE a 243 " pdb=" C ILE a 243 " pdb=" CB ILE a 243 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE A 308 " pdb=" N ILE A 308 " pdb=" C ILE A 308 " pdb=" CB ILE A 308 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1643 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP a 208 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.78e+00 pdb=" C ASP a 208 " -0.034 2.00e-02 2.50e+03 pdb=" O ASP a 208 " 0.013 2.00e-02 2.50e+03 pdb=" N THR a 209 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP a 208 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.26e+00 pdb=" CG ASP a 208 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP a 208 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP a 208 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 208 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C ASP B 208 " 0.030 2.00e-02 2.50e+03 pdb=" O ASP B 208 " -0.011 2.00e-02 2.50e+03 pdb=" N THR B 209 " -0.010 2.00e-02 2.50e+03 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 977 2.74 - 3.28: 9496 3.28 - 3.82: 16318 3.82 - 4.36: 19784 4.36 - 4.90: 36712 Nonbonded interactions: 83287 Sorted by model distance: nonbonded pdb=" OG SER b 59 " pdb=" OD2 ASP b 136 " model vdw 2.204 3.040 nonbonded pdb=" O GLY b 266 " pdb=" OG SER b 348 " model vdw 2.216 3.040 nonbonded pdb=" O SER A 233 " pdb=" OG SER A 233 " model vdw 2.237 3.040 nonbonded pdb=" OG SER a 59 " pdb=" OD2 ASP a 136 " model vdw 2.250 3.040 nonbonded pdb=" O SER a 233 " pdb=" OG SER a 233 " model vdw 2.261 3.040 ... (remaining 83282 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 17 through 352) selection = (chain 'a' and resid 17 through 352) selection = chain 'b' } 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: 5.630 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.960 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 0.029 11293 Z= 0.098 Angle : 0.460 6.951 15328 Z= 0.243 Chirality : 0.041 0.193 1646 Planarity : 0.003 0.040 1944 Dihedral : 17.938 85.972 4138 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.81 % Allowed : 30.05 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.23), residues: 1368 helix: 2.59 (0.45), residues: 154 sheet: -1.50 (0.32), residues: 272 loop : -1.31 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 105 TYR 0.008 0.001 TYR A 323 PHE 0.008 0.001 PHE a 20 TRP 0.009 0.001 TRP A 225 HIS 0.004 0.000 HIS b 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (11272) covalent geometry : angle 0.45881 / 0.24 (15286) SS BOND : bond 0.00168 / 0.11 ( 21) SS BOND : angle 0.80506 / 0.48 ( 42) hydrogen bonds : bond 0.23290 / 15.77 ( 247) hydrogen bonds : angle 7.78409 / 5.54 ( 660) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 136 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: a 30 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7485 (mt-10) REVERT: a 105 ARG cc_start: 0.8020 (mtm-85) cc_final: 0.7269 (mtt-85) REVERT: a 110 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7915 (mt-10) REVERT: a 130 ASN cc_start: 0.7942 (t0) cc_final: 0.7454 (t0) REVERT: a 170 LYS cc_start: 0.7809 (ptmt) cc_final: 0.7287 (pttp) REVERT: b 112 LYS cc_start: 0.8454 (ptpt) cc_final: 0.7567 (pttm) REVERT: b 116 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8116 (mptt) REVERT: b 123 MET cc_start: 0.6473 (ttm) cc_final: 0.5527 (pmm) REVERT: b 321 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7232 (tt) REVERT: B 120 LYS cc_start: 0.7361 (mttt) cc_final: 0.7134 (mttp) REVERT: B 127 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6639 (tt0) REVERT: B 130 ASN cc_start: 0.6821 (t0) cc_final: 0.6556 (t0) REVERT: B 175 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7738 (pt0) REVERT: B 289 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8760 (tp30) REVERT: B 329 CYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8022 (t) REVERT: A 97 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7431 (mmm) REVERT: A 174 ARG cc_start: 0.7333 (mtm180) cc_final: 0.6456 (ptt-90) REVERT: A 219 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8578 (pt0) REVERT: A 326 GLU cc_start: 0.7575 (pm20) cc_final: 0.7327 (pm20) outliers start: 46 outliers final: 35 residues processed: 176 average time/residue: 0.1270 time to fit residues: 30.2680 Evaluate side-chains 175 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 40 SER Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 109 THR Chi-restraints excluded: chain a residue 123 MET Chi-restraints excluded: chain a residue 236 VAL Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain a residue 309 THR Chi-restraints excluded: chain a residue 331 TYR Chi-restraints excluded: chain b residue 59 SER Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 126 THR Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 