Starting phenix.real_space_refine on Sat Aug 23 10:09:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gd9_29943/08_2025/8gd9_29943_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gd9_29943/08_2025/8gd9_29943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gd9_29943/08_2025/8gd9_29943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gd9_29943/08_2025/8gd9_29943.map" model { file = "/net/cci-nas-00/data/ceres_data/8gd9_29943/08_2025/8gd9_29943_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gd9_29943/08_2025/8gd9_29943_neut.cif" } resolution = 3.2 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= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5199 atoms to isotropic. 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 45 5.16 5 C 4670 2.51 5 N 1281 2.21 5 O 1313 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7309 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1603 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 9, 'GLN:plan1': 3, 'ARG:plan': 6, 'ASN:plan1': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 126 Chain: "B" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2430 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 222 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 13, 'GLN:plan1': 3, 'ARG:plan': 8, 'ASN:plan1': 3, 'HIS:plan': 1, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 138 Chain: "G" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 362 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "N" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 905 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 1979 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 5, 'GLN:plan1': 3, 'PHE:plan': 3, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 98 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'Z2C': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.62, per 1000 atoms: 0.22 Number of scatterers: 7309 At special positions: 0 Unit cell: (98.6, 115.6, 96.9, 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 45 16.00 O 1313 8.00 N 1281 7.00 C 4670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.05 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.05 Simple disulfide: pdb=" SG CYS R 92 " - pdb=" SG CYS R 170 " distance=2.05 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: 0.53 Conformation dependent library (CDL) restraints added in 383.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1910 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 11 sheets defined 40.1% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 removed outlier: 3.833A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.687A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.874A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 389 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.637A pdb=" N ARG B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 23 removed outlier: 3.528A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.559A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.790A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 44 removed outlier: 3.611A pdb=" N LYS R 44 " --> pdb=" O VAL R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 52 removed outlier: 3.732A pdb=" N GLU R 51 " --> pdb=" O GLU R 48 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR R 52 " --> pdb=" O GLN R 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 48 through 52' Processing helix chain 'R' and resid 53 through 83 removed outlier: 3.623A pdb=" N LEU R 57 " --> pdb=" O THR R 53 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU R 66 " --> pdb=" O ALA R 62 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL R 72 " --> pdb=" O GLY R 68 " (cutoff:3.500A) Proline residue: R 74 - end of helix removed outlier: 3.925A pdb=" N LYS R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 123 removed outlier: 3.604A pdb=" N PHE R 97 " --> pdb=" O GLU R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 131 Processing helix chain 'R' and resid 134 through 153 removed outlier: 3.586A pdb=" N ALA R 142 " --> pdb=" O LEU R 138 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE R 150 " --> pdb=" O SER R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 