Starting phenix.real_space_refine on Thu Jul 2 17:03:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vaw_64907/07_2026/9vaw_64907.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vaw_64907/07_2026/9vaw_64907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vaw_64907/07_2026/9vaw_64907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vaw_64907/07_2026/9vaw_64907.map" model { file = "/net/cci-nas-00/data/ceres_data/9vaw_64907/07_2026/9vaw_64907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vaw_64907/07_2026/9vaw_64907.cif" } resolution = 2.24 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= 0.005 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 62 5.16 5 C 5818 2.51 5 N 1555 2.21 5 O 1900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9335 Number of models: 1 Model: "" Number of chains: 11 Chain: "R" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2478 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 305} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 1836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1836 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 5, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2583 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 338, 2577 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 338, 2577 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 2616 Chain: "C" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 405 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1775 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "B" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Time building chain proxies: 2.36, per 1000 atoms: 0.25 Number of scatterers: 9335 At special positions: 0 Unit cell: (101.76, 125.08, 121.9, 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 62 16.00 O 1900 8.00 N 1555 7.00 C 5818 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.04 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.17 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: 1.04 Conformation dependent library (CDL) restraints added in 464.8 milliseconds 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2206 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 15 sheets defined 40.2% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'R' and resid 59 through 90 Processing helix chain 'R' and resid 100 through 127 removed outlier: 3.977A pdb=" N HIS R 104 " --> pdb=" O THR R 100 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 137 through 172 removed outlier: 3.618A pdb=" N TYR R 145 " --> pdb=" O CYS R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 180 Processing helix chain 'R' and resid 181 through 201 Processing helix chain 'R' and resid 201 through 206 removed outlier: 3.914A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 220 No H-bonds generated for 'chain 'R' and resid 218 through 220' Processing helix chain 'R' and resid 229 through 245 removed outlier: 3.608A pdb=" N VAL R 235 " --> pdb=" O ALA R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 273 Processing helix chain 'R' and resid 293 through 329 removed outlier: 3.500A pdb=" N ALA R 297 " --> pdb=" O GLY R 293 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 3.512A pdb=" N CYS R 327 " --> pdb=" O ARG R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 365 removed outlier: 3.501A pdb=" N HIS R 343 " --> pdb=" O TYR R 339 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET R 347 " --> pdb=" O HIS R 343 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR R 358 " --> pdb=" O TYR R 354 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 368 through 381 Processing helix chain 'A' and resid 12 through 37 removed outlier: 3.515A pdb=" N ARG A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 212 through 221 removed outlier: 4.454A pdb=" N ILE A 217 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N HIS A 218 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 246 through 261 Processing helix chain 'A' and resid 262 through 265 removed outlier: 3.581A pdb=" N GLN A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 275 through 283 removed outlier: 3.569A pdb=" N GLU A 281 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 316 removed outlier: 3.708A pdb=" N LEU A 316 " --> pdb=" O MET A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 45 Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 208 through 212 Processing sheet with id=AA1, first strand: chain 'R' and resid 207 through 211 Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 195 removed outlier: 6.473A pdb=" N LEU A 40 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL A 204 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU A 42 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N SER A 225 