166 ASN Chi-restraints excluded: chain b residue 185 SER Chi-restraints excluded: chain b residue 236 VAL Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain b residue 312 CYS Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 288 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 35 GLN a 65 ASN b 35 GLN B 47 GLN A 31 GLN A 344 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.126707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.090610 restraints weight = 12643.116| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.10 r_work: 0.2823 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 11293 Z= 0.227 Angle : 0.581 6.476 15328 Z= 0.305 Chirality : 0.045 0.199 1646 Planarity : 0.004 0.039 1944 Dihedral : 7.233 59.412 1531 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 6.13 % Allowed : 27.24 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.22), residues: 1368 helix: 2.46 (0.44), residues: 154 sheet: -1.13 (0.30), residues: 306 loop : -1.55 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 105 TYR 0.014 0.002 TYR b 32 PHE 0.012 0.001 PHE a 20 TRP 0.015 0.001 TRP A 225 HIS 0.004 0.001 HIS b 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.23 (11272) covalent geometry : angle 0.57848 / 0.30 (15286) SS BOND : bond 0.00262 / 0.19 ( 21) SS BOND : angle 1.17362 / 0.70 ( 42) hydrogen bonds : bond 0.04935 / 3.43 ( 247) hydrogen bonds : angle 5.53690 / 3.95 ( 660) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 125 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 24 ASN cc_start: 0.7812 (t0) cc_final: 0.7392 (t0) REVERT: a 63 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8255 (mp) REVERT: a 130 ASN cc_start: 0.8240 (t0) cc_final: 0.7761 (t0) REVERT: a 170 LYS cc_start: 0.8742 (ptmt) cc_final: 0.8400 (pttp) REVERT: b 112 LYS cc_start: 0.8625 (ptpt) cc_final: 0.8005 (pttm) REVERT: b 116 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8383 (mptt) REVERT: b 123 MET cc_start: 0.6518 (OUTLIER) cc_final: 0.5887 (pmm) REVERT: b 175 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7412 (tt0) REVERT: b 321 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8222 (tt) REVERT: B 24 ASN cc_start: 0.7526 (m-40) cc_final: 0.6871 (t0) REVERT: B 120 LYS cc_start: 0.8364 (mttt) cc_final: 0.8082 (mttp) REVERT: B 130 ASN cc_start: 0.7066 (t0) cc_final: 0.6862 (t0) REVERT: B 175 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7907 (pt0) REVERT: A 174 ARG cc_start: 0.7872 (mtm180) cc_final: 0.7027 (ptt-90) REVERT: A 326 GLU cc_start: 0.7812 (pm20) cc_final: 0.7577 (pm20) outliers start: 74 outliers final: 48 residues processed: 188 average time/residue: 0.1181 time to fit residues: 30.3671 Evaluate side-chains 179 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 126 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 123 MET Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 236 VAL Chi-restraints excluded: chain a residue 246 ASN Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 297 SER Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 331 TYR Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 351 THR Chi-restraints excluded: chain b residue 80 THR Chi-restraints excluded: chain b residue 123 MET Chi-restraints excluded: chain b residue 132 THR Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 175 GLN Chi-restraints excluded: chain b residue 181 SER Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 236 VAL Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain b residue 284 THR Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 345 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 42 optimal weight: 0.9990 chunk 125 optimal weight: 0.0000 chunk 105 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 35 GLN b 35 GLN b 175 GLN A 35 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.131041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.094184 restraints weight = 12662.917| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.17 r_work: 0.2749 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11293 Z= 0.098 Angle : 0.470 6.355 15328 Z= 0.250 Chirality : 0.041 0.183 1646 Planarity : 0.003 0.039 1944 Dihedral : 5.701 57.424 1493 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.81 % Allowed : 29.22 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.23), residues: 1368 helix: 2.61 (0.44), residues: 154 sheet: -1.19 (0.31), residues: 302 loop : -1.33 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 105 TYR 0.009 0.001 TYR A 323 PHE 0.009 0.001 PHE a 20 TRP 0.009 0.001 TRP A 225 HIS 0.004 0.001 HIS b 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (11272) covalent geometry : angle 0.46843 / 0.25 (15286) SS BOND : bond 0.00201 / 0.13 ( 21) SS BOND : angle 0.87809 / 0.51 ( 42) hydrogen