157 Processing helix chain 'R' and resid 178 through 221 removed outlier: 3.583A pdb=" N ALA R 182 " --> pdb=" O VAL R 178 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA R 189 " --> pdb=" O SER R 185 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS R 207 " --> pdb=" O ASN R 203 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA R 209 " --> pdb=" O LEU R 205 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG R 212 " --> pdb=" O GLY R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 298 Proline residue: R 287 - end of helix removed outlier: 3.779A pdb=" N LEU R 297 " --> pdb=" O PHE R 293 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR R 298 " --> pdb=" O VAL R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 309 through 319 removed outlier: 3.909A pdb=" N ILE R 315 " --> pdb=" O ASP R 311 " (cutoff:3.500A) Processing helix chain 'R' and resid 319 through 330 removed outlier: 4.274A pdb=" N ILE R 323 " --> pdb=" O SER R 319 " (cutoff:3.500A) Proline residue: R 326 - end of helix Processing helix chain 'R' and resid 333 through 341 removed outlier: 4.243A pdb=" N LEU R 337 " --> pdb=" O ARG R 333 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.602A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.699A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.867A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.987A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.647A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.954A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.525A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.629A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.778A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 162 through 163 374 hydrogen bonds defined for protein. 1083 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: 0.80 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1185 1.31 - 1.45: 2128 1.45 - 1.59: 4078 1.59 - 1.72: 2 1.72 - 1.86: 60 Bond restraints: 7453 Sorted by residual: bond pdb=" C8 Z2C R 501 " pdb=" C9 Z2C R 501 " ideal model delta sigma weight residual 1.566 1.310 0.256 2.00e-02 2.50e+03 1.64e+02 bond pdb=" C12 Z2C R 501 " pdb=" C6 Z2C R 501 " ideal model delta sigma weight residual 1.535 1.317 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C12 Z2C R 501 " pdb=" C8 Z2C R 501 " ideal model delta sigma weight residual 1.551 1.691 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" CA THR B 87 " pdb=" C THR B 87 " ideal model delta sigma weight residual 1.527 1.459 0.068 1.27e-02 6.20e+03 2.85e+01 bond pdb=" N ASN B 88 " pdb=" CA ASN B 88 " ideal model delta sigma weight residual 1.456 1.393 0.064 1.21e-02 6.83e+03 2.75e+01 ... (remaining 7448 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 9717 2.19 - 4.39: 363 4.39 - 6.58: 69 6.58 - 8.77: 19 8.77 - 10.97: 8 Bond angle restraints: 10176 Sorted by residual: angle pdb=" N LYS G 14 " pdb=" CA LYS G 14 " pdb=" C LYS G 14 " ideal model delta sigma weight residual 111.36 119.25 -7.89 1.09e+00 8.42e-01 5.24e+01 angle pdb=" N LYS R 334 " pdb=" CA LYS R 334 " pdb=" C LYS R 334 " ideal model delta sigma weight residual 111.71 120.03 -8.32 1.15e+00 7.56e-01 5.23e+01 angle pdb=" N ALA B 309 " pdb=" CA ALA B 309 " pdb=" C ALA B 309 " ideal model delta sigma weight residual 113.17 122.24 -9.07 1.26e+00 6.30e-01 5.19e+01 angle pdb=" N THR R 335 " pdb=" CA THR R 335 " pdb=" C THR R 335 " ideal model delta sigma weight residual 111.07 118.62 -7.55 1.07e+00 8.73e-01 4.98e+01 angle pdb=" N TYR A 358 " pdb=" CA TYR A 358 " pdb=" C TYR A 358 " ideal model delta sigma weight residual 111.28 120.41 -9.13 1.35e+00 5.49e-01 4.58e+01 ... (remaining 10171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 4028 17.35 - 34.71: 265 34.71 - 52.06: 55 52.06 - 69.41: 15 69.41 - 86.77: 5 Dihedral angle restraints: 4368 sinusoidal: 1418 harmonic: 2950 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 153.74 26.26 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ILE R 330 " pdb=" C ILE R 330 " pdb=" N LEU R 331 " pdb=" CA LEU R 331 " ideal model delta harmonic sigma weight residual 180.00 -157.93 -22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA HIS R 129 " pdb=" C