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LYS A 41 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N MET A 227 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU A 43 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU A 229 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU A 45 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N ALA A 231 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE A 226 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N PHE A 272 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE A 228 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASN A 274 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A 230 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.516A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.621A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.778A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.833A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.711A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.598A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.760A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.085A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.085A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.296A pdb=" N VAL D 135 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY D 213 " --> pdb=" O LEU D 233 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.296A pdb=" N VAL D 135 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY D 213 " --> pdb=" O LEU D 233 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR D 226 " --> pdb=" O GLN D 219 " (cutoff:3.500A) 487 hydrogen bonds defined for protein. 1364 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: 1.63 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2479 1.34 - 1.46: 2811 1.46 - 1.59: 3943 1.59 - 1.72: 0 1.72 - 1.84: 94 Bond restraints: 9327 Sorted by residual: bond pdb=" CA SER B 227 " pdb=" CB SER B 227 " ideal model delta sigma weight residual 1.535 1.491 0.044 1.32e-02 5.74e+03 1.09e+01 bond pdb=" CA SER B 122 " pdb=" CB SER B 122 " ideal model delta sigma weight residual 1.530 1.489 0.041 1.43e-02 4.89e+03 8.27e+00 bond pdb=" CA SER D 181 " pdb=" CB SER D 181 " ideal model delta sigma weight residual 1.536 1.496 0.040 1.46e-02 4.69e+03 7.61e+00 bond pdb=" CA SER A 22 " pdb=" CB SER A 22 " ideal model delta sigma weight residual 1.528 1.487 0.041 1.56e-02 4.11e+03 6.93e+00 bond pdb=" CA ALA B 240 " pdb=" CB ALA B 240 " ideal model delta sigma weight residual 1.533 1.493 0.040 1.65e-02 3.67e+03 5.83e+00 ... (remaining 9322 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 12473 3.28 - 6.56: 178 6.56 - 9.84: 5 9.84 - 13.12: 0 13.12 - 16.40: 1 Bond angle restraints: 12657 Sorted by residual: angle pdb=" CG ARG R 142 " pdb=" CD ARG R 142 " pdb=" NE ARG R 142 " ideal model delta sigma weight residual 112.00 95.60 16.40 2.20e+00 2.07e-01 5.56e+01 angle pdb=" CA ASP A 236 " pdb=" CB ASP A 236 " pdb=" CG ASP A 236 " ideal model delta sigma weight residual 112.60 117.48 -4.88 1.00e+00 1.00e+00 2.38e+01 angle pdb=" CA ASP B 333 " pdb=" CB ASP B 333 " pdb=" CG ASP B 333 " ideal model delta sigma weight residual 112.60 117.04 -4.44 1.00e+00 1.00e+00 1.97e+01 angle pdb=" CA PHE D 27 " pdb=" CB PHE D 27 " pdb=" CG PHE D 27 " ideal model delta sigma weight residual 113.80 118.18 -4.38 1.00e+00 1.00e+00 1.92e+01 angle pdb=" CA ASN B 340 " pdb=" CB ASN B 340 " pdb=" CG ASN B 340 " ideal model delta sigma weight residual 112.60 116.87 -4.27 1.00e+00 1.00e+00 1.82e+01 ... (remaining 12652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.12: 5046 16.12 - 32.25: 372 32.25 - 48.37: 69 48.37 - 64.50: 30 64.50 - 80.62: 8 Dihedral angle restraints: 5525 sinusoidal: 2107 harmonic: 3418 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 153.45 26.55 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA PHE D 32 " pdb=" C PHE D 32 " pdb=" N GLY D 33 " pdb=" CA GLY D 33 " ideal model delta harmonic sigma weight residual 180.00 155.76 24.24 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA ALA B 309 " pdb=" C ALA B 309 " pdb=" N GLY B 310 " pdb=" CA GLY B 310 " ideal model delta harmonic sigma weight residual -180.00 -157.94 -22.06 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 5522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 859 0.061 - 0.123: 480 0.123 - 0.184: 102 0.184 - 0.245: 6 0.245 - 0.307: 2 Chirality restraints: 1449 Sorted by residual: chirality pdb=" CG LEU D 162 " pdb=" CB LEU D 162 " pdb=" CD1 LEU D 162 " pdb=" CD2 LEU D 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA GLN B 75 " pdb=" N GLN B 75 " pdb=" C GLN B 75 " pdb=" CB GLN B 75 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA SER D 55 " pdb=" N SER D 55 " pdb=" C SER D 55 " pdb=" CB SER D 55 