bonds : bond 0.03319 / 2.29 ( 247) hydrogen bonds : angle 5.07499 / 3.62 ( 660) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 137 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: a 130 ASN cc_start: 0.8241 (t0) cc_final: 0.7782 (t0) REVERT: a 170 LYS cc_start: 0.8660 (ptmt) cc_final: 0.8292 (pttp) REVERT: b 23 ASP cc_start: 0.7927 (t70) cc_final: 0.7352 (t0) REVERT: b 112 LYS cc_start: 0.8632 (ptpt) cc_final: 0.7927 (pttm) REVERT: b 116 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8339 (mptt) REVERT: b 123 MET cc_start: 0.6537 (OUTLIER) cc_final: 0.5925 (pmm) REVERT: b 175 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: b 321 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7942 (tt) REVERT: B 24 ASN cc_start: 0.7454 (m-40) cc_final: 0.6801 (t0) REVERT: B 105 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7947 (mtt-85) REVERT: B 120 LYS cc_start: 0.8273 (mttt) cc_final: 0.7999 (mttp) REVERT: A 174 ARG cc_start: 0.7774 (mtm180) cc_final: 0.6979 (ptt-90) REVERT: A 326 GLU cc_start: 0.7802 (pm20) cc_final: 0.7601 (pm20) outliers start: 46 outliers final: 31 residues processed: 177 average time/residue: 0.1276 time to fit residues: 30.5259 Evaluate side-chains 167 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 123 MET Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 236 VAL Chi-restraints excluded: chain a residue 246 ASN Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 123 MET Chi-restraints excluded: chain b residue 132 THR Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 175 GLN Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 236 VAL Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain b residue 312 CYS Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 331 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 43 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 35 GLN b 175 GLN A 344 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.128623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.092767 restraints weight = 12731.518| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.17 r_work: 0.2758 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11293 Z= 0.163 Angle : 0.515 6.307 15328 Z= 0.271 Chirality : 0.043 0.185 1646 Planarity : 0.003 0.038 1944 Dihedral : 5.467 58.650 1487 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.46 % Allowed : 27.40 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.23), residues: 1368 helix: 2.62 (0.44), residues: 154 sheet: -1.16 (0.31), residues: 302 loop : -1.40 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG b 105 TYR 0.010 0.001 TYR A 323 PHE 0.012 0.001 PHE a 20 TRP 0.011 0.001 TRP A 225 HIS 0.004 0.001 HIS b 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.16 (11272) covalent geometry : angle 0.51314 / 0.27 (15286) SS BOND : bond 0.00220 / 0.16 ( 21) SS BOND : angle 0.96855 / 0.57 ( 42) hydrogen bonds : bond 0.03890 / 2.69 ( 247) hydrogen bonds : angle 5.03391 / 3.58 ( 660) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 129 time to evaluate : 0.466 Fit side-chains REVERT: a 24 ASN cc_start: 0.7837 (t0) cc_final: 0.7374 (t0) REVERT: a 63 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8209 (mp) REVERT: a 105 ARG cc_start: 0.8592 (mtm-85) cc_final: 0.7969 (mtt-85) REVERT: a 130 ASN cc_start: 0.8225 (t0) cc_final: 0.7766 (t0) REVERT: a 170 LYS cc_start: 0.8707 (ptmt) cc_final: 0.8362 (pttp) REVERT: b 23 ASP cc_start: 0.8006 (t70) cc_final: 0.7427 (t0) REVERT: b 112 LYS cc_start: 0.8643 (ptpt) cc_final: 0.7980 (pttm) REVERT: b 116 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8364 (mptt) REVERT: b 123 MET cc_start: 0.6517 (OUTLIER) cc_final: 0.5901 (pmm) REVERT: b 321 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7995 (tt) REVERT: B 24 ASN cc_start: 0.7470 (m-40) cc_final: 0.6807 (t0) REVERT: B 105 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8022 (mtt-85) REVERT: B 120 LYS cc_start: 0.8345 (mttt) cc_final: 0.8058 (mttp) REVERT: B 123 MET cc_start: 0.5748 (OUTLIER) cc_final: 0.5302 (ppp) REVERT: A 35 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7570 (mp10) REVERT: A 97 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8055 (mtm) REVERT: A 169 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8926 (mt) REVERT: A 174 ARG cc_start: 0.7827 (mtm180) cc_final: 0.7027 (ptt-90) outliers start: 66 outliers final: 39 residues processed: 185 average time/residue: 0.1237 time to fit residues: 31.1725 Evaluate side-chains 177 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 130 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 123 MET Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 236 VAL Chi-restraints excluded: chain a residue 246 ASN Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 297 