HIS R 129 " pdb=" N TYR R 130 " pdb=" CA TYR R 130 " ideal model delta harmonic sigma weight residual -180.00 -161.23 -18.77 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 4365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1049 0.090 - 0.179: 146 0.179 - 0.269: 12 0.269 - 0.358: 4 0.358 - 0.448: 2 Chirality restraints: 1213 Sorted by residual: chirality pdb=" CA ASN R 35 " pdb=" N ASN R 35 " pdb=" C ASN R 35 " pdb=" CB ASN R 35 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" CA THR B 87 " pdb=" N THR B 87 " pdb=" C THR B 87 " pdb=" CB THR B 87 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA LYS G 14 " pdb=" N LYS G 14 " pdb=" C LYS G 14 " pdb=" CB LYS G 14 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 1210 not shown) Planarity restraints: 1296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS R 151 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C CYS R 151 " -0.059 2.00e-02 2.50e+03 pdb=" O CYS R 151 " 0.022 2.00e-02 2.50e+03 pdb=" N ALA R 152 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 185 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C SER R 185 " 0.055 2.00e-02 2.50e+03 pdb=" O SER R 185 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR R 186 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 85 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.79e+00 pdb=" C TYR B 85 " 0.051 2.00e-02 2.50e+03 pdb=" O TYR B 85 " -0.019 2.00e-02 2.50e+03 pdb=" N THR B 86 " -0.017 2.00e-02 2.50e+03 ... (remaining 1293 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1055 2.76 - 3.29: 6695 3.29 - 3.83: 11603 3.83 - 4.36: 13575 4.36 - 4.90: 24301 Nonbonded interactions: 57229 Sorted by model distance: nonbonded pdb=" O ASN R 321 " pdb=" OD2 ASP R 325 " model vdw 2.224 3.040 nonbonded pdb=" O LEU A 346 " pdb=" OG1 THR A 350 " model vdw 2.251 3.040 nonbonded pdb=" O GLY B 224 " pdb=" NH1 ARG B 251 " model vdw 2.336 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.348 3.040 nonbonded pdb=" O PHE N 29 " pdb=" NH2 ARG N 72 " model vdw 2.361 3.120 ... (remaining 57224 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.410 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 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 : 0.009 0.256 7456 Z= 0.498 Angle : 1.047 10.965 10182 Z= 0.637 Chirality : 0.064 0.448 1213 Planarity : 0.006 0.063 1296 Dihedral : 13.200 86.765 2449 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.30 % Allowed : 0.91 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.25), residues: 995 helix: 0.19 (0.26), residues: 371 sheet: -0.38 (0.34), residues: 229 loop : -1.73 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 150 TYR 0.019 0.002 TYR R 298 PHE 0.024 0.003 PHE A 246 TRP 0.022 0.003 TRP B 339 HIS 0.007 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00868 ( 7453) covalent geometry : angle 1.04086 (10176) SS BOND : bond 0.02197 ( 3) SS BOND : angle 4.89295 ( 6) hydrogen bonds : bond 0.16447 ( 374) hydrogen bonds : angle 6.21450 ( 1083) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8081 (tt) cc_final: 0.7878 (tp) REVERT: B 137 ARG cc_start: 0.7335 (tpp-160) cc_final: 0.7092 (tpp80) REVERT: B 239 ASN cc_start: 0.8148 (m110) cc_final: 0.7752 (m-40) REVERT: R 169 TRP cc_start: 0.8035 (p-90) cc_final: 0.7691 (p-90) REVERT: R 270 MET cc_start: 0.7692 (tpt) cc_final: 0.7390 (tpt) outliers start: 2 outliers final: 2 residues processed: 167 average time/residue: 0.0833 time to fit residues: 18.2524 Evaluate side-chains 158 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 88 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.0270 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 220 GLN R 216 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.129065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.108142 restraints weight = 10171.900| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.60 r_work: 0.3146 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7456 Z= 0.133 Angle : 0.539 5.537 10182 Z= 0.293 Chirality : 0.043 0.140 1213 Planarity : 0.004 0.054 1296 Dihedral : 5.914 54.788 1127 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.67 % Allowed : 8.83 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.27), residues: 