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1446 not shown) Planarity restraints: 1598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 142 " -0.390 9.50e-02 1.11e+02 1.79e-01 3.70e+01 pdb=" NE ARG R 142 " 0.048 2.00e-02 2.50e+03 pdb=" CZ ARG R 142 " -0.069 2.00e-02 2.50e+03 pdb=" NH1 ARG R 142 " 0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG R 142 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 110 " 0.050 2.00e-02 2.50e+03 3.20e-02 1.80e+01 pdb=" CG PHE D 110 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE D 110 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE D 110 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE D 110 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 110 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE D 110 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 103 " 0.037 2.00e-02 2.50e+03 2.43e-02 1.18e+01 pdb=" CG TYR D 103 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR D 103 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR D 103 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR D 103 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 103 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR D 103 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR D 103 " -0.001 2.00e-02 2.50e+03 ... (remaining 1595 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 284 2.67 - 3.23: 9348 3.23 - 3.78: 15621 3.78 - 4.34: 22494 4.34 - 4.90: 35577 Nonbonded interactions: 83324 Sorted by model distance: nonbonded pdb=" OH TYR B 124 " pdb=" O HOH B 401 " model vdw 2.112 3.040 nonbonded pdb=" O GLY B 131 " pdb=" O HOH B 402 " model vdw 2.128 3.040 nonbonded pdb=" OE2 GLU A 14 " pdb=" OH TYR D 163 " model vdw 2.244 3.040 nonbonded pdb=" O HOH A 423 " pdb=" O HOH D 350 " model vdw 2.257 3.040 nonbonded pdb=" O GLY D 112 " pdb=" OG SER D 172 " model vdw 2.257 3.040 ... (remaining 83319 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=0.50 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: 0.350 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.860 Find NCS groups from input model: 0.060 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:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0220 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 : 0.008 0.135 9329 Z= 0.499 Angle : 1.186 16.404 12661 Z= 0.797 Chirality : 0.070 0.307 1449 Planarity : 0.009 0.179 1598 Dihedral : 12.828 80.622 3313 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.78 % Rotamer: Outliers : 0.91 % Allowed : 4.77 % Favored : 94.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.59 (0.23), residues: 1151 helix: -1.53 (0.21), residues: 412 sheet: -0.19 (0.28), residues: 291 loop : -0.94 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.074 0.005 ARG R 142 TYR 0.052 0.006 TYR D 103 PHE 0.057 0.006 PHE D 110 TRP 0.038 0.008 TRP B 99 HIS 0.020 0.004 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00753 / 0.49 ( 9327) covalent geometry : angle 1.18134 / 0.80 (12657) SS BOND : bond 0.09570 / 6.83 ( 2) SS BOND : angle 5.87883 / 5.22 ( 4) hydrogen bonds : bond 0.17166 / 11.72 ( 480) hydrogen bonds : angle 7.51115 / 5.39 ( 1364) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 120 MET cc_start: -0.3361 (tpp) cc_final: -0.3865 (tpp) REVERT: A 24 MET cc_start: -0.0327 (mmm) cc_final: -0.3054 (tmt) REVERT: A 312 MET cc_start: 0.0710 (mtm) cc_final: 0.0299 (ptt) REVERT: B 118 ASP cc_start: 0.1718 (p0) cc_final: 0.1221 (t70) outliers start: 9 outliers final: 2 residues processed: 112 average time/residue: 0.5379 time to fit residues: 64.9452 Evaluate side-chains 75 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain C residue 40 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 57 ASN R 218 HIS ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 261 ASN R 269 GLN R 343 HIS A 218 HIS B 6 GLN B 32 GLN B 44 GLN B 176 GLN B 220 GLN B 259 GLN B 268 ASN B 293 ASN B 313 ASN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5209 r_free = 0.5209 target = 0.264142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5104 r_free = 0.5104 target = 0.240494 restraints weight = 62028.237| |-----------------------------------------------------------------------------| r_work (start): 0.4972 rms_B_bonded: 6.38 r_work (final): 0.4972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4973 r_free = 0.4973 target_work(ls_wunit_k1) = 0.233 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4973 r_free = 0.4973 target_work(ls_wunit_k1) = 0.233 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0615 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9329 Z= 0.145 Angle : 0.638 9.389 12661 Z= 0.339 Chirality : 0.044 0.197 1449 Planarity : 0.005 0.045 1598 Dihedral : 4.987 26.148 1283 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.91 % Allowed : 8.72 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.62 (0.24), residues: 1151 helix: 1.40 (0.24), residues: 424 sheet: 0.24 (0.30), residues: 283 loop : -0.33 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 148 TYR 0.020 0.002 TYR R 153 PHE 0.022 0.002 PHE R 205 TRP 0.032 0.002 TRP B 339 HIS 0.010 0.002 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 9327) covalent geometry : angle 0.63758 / 0.34 (12657) SS BOND : bond 0.00447 / 0.32 ( 2) SS BOND : angle 1.16176 / 0.88 ( 4) hydrogen bonds : bond 0.04442 / 2.97 ( 480) hydrogen bonds : angle 4.92734 / 3.62 ( 1364) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.324 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: R 55 ASP cc_start: 0.2151 (m-30) cc_final: 0.1325 (p0) REVERT: R 120 MET cc_start: -0.3563 (tpp) cc_final: -0.3884 (tpp) REVERT: A 24 MET cc_start: 0.0849 (mmm) cc_final: -0.3385 (tmt) REVERT: A 227 MET cc_start: -0.0037 (tpp) cc_final: -0.3295 (ptp) REVERT: A 246 ASN cc_start: 0.7169 (t0) cc_final: 0.6964 (t0) REVERT: A 312 MET cc_start: 0.1616 (mtm) cc_final: 0.0405 (ppp) REVERT: B 101 MET cc_start: 0.1825 (OUTLIER) cc_final: 0.1612 (tmt) REVERT: B 118 ASP cc_start: 0.2005 (p0) cc_final: 0.1754 (t70) REVERT: B 229 ILE cc_start: -0.0671 (mm) cc_final: -0.0925 (mm) outliers start: 9 outliers final: 2 residues processed: 91 average time/residue: 0.4409 time to fit residues: 43.9383 Evaluate side-chains 72 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 ASN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain D residue 45 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 57 ASN ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN C 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5205 r_free = 0.5205 target = 0.263412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5120 r_free = 0.5120 target = 0.242392 restraints weight = 46341.344| |-----------------------------------------------------------------------------| r_work (start): 0.4989 rms_B_bonded: 5.05 r_work (final): 0.4989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4989 r_free = 0.4989 target_work(ls_wunit_k1) = 0.235 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4989 r_free = 0.4989 target_work(ls_wunit_k1) = 0.235 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.4989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0920 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9329 Z= 0.144 Angle : 0.623 8.056 12661 Z= 0.325 Chirality : 0.043 0.206 1449 Planarity : 0.005 0.042 1598 Dihedral : 4.643 22.223 1277 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.32 % Allowed : 10.14 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.95 (0.25), residues: 1151 helix: 1.82 (0.25), residues: 427 sheet: 0.46 (0.31), residues: 268 loop : -0.34 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 60 TYR 0.019 0.002 TYR R 153 PHE 0.041 0.002 PHE B 292 TRP 0.026 0.002 TRP B 339 HIS 0.008 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 9327) covalent geometry : angle 0.62249 / 0.33 (12657) SS BOND : bond 0.00572 / 0.41 ( 2) SS BOND : angle 1.06725 / 0.80 ( 4) hydrogen bonds : bond 0.03866 / 2.60 ( 480) hydrogen bonds : angle 4.92380 / 3.61 ( 1364) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.201 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 120 MET cc_start: -0.2926 (tpp) cc_final: -0.3407 (tpp) REVERT: A 24 MET cc_start: 0.1243 (mmm) cc_final: -0.3472 (tmt) REVERT: A 57 LYS cc_start: 0.7720 (tppt) cc_final: 0.7502 (tttt) REVERT: A 227 MET cc_start: 0.0057 (tpp) cc_final: -0.3956 (pmm) REVERT: A 312 MET cc_start: 0.2119 (mtm) cc_final: 0.1133 (mpm) REVERT: B 229 ILE cc_start: 0.0506 (mm) cc_final: 0.0210 (mm) outliers start: 13 outliers final: 7 residues processed: 76 average time/residue: 0.3983 time to fit residues: 33.0760 Evaluate side-chains 66 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 44 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 67 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 72 optimal weight: 0.0470 chunk 74 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 98 optimal weight: 0.1980 chunk 104 optimal weight: 0.2980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 343 HIS A 287 HIS A 299 GLN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5206 r_free = 0.5206 target = 0.263017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5117 r_free = 0.5117 target = 0.242491 restraints weight = 45722.487| |-----------------------------------------------------------------------------| r_work (start): 0.5001 rms_B_bonded: 4.91 r_work (final): 0.5001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5001 r_free = 0.5001 target_work(ls_wunit_k1) = 0.236 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5001 r_free = 0.5001 target_work(ls_wunit_k1) = 0.236 