SER Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 331 TYR Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 351 THR Chi-restraints excluded: chain b residue 123 MET Chi-restraints excluded: chain b residue 132 THR Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 175 GLN Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 236 VAL Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain b residue 312 CYS Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 331 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 27 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 45 optimal weight: 0.0470 chunk 121 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 26 HIS b 35 GLN b 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.091480 restraints weight = 12676.423| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.13 r_work: 0.2741 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11293 Z= 0.170 Angle : 0.522 6.260 15328 Z= 0.276 Chirality : 0.043 0.184 1646 Planarity : 0.003 0.039 1944 Dihedral : 5.551 58.716 1487 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 5.63 % Allowed : 26.90 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.23), residues: 1368 helix: 2.60 (0.44), residues: 154 sheet: -1.02 (0.32), residues: 292 loop : -1.46 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 105 TYR 0.011 0.001 TYR b 32 PHE 0.012 0.001 PHE a 20 TRP 0.012 0.001 TRP A 225 HIS 0.004 0.001 HIS b 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.17 (11272) covalent geometry : angle 0.52046 / 0.28 (15286) SS BOND : bond 0.00224 / 0.16 ( 21) SS BOND : angle 0.99957 / 0.59 ( 42) hydrogen bonds : bond 0.03941 / 2.74 ( 247) hydrogen bonds : angle 5.00225 / 3.56 ( 660) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 134 time to evaluate : 0.438 Fit side-chains REVERT: a 24 ASN cc_start: 0.7738 (t0) cc_final: 0.7267 (t0) REVERT: a 63 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8166 (mp) REVERT: a 105 ARG cc_start: 0.8585 (mtm-85) cc_final: 0.7922 (mtt-85) REVERT: a 130 ASN cc_start: 0.8230 (t0) cc_final: 0.7764 (t0) REVERT: a 170 LYS cc_start: 0.8686 (ptmt) cc_final: 0.8319 (pttp) REVERT: b 23 ASP cc_start: 0.7976 (t70) cc_final: 0.7388 (t0) REVERT: b 112 LYS cc_start: 0.8638 (ptpt) cc_final: 0.7996 (pttm) REVERT: b 116 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8342 (mptt) REVERT: b 123 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.5863 (pmm) REVERT: b 321 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8099 (tt) REVERT: B 24 ASN cc_start: 0.7434 (m-40) cc_final: 0.6738 (t0) REVERT: B 105 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7977 (mtt-85) REVERT: B 120 LYS cc_start: 0.8304 (mttt) cc_final: 0.8021 (mttp) REVERT: B 123 MET cc_start: 0.5760 (OUTLIER) cc_final: 0.5318 (ppp) REVERT: A 35 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7739 (mp10) REVERT: A 97 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8048 (mtm) REVERT: A 174 ARG cc_start: 0.7800 (mtm180) cc_final: 0.7013 (ptt-90) REVERT: A 219 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8697 (pt0) outliers start: 68 outliers final: 46 residues processed: 193 average time/residue: 0.1222 time to fit residues: 32.1236 Evaluate side-chains 184 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 130 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 123 MET Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 236 VAL Chi-restraints excluded: chain a residue 246 ASN Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 297 SER Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 331 TYR Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 351 THR Chi-restraints excluded: chain b residue 123 MET Chi-restraints excluded: chain b residue 132 THR Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 175 GLN Chi-restraints excluded: chain b residue 181 SER Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 236 VAL Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain b residue 312 CYS Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 331 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 126 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 123 optimal weight: 0.1980 chunk 52 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 69 optimal weight: 0.0770 chunk 19 optimal weight: 0.6980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 35 GLN b 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.129878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.094043 restraints weight = 12719.727| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.15 r_work: 0.2761 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11293 Z= 0.118 Angle : 0.490 6.637 15328 Z= 0.259 Chirality : 0.042 0.199 1646 Planarity : 0.003 0.039 1944 Dihedral : 5.431 57.691 1487 