995 helix: 1.49 (0.27), residues: 375 sheet: -0.12 (0.34), residues: 225 loop : -1.47 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 72 TYR 0.013 0.001 TYR A 339 PHE 0.014 0.002 PHE R 54 TRP 0.016 0.002 TRP B 339 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 7453) covalent geometry : angle 0.53832 (10176) SS BOND : bond 0.00306 ( 3) SS BOND : angle 0.86526 ( 6) hydrogen bonds : bond 0.04323 ( 374) hydrogen bonds : angle 4.36229 ( 1083) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8136 (tt) cc_final: 0.7874 (tp) REVERT: B 239 ASN cc_start: 0.8209 (m110) cc_final: 0.7799 (m-40) REVERT: B 291 ASP cc_start: 0.7608 (p0) cc_final: 0.7394 (p0) REVERT: B 329 THR cc_start: 0.8292 (p) cc_final: 0.7945 (m) REVERT: G 19 LEU cc_start: 0.7672 (mt) cc_final: 0.7305 (mp) REVERT: N 21 SER cc_start: 0.8308 (m) cc_final: 0.8029 (t) REVERT: R 27 MET cc_start: 0.6478 (mtp) cc_final: 0.6251 (mtp) outliers start: 11 outliers final: 8 residues processed: 178 average time/residue: 0.0812 time to fit residues: 18.9633 Evaluate side-chains 175 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 167 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 275 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.104894 restraints weight = 10174.993| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.55 r_work: 0.3132 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7456 Z= 0.147 Angle : 0.544 8.314 10182 Z= 0.291 Chirality : 0.043 0.154 1213 Planarity : 0.004 0.050 1296 Dihedral : 5.466 53.166 1124 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.83 % Allowed : 13.39 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.27), residues: 995 helix: 1.93 (0.27), residues: 378 sheet: 0.04 (0.34), residues: 228 loop : -1.20 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.014 0.001 TYR N 95 PHE 0.029 0.002 PHE N 108 TRP 0.015 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7453) covalent geometry : angle 0.54286 (10176) SS BOND : bond 0.00335 ( 3) SS BOND : angle 1.62846 ( 6) hydrogen bonds : bond 0.04325 ( 374) hydrogen bonds : angle 4.10775 ( 1083) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.271 Fit side-chains REVERT: A 211 LYS cc_start: 0.8191 (mmtm) cc_final: 0.7618 (mmtm) REVERT: A 220 HIS cc_start: 0.7679 (t-170) cc_final: 0.7319 (t-170) REVERT: B 239 ASN cc_start: 0.8163 (m110) cc_final: 0.7859 (m-40) REVERT: B 289 TYR cc_start: 0.8279 (m-80) cc_final: 0.7813 (m-80) REVERT: B 329 THR cc_start: 0.8256 (p) cc_final: 0.7912 (m) REVERT: N 21 SER cc_start: 0.8322 (m) cc_final: 0.8010 (t) REVERT: R 107 LEU cc_start: 0.8385 (tp) cc_final: 0.8086 (tp) outliers start: 12 outliers final: 9 residues processed: 166 average time/residue: 0.0779 time to fit residues: 17.0021 Evaluate side-chains 168 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 275 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 30 optimal weight: 0.0020 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 chunk 39 optimal weight: 0.9980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 181 HIS R 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.108364 restraints weight = 10346.590| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.59 r_work: 0.3180 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7456 Z= 0.107 Angle : 0.485 5.297 10182 Z= 0.262 Chirality : 0.041 0.139 1213 Planarity : 0.003 0.042 1296 Dihedral : 4.940 50.299 1124 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.98 % Allowed : 15.98 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.27), residues: 995 helix: 2.21 (0.27), residues: 383 sheet: 0.13 (0.35), residues: 229 loop : -1.15 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.012 0.001 TYR A 339 PHE 0.019 0.001 PHE R 54 TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 7453) covalent geometry : angle 0.48358 (10176) SS BOND : bond 0.00283 ( 3) SS BOND : angle 1.73511 ( 6) hydrogen bonds : bond 0.03601 ( 374) hydrogen bonds : angle 3.87354 ( 1083) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 220 HIS cc_start: 0.7658 (t-170) cc_final: 0.7382 (t70) REVERT: B 237 ASN cc_start: 0.8398 (p0) cc_final: 0.8190 (p0) REVERT: B 239 ASN cc_start: 0.8183 (m110) cc_final: 0.7822 (m-40) REVERT: B 289 TYR cc_start: 0.8262 (m-80) cc_final: 0.7791 (m-80) REVERT: B 291 ASP cc_start: 0.7501 (p0) cc_final: 0.7215 (p0) REVERT: B 329 THR cc_start: 0.8287 (p) cc_final: 0.7949 (m) REVERT: R 107 LEU cc_start: 0.8386 (tp) cc_final: 0.8054 (tp) REVERT: R 282 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7957 (mt) outliers start: 13 outliers final: 8 residues processed: 161 average time/residue: 0.0866 time to fit residues: 18.2301 Evaluate side-chains 170 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 218 MET Chi-restraints excluded: chain R residue 275 ILE Chi-restraints excluded: chain R residue 282 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 0.0050 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.106605 restraints weight = 10200.384| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.55 r_work: 0.3159 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7456 Z= 0.141 Angle : 0.517 6.066 10182 Z= 0.277 Chirality : 0.042 0.138 1213 Planarity : 0.004 0.043 1296 Dihedral : 4.999 48.990 1124 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.74 % Allowed : 17.50 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.27), residues: 995 helix: 2.31 (0.27), residues: 382 sheet: 0.24 (0.35), residues: 225 loop : -1.09 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.015 0.001 TYR N 95 PHE 0.018 0.002 PHE N 108 TRP 0.014 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7453) covalent geometry : angle 0.51546 (10176) SS BOND : bond 0.00405 ( 3) SS BOND : angle 1.77104 ( 6) hydrogen bonds : bond 0.04042 ( 374) hydrogen bonds : angle 3.87767 ( 1083) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8084 (mtm-85) cc_final: 0.7751 (mtm-85) REVERT: A 220 HIS cc_start: 0.7668 (t-170) cc_final: 0.7371 (t70) REVERT: B 291 ASP cc_start: 0.7517 (p0) cc_final: 0.7189 (p0) REVERT: B 329 THR cc_start: 0.8289 (p) cc_final: 0.7963 (m) REVERT: R 107 LEU cc_start: 0.8345 (tp) cc_final: 0.8038 (tp) outliers start: 18 outliers final: 14 residues processed: 167 average time/residue: 0.0835 time to fit residues: 18.4352 Evaluate side-chains 176 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 275 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 76 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 42 optimal weight: 0.0770 chunk 63 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.105406 restraints weight = 10142.154| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.53 r_work: 0.3148 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7456 Z= 0.131 Angle : 0.504 5.568 10182 Z= 0.271 Chirality : 0.042 0.138 1213 Planarity : 0.003 0.042 1296 Dihedral : 4.928 47.740 1124 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.20 % Allowed : 17.66 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.27), residues: 995 helix: 2.40 (0.27), residues: 382 sheet: 0.30 (0.35), residues: 225 loop : -1.03 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.014 0.001 TYR N 95 PHE 0.017 0.002 PHE R 54 TRP 0.014 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7453) covalent geometry : angle 0.50252 (10176) SS BOND : bond 0.00411 ( 3) SS BOND : angle 1.72937 ( 6) hydrogen bonds : bond 0.03913 ( 374) hydrogen bonds : angle 3.81344 ( 1083) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8085 (mtm-85) cc_final: 0.7719 (mtm-85) REVERT: A 220 HIS cc_start: 0.7669 (t-170) cc_final: 0.7401 (t70) REVERT: B 237 ASN cc_start: 0.8422 (p0) cc_final: 0.8137 (p0) REVERT: B 239 ASN cc_start: 0.8148 (m-40) cc_final: 0.7884 (m-40) REVERT: B 291 ASP cc_start: 0.7506 (p0) cc_final: 0.7181 (p0) REVERT: B 329 THR cc_start: 0.8244 (p) cc_final: 0.7942 (m) REVERT: N 21 SER cc_start: 0.8308 (m) cc_final: 0.7843 (p) REVERT: R 91 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6266 (tp) REVERT: R 107 LEU cc_start: 0.8374 (tp) cc_final: 0.8079 (tp) outliers start: 21 outliers final: 17 residues processed: 172 average time/residue: 0.0839 time to fit residues: 19.1016 Evaluate side-chains 181 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 275 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 32 optimal weight: 0.0980 chunk 93 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.127945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.107303 