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.22 % Allowed : 27.48 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.23), residues: 1368 helix: 2.65 (0.44), residues: 154 sheet: -1.12 (0.31), residues: 306 loop : -1.37 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 105 TYR 0.009 0.001 TYR B 323 PHE 0.011 0.001 PHE a 20 TRP 0.010 0.001 TRP A 225 HIS 0.004 0.001 HIS b 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (11272) covalent geometry : angle 0.48814 / 0.26 (15286) SS BOND : bond 0.00183 / 0.13 ( 21) SS BOND : angle 0.94244 / 0.54 ( 42) hydrogen bonds : bond 0.03364 / 2.33 ( 247) hydrogen bonds : angle 4.85979 / 3.45 ( 660) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 138 time to evaluate : 0.417 Fit side-chains REVERT: a 63 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8171 (mp) REVERT: a 105 ARG cc_start: 0.8585 (mtm-85) cc_final: 0.7923 (mtt-85) REVERT: a 130 ASN cc_start: 0.8242 (t0) cc_final: 0.7765 (t0) REVERT: a 170 LYS cc_start: 0.8662 (ptmt) cc_final: 0.8297 (pttp) REVERT: b 23 ASP cc_start: 0.7922 (t70) cc_final: 0.7348 (t0) REVERT: b 112 LYS cc_start: 0.8636 (ptpt) cc_final: 0.7977 (pttm) REVERT: b 116 LYS cc_start: 0.8787 (mmtt) cc_final: 0.8346 (mptt) REVERT: b 123 MET cc_start: 0.6510 (OUTLIER) cc_final: 0.5879 (pmm) REVERT: b 238 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: b 321 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7973 (tt) REVERT: B 24 ASN cc_start: 0.7403 (m-40) cc_final: 0.6746 (t0) REVERT: B 105 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7984 (mtt-85) REVERT: B 120 LYS cc_start: 0.8301 (mttt) cc_final: 0.8009 (mttp) REVERT: B 123 MET cc_start: 0.5779 (OUTLIER) cc_final: 0.5333 (ppp) REVERT: A 35 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7820 (mp10) REVERT: A 97 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.7864 (mmm) REVERT: A 174 ARG cc_start: 0.7783 (mtm180) cc_final: 0.7016 (ptt-90) REVERT: A 219 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8658 (pt0) outliers start: 63 outliers final: 42 residues processed: 193 average time/residue: 0.1200 time to fit residues: 31.9949 Evaluate side-chains 185 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 134 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 123 MET Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 216 SER Chi-restraints excluded: chain a residue 236 VAL Chi-restraints excluded: chain a residue 246 ASN Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 297 SER Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 331 TYR Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain b residue 123 MET Chi-restraints excluded: chain b residue 132 THR Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 175 GLN Chi-restraints excluded: chain b residue 181 SER Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 236 VAL Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain b residue 312 CYS Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 331 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 41 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 128 optimal weight: 0.3980 chunk 101 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 57 optimal weight: 0.0570 chunk 30 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.8904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 35 GLN b 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.091715 restraints weight = 12788.378| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.12 r_work: 0.2695 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11293 Z= 0.196 Angle : 0.552 6.660 15328 Z= 0.291 Chirality : 0.044 0.202 1646 Planarity : 0.003 0.039 1944 Dihedral : 5.680 58.830 1487 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 5.71 % Allowed : 26.82 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.23), residues: 1368 helix: 2.56 (0.44), residues: 154 sheet: -0.98 (0.31), residues: 312 loop : -1.54 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 174 TYR 0.012 0.001 TYR b 32 PHE 0.013 0.001 PHE a 20 TRP 0.012 0.001 TRP A 225 HIS 0.004 0.001 HIS b 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.20 (11272) covalent geometry : angle 0.54911 / 0.29 (15286) SS BOND : bond 0.00243 / 0.18 ( 21) SS BOND : angle 1.14061 / 0.67 ( 42) hydrogen bonds : bond 0.04162 / 2.89 ( 247) hydrogen bonds : angle 4.98511 / 3.54 ( 660) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 126 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: a 30 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7580 (mt-10) REVERT: a 63 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8178 (mp) REVERT: a 130 ASN cc_start: 0.8228 (t0) cc_final: 0.7751 (t0) REVERT: a 170 LYS cc_start: 0.8701 (ptmt) cc_final: 0.8326 (pttp) REVERT: b 23 ASP cc_start: 