restraints weight = 10157.665| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.52 r_work: 0.3154 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7456 Z= 0.120 Angle : 0.490 5.344 10182 Z= 0.263 Chirality : 0.041 0.140 1213 Planarity : 0.003 0.043 1296 Dihedral : 4.800 44.751 1124 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.50 % Allowed : 17.20 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.27), residues: 995 helix: 2.49 (0.27), residues: 382 sheet: 0.34 (0.36), residues: 219 loop : -0.92 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.013 0.001 TYR N 95 PHE 0.017 0.002 PHE R 54 TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7453) covalent geometry : angle 0.48832 (10176) SS BOND : bond 0.00380 ( 3) SS BOND : angle 1.61819 ( 6) hydrogen bonds : bond 0.03751 ( 374) hydrogen bonds : angle 3.77336 ( 1083) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7642 (mtm-85) REVERT: A 220 HIS cc_start: 0.7654 (t-170) cc_final: 0.7386 (t70) REVERT: B 59 TYR cc_start: 0.7584 (OUTLIER) cc_final: 0.6882 (m-80) REVERT: B 150 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7909 (mmt180) REVERT: B 291 ASP cc_start: 0.7503 (p0) cc_final: 0.7197 (p0) REVERT: B 329 THR cc_start: 0.8229 (p) cc_final: 0.7933 (m) REVERT: N 21 SER cc_start: 0.8301 (m) cc_final: 0.7848 (p) REVERT: R 91 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.6208 (tp) REVERT: R 107 LEU cc_start: 0.8380 (tp) cc_final: 0.8110 (tp) outliers start: 23 outliers final: 18 residues processed: 168 average time/residue: 0.0852 time to fit residues: 18.7630 Evaluate side-chains 180 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 275 ILE Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 57 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 0.0370 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.128240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.107664 restraints weight = 10170.526| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.53 r_work: 0.3168 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7456 Z= 0.111 Angle : 0.482 5.310 10182 Z= 0.260 Chirality : 0.041 0.142 1213 Planarity : 0.003 0.043 1296 Dihedral : 4.725 43.195 1124 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.65 % Allowed : 17.96 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.27), residues: 995 helix: 2.57 (0.27), residues: 382 sheet: 0.41 (0.36), residues: 219 loop : -0.90 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.012 0.001 TYR N 95 PHE 0.018 0.001 PHE R 54 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7453) covalent geometry : angle 0.48039 (10176) SS BOND : bond 0.00365 ( 3) SS BOND : angle 1.47257 ( 6) hydrogen bonds : bond 0.03607 ( 374) hydrogen bonds : angle 3.73329 ( 1083) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7811 (mtm-85) REVERT: B 59 TYR cc_start: 0.7587 (OUTLIER) cc_final: 0.6955 (m-80) REVERT: B 150 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7891 (mmt180) REVERT: B 291 ASP cc_start: 0.7494 (p0) cc_final: 0.7178 (p0) REVERT: B 329 THR cc_start: 0.8216 (p) cc_final: 0.7934 (m) REVERT: R 91 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.6164 (tp) REVERT: R 107 LEU cc_start: 0.8381 (tp) cc_final: 0.8101 (tp) outliers start: 24 outliers final: 20 residues processed: 168 average time/residue: 0.0876 time to fit residues: 19.2308 Evaluate side-chains 183 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 218 MET Chi-restraints excluded: chain R residue 275 ILE Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 26 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.128504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.108018 restraints weight = 10042.686| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.51 r_work: 0.3186 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7456 Z= 0.123 Angle : 0.500 6.940 10182 Z= 0.267 Chirality : 0.042 0.155 1213 Planarity : 0.003 0.043 1296 Dihedral : 4.759 42.486 1124 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.11 % Allowed : 17.35 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.27), residues: 995 helix: 2.53 (0.27), residues: 384 sheet: 0.40 (0.36), residues: 219 loop : -0.91 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.013 0.001 TYR N 95 PHE 0.018 0.002 PHE R 54 TRP 0.013 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7453) covalent geometry : angle 0.49926 (10176) SS BOND : bond 0.00375 ( 3) SS BOND : angle 1.50495 ( 6) hydrogen bonds : bond 0.03734 ( 374) hydrogen bonds : angle 3.75384 ( 1083) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8051 (mtm-85) cc_final: 0.7766 (mtm-85) REVERT: B 59 TYR cc_start: 0.7586 (OUTLIER) cc_final: 0.6943 (m-80) REVERT: B 150 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7900 (mmt180) REVERT: B 291 ASP cc_start: 0.7484 (p0) cc_final: 0.7164 (p0) REVERT: B 329 THR cc_start: 0.8249 (p) cc_final: 0.7956 (m) REVERT: N 21 SER cc_start: 0.8301 (m) cc_final: 0.7837 (p) REVERT: R 91 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.6174 (tp) REVERT: R 107 LEU cc_start: 0.8335 (tp) cc_final: 0.8042 (tp) outliers start: 27 outliers final: 20 residues processed: 169 average time/residue: 0.0831 time to fit residues: 18.5265 Evaluate side-chains 182 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 275 ILE Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 42 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 chunk 45 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.126991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.106377 restraints weight = 10163.043| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.53 r_work: 0.3132 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7456 Z= 0.161 Angle : 0.552 9.583 10182 Z= 0.292 Chirality : 0.043 0.161 1213 Planarity : 0.004 0.044 1296 Dihedral : 4.995 44.139 1124 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.65 % Allowed : 18.11 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.27), residues: 995 helix: 2.42 (0.27), residues: 384 sheet: 0.42 (0.36), residues: 225 loop : -0.93 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.017 0.002 TYR N 95 PHE 0.018 0.002 PHE N 108 TRP 0.016 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 7453) covalent geometry : angle 0.55084 (10176) SS BOND : bond 0.00510 ( 3) SS BOND : angle 1.74208 ( 6) hydrogen bonds : bond 0.04189 ( 374) hydrogen bonds : angle 3.86428 ( 1083) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 274 ASP cc_start: 0.8337 (t0) cc_final: 0.8119 (t0) REVERT: B 59 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.6941 (m-80) REVERT: B 150 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7996 (mmt180) REVERT: B 291 ASP cc_start: 0.7535 (p0) cc_final: 0.7206 (p0) REVERT: B 329 THR cc_start: 0.8218 (p) cc_final: 0.7925 (m) REVERT: N 21 SER cc_start: 0.8285 (m) cc_final: 0.7849 (p) REVERT: R 91 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6287 (tp) REVERT: R 107 LEU cc_start: 0.8330 (tp) cc_final: 0.8051 (tp) outliers start: 24 outliers final: 19 residues processed: 170 average time/residue: 0.0859 time to fit residues: 19.1601 Evaluate side-chains 184 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 275 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 0.0670 chunk 64 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.127609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.107102 restraints weight = 10052.130| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.51 r_work: 0.3184 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7456 Z= 0.119 Angle : 0.513 9.074 10182 Z= 0.272 Chirality : 0.042 0.148 1213 Planarity : 0.003 0.045 1296 Dihedral : 4.852 42.579 1124 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.50 % Allowed : 18.11 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.27), residues: 995 helix: 2.51 (0.27), residues: 384 sheet: 0.40 (0.36), residues: 219 loop : -0.93 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.013 0.001 TYR N 95 PHE 0.018 0.002 PHE A 212 TRP 0.013 0.002 TRP A 234 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 7453) covalent geometry : angle 0.51207 (10176) SS BOND : bond 0.00375 ( 3) SS BOND : angle 1.47863 ( 6) hydrogen bonds : bond 0.03751 ( 374) hydrogen bonds : angle 3.78907 ( 1083) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1803.61 seconds wall clock time: 31 minutes 22.34 seconds (1882.34 seconds total)