0.7971 (t70) cc_final: 0.7363 (t0) REVERT: b 112 LYS cc_start: 0.8621 (ptpt) cc_final: 0.7993 (pttm) REVERT: b 116 LYS cc_start: 0.8795 (mmtt) cc_final: 0.8360 (mptt) REVERT: b 123 MET cc_start: 0.6472 (OUTLIER) cc_final: 0.5842 (pmm) REVERT: b 175 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7311 (tt0) REVERT: b 238 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: b 321 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8142 (tt) REVERT: B 24 ASN cc_start: 0.7423 (m-40) cc_final: 0.6754 (t0) REVERT: B 105 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8006 (mtt-85) REVERT: B 120 LYS cc_start: 0.8336 (mttt) cc_final: 0.8029 (mttp) REVERT: B 123 MET cc_start: 0.5843 (OUTLIER) cc_final: 0.5389 (ppp) REVERT: A 97 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8078 (mtm) REVERT: A 174 ARG cc_start: 0.7792 (mtm180) cc_final: 0.7012 (ptt-90) REVERT: A 219 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8703 (pt0) outliers start: 69 outliers final: 44 residues processed: 188 average time/residue: 0.1238 time to fit residues: 31.8586 Evaluate side-chains 176 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 123 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 123 MET Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 146 THR Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 216 SER Chi-restraints excluded: chain a residue 236 VAL Chi-restraints excluded: chain a residue 246 ASN Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 297 SER Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 331 TYR Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 351 THR Chi-restraints excluded: chain b residue 123 MET Chi-restraints excluded: chain b residue 132 THR Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 175 GLN Chi-restraints excluded: chain b residue 181 SER Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 236 VAL Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain b residue 312 CYS Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 35 GLN b 175 GLN A 35 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.130414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.094124 restraints weight = 12582.158| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.18 r_work: 0.2748 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11293 Z= 0.104 Angle : 0.483 6.666 15328 Z= 0.257 Chirality : 0.041 0.193 1646 Planarity : 0.003 0.039 1944 Dihedral : 5.434 57.106 1487 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.47 % Allowed : 28.23 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.23), residues: 1368 helix: 2.66 (0.45), residues: 154 sheet: -1.06 (0.32), residues: 302 loop : -1.37 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG b 174 TYR 0.009 0.001 TYR A 323 PHE 0.010 0.001 PHE a 20 TRP 0.010 0.001 TRP A 225 HIS 0.004 0.001 HIS b 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 (11272) covalent geometry : angle 0.48178 / 0.26 (15286) SS BOND : bond 0.00184 / 0.13 ( 21) SS BOND : angle 0.88568 / 0.53 ( 42) hydrogen bonds : bond 0.03156 / 2.18 ( 247) hydrogen bonds : angle 4.79045 / 3.40 ( 660) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 133 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: a 30 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7541 (mt-10) REVERT: a 130 ASN cc_start: 0.8240 (t0) cc_final: 0.7768 (t0) REVERT: a 170 LYS cc_start: 0.8601 (ptmt) cc_final: 0.8219 (pttp) REVERT: b 23 ASP cc_start: 0.7916 (t70) cc_final: 0.7344 (t0) REVERT: b 112 LYS cc_start: 0.8643 (ptpt) cc_final: 0.7948 (pttm) REVERT: b 116 LYS cc_start: 0.8795 (mmtt) cc_final: 0.8343 (mptt) REVERT: b 123 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.5859 (pmm) REVERT: b 175 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7256 (tt0) REVERT: b 238 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: b 321 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7888 (tt) REVERT: B 24 ASN cc_start: 0.7336 (m-40) cc_final: 0.6691 (t0) REVERT: B 105 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7988 (mtt-85) REVERT: B 120 LYS cc_start: 0.8305 (mttt) cc_final: 0.8003 (mttp) REVERT: B 123 MET cc_start: 0.5809 (OUTLIER) cc_final: 0.5383 (ppp) REVERT: A 97 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.7872 (mmm) REVERT: A 174 ARG cc_start: 0.7763 (mtm180) cc_final: 0.7006 (ptt-90) REVERT: A 219 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8664 (pt0) outliers start: 54 outliers final: 42 residues processed: 179 average time/residue: 0.1272 time to fit residues: 31.2484 Evaluate side-chains 184 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 134 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 123 MET Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 216 SER Chi-restraints excluded: chain a residue 236 VAL Chi-restraints excluded: chain a residue 246 ASN Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 297 SER Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 331 TYR Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 351 THR Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 123 MET Chi-restraints excluded: chain b residue 132 THR Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 175 GLN Chi-restraints excluded: chain b residue 181 SER Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 236 VAL Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain b residue 312 CYS Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 329 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 35 GLN b 175 GLN A 35 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.126998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.091210 restraints weight = 12609.513| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.11 r_work: 0.2721 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11293 Z= 0.222 Angle : 0.570 6.698 15328 Z= 0.300 Chirality : 0.045 0.203 1646 Planarity : 0.003 0.039 1944 Dihedral : 5.700 58.768 1487 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 5.05 % Allowed : 27.48 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.23), residues: 1368 helix: 2.55 (0.44), residues: 154 sheet: -0.90 (0.32), residues: 306 loop : -1.57 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG b 322 TYR 0.013 0.001 TYR b 32 PHE 0.013 0.001 PHE a 20 TRP 0.011 0.001 TRP A 225 HIS 0.004 0.001 HIS b 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.22 (11272) covalent geometry : angle 0.56743 / 0.30 (15286) SS BOND : bond 0.00266 / 0.20 ( 21) SS BOND : angle 1.19835 / 0.71 ( 42) hydrogen bonds : bond 0.04332 / 3.01 ( 247) hydrogen bonds : angle 4.97383 / 3.54 ( 660) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 126 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: a 30 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7666 (mt-10) REVERT: a 63 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8170 (mp) REVERT: a 130 ASN cc_start: 0.8230 (t0) cc_final: 0.7757 (t0) REVERT: a 170 LYS cc_start: 0.8694 (ptmt) cc_final: 0.8318 (pttp) REVERT: b 23 ASP cc_start: 0.7980 (t70) cc_final: 0.7374 (t0) REVERT: b 112 LYS cc_start: 0.8614 (ptpt) cc_final: 0.7988 (pttm) REVERT: b 116 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8358 (mptt) REVERT: b 123 MET cc_start: 0.6483 (OUTLIER) cc_final: 0.5850 (pmm) REVERT: b 175 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7357 (tt0) REVERT: b 238 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: b 321 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8152 (tt) REVERT: B 24 ASN cc_start: 0.7397 (m-40) cc_final: 0.6741 (t0) REVERT: B 105 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8003 (mtt-85) REVERT: B 120 LYS cc_start: 0.8332 (mttt) cc_final: 0.8035 (mttp) REVERT: B 123 MET cc_start: 0.5847 (OUTLIER) cc_final: 0.5379 (ppp) REVERT: B 289 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8621 (mm-30) REVERT: A 97 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8114 (mtm) REVERT: A 174 ARG cc_start: 0.7810 (mtm180) cc_final: 0.7025 (ptt-90) REVERT: A 219 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8722 (pt0) outliers start: 61 outliers final: 44 residues processed: 180 average time/residue: 0.1203 time to fit residues: 29.6396 Evaluate side-chains 177 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 124 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 123 MET Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 146 THR Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 216 SER Chi-restraints excluded: chain a residue 236 VAL Chi-restraints excluded: chain a residue 246 ASN Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 297 SER Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 331 TYR Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 351 THR Chi-restraints excluded: chain b residue 123 MET Chi-restraints excluded: chain b residue 132 THR Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 175 GLN Chi-restraints excluded: chain b residue 181 SER Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 236 VAL Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain b residue 312 CYS Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 329 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 23 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 11 optimal weight: 0.0370 chunk 91 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 35 GLN b 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.129087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.092730 restraints weight = 12632.473| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.18 r_work: 0.2826 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11293 Z= 0.135 Angle : 0.511 6.679 15328 Z= 0.271 Chirality : 0.042 0.195 1646 Planarity : 0.003 0.039 1944 Dihedral : 5.544 57.618 1487 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.47 % Allowed : 28.23 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.23), residues: 1368 helix: 2.60 (0.44), residues: 154 sheet: -0.84 (0.34), residues: 276 loop : -1.48 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 174 TYR 0.009 0.001 TYR B 323 PHE 0.011 0.001 PHE a 20 TRP 0.012 0.001 TRP A 225 HIS 0.004 0.001 HIS b 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.13 (11272) covalent geometry : angle 0.50936 / 0.27 (15286) SS BOND : bond 0.00210 / 0.15 ( 21) SS BOND : angle 0.99177 / 0.59 ( 42) hydrogen bonds : bond 0.03484 / 2.41 ( 247) hydrogen bonds : angle 4.85523 / 3.45 ( 660) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 132 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: a 30 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7705 (mt-10) REVERT: a 63 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8156 (mp) REVERT: a 130 ASN cc_start: 0.8240 (t0) cc_final: 0.7764 (t0) REVERT: a 170 LYS cc_start: 0.8686 (ptmt) cc_final: 0.8321 (pttp) REVERT: b 23 ASP cc_start: 0.7959 (t70) cc_final: 0.7361 (t0) REVERT: b 112 LYS cc_start: 0.8634 (ptpt) cc_final: 0.7967 (pttm) REVERT: b 116 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8344 (mptt) REVERT: b 123 MET cc_start: 0.6528 (OUTLIER) cc_final: 0.5865 (pmm) REVERT: b 175 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: b 238 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8417 (mt-10) REVERT: b 321 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7940 (tt) REVERT: B 24 ASN cc_start: 0.7327 (m-40) cc_final: 0.6685 (t0) REVERT: B 105 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7981 (mtt-85) REVERT: B 120 LYS cc_start: 0.8302 (mttt) cc_final: 0.7998 (mttp) REVERT: B 123 MET cc_start: 0.5796 (OUTLIER) cc_final: 0.5350 (ppp) REVERT: B 289 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8655 (mm-30) REVERT: A 97 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.7919 (mmm) REVERT: A 174 ARG cc_start: 0.7789 (mtm180) cc_final: 0.7029 (ptt-90) REVERT: A 219 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8717 (pt0) outliers start: 54 outliers final: 41 residues processed: 179 average time/residue: 0.1234 time to fit residues: 30.2952 Evaluate side-chains 176 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 126 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 123 MET Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 216 SER Chi-restraints excluded: chain a residue 236 VAL Chi-restraints excluded: chain a residue 246 ASN Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 297 SER Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 331 TYR Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 351 THR Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 123 MET Chi-restraints excluded: chain b residue 132 THR Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 175 GLN Chi-restraints excluded: chain b residue 181 SER Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 236 VAL Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain b residue 312 CYS Chi-restraints excluded: chain b residue 321 LEU Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 329 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 112 optimal weight: 0.0070 chunk 122 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 overall best weight: 1.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 35 GLN b 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.092462 restraints weight = 12659.848| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.21 r_work: 0.2713 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11293 Z= 0.160 Angle : 0.535 6.659 15328 Z= 0.284 Chirality : 0.043 0.197 1646 Planarity : 0.003 0.039 1944 Dihedral : 5.537 58.328 1486 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.47 % Allowed : 28.23 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.23), residues: 1368 helix: 2.57 (0.44), residues: 154 sheet: -0.85 (0.34), residues: 276 loop : -1.50 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG b 105 TYR 0.010 0.001 TYR b 32 PHE 0.012 0.001 PHE a 20 TRP 0.011 0.001 TRP A 225 HIS 0.004 0.001 HIS b 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 (11272) covalent geometry : angle 0.53315 / 0.28 (15286) SS BOND : bond 0.00219 / 0.16 ( 21) SS BOND : angle 1.05326 / 0.63 ( 42) hydrogen bonds : bond 0.03726 / 2.58 ( 247) hydrogen bonds : angle 4.86058 / 3.45 ( 660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2950.32 seconds wall clock time: 51 minutes 15.64 seconds (3075.64 seconds total)