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.5001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0815 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9329 Z= 0.110 Angle : 0.527 6.422 12661 Z= 0.281 Chirality : 0.041 0.148 1449 Planarity : 0.004 0.046 1598 Dihedral : 4.237 20.566 1277 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.62 % Allowed : 11.05 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.14 (0.25), residues: 1151 helix: 2.05 (0.25), residues: 426 sheet: 0.51 (0.31), residues: 269 loop : -0.28 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.013 0.001 TYR D 216 PHE 0.028 0.001 PHE B 292 TRP 0.028 0.002 TRP D 164 HIS 0.016 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 ( 9327) covalent geometry : angle 0.52675 / 0.28 (12657) SS BOND : bond 0.00411 / 0.29 ( 2) SS BOND : angle 0.90951 / 0.75 ( 4) hydrogen bonds : bond 0.03473 / 2.30 ( 480) hydrogen bonds : angle 4.64115 / 3.40 ( 1364) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.240 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 120 MET cc_start: -0.3009 (tpp) cc_final: -0.3488 (tpp) REVERT: A 24 MET cc_start: 0.0981 (mmm) cc_final: -0.3412 (tmt) REVERT: A 227 MET cc_start: 0.0181 (tpp) cc_final: -0.3552 (pmm) REVERT: B 229 ILE cc_start: 0.0363 (mm) cc_final: 0.0084 (mm) REVERT: B 262 MET cc_start: -0.2347 (OUTLIER) cc_final: -0.2759 (mtm) outliers start: 16 outliers final: 8 residues processed: 77 average time/residue: 0.4004 time to fit residues: 33.8342 Evaluate side-chains 72 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain D residue 143 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 66 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 111 optimal weight: 20.0000 chunk 73 optimal weight: 0.1980 chunk 101 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 95 optimal weight: 0.0970 chunk 4 optimal weight: 5.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 350 ASN A 327 HIS ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5205 r_free = 0.5205 target = 0.262570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5123 r_free = 0.5123 target = 0.243242 restraints weight = 40604.630| |-----------------------------------------------------------------------------| r_work (start): 0.5013 rms_B_bonded: 4.43 r_work (final): 0.5013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5012 r_free = 0.5012 target_work(ls_wunit_k1) = 0.238 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5012 r_free = 0.5012 target_work(ls_wunit_k1) = 0.238 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.5012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0945 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9329 Z= 0.119 Angle : 0.541 8.097 12661 Z= 0.286 Chirality : 0.041 0.150 1449 Planarity : 0.004 0.042 1598 Dihedral : 4.174 19.491 1277 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.83 % Allowed : 11.56 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 (0.25), residues: 1151 helix: 2.23 (0.25), residues: 420 sheet: 0.54 (0.30), residues: 275 loop : -0.25 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 30 TYR 0.023 0.002 TYR D 216 PHE 0.027 0.002 PHE B 292 TRP 0.039 0.002 TRP D 164 HIS 0.019 0.002 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 9327) covalent geometry : angle 0.54035 / 0.29 (12657) SS BOND : bond 0.00679 / 0.48 ( 2) SS BOND : angle 0.92345 / 0.76 ( 4) hydrogen bonds : bond 0.03413 / 2.25 ( 480) hydrogen bonds : angle 4.59281 / 3.37 ( 1364) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.318 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: R 99 SER cc_start: 0.4798 (p) cc_final: 0.4552 (p) REVERT: R 120 MET cc_start: -0.2617 (tpp) cc_final: -0.3162 (tpp) REVERT: A 227 MET cc_start: 0.0367 (tpp) cc_final: -0.3593 (pmm) REVERT: A 284 MET cc_start: 0.1934 (mtp) cc_final: 0.1622 (mtm) REVERT: A 312 MET cc_start: 0.2103 (mtm) cc_final: 0.1057 (mpm) REVERT: B 61 MET cc_start: -0.2146 (tpp) cc_final: -0.3587 (mtt) REVERT: B 229 ILE cc_start: 0.0579 (mm) cc_final: 0.0290 (mm) outliers start: 18 outliers final: 8 residues processed: 74 average time/residue: 0.3767 time to fit residues: 30.9852 Evaluate side-chains 70 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 143 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 30 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 37 optimal weight: 0.3980 chunk 102 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 0.0770 chunk 43 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5198 r_free = 0.5198 target = 0.261540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.5113 r_free = 0.5113 target = 0.241560 restraints weight = 44268.436| |-----------------------------------------------------------------------------| r_work (start): 0.5005 rms_B_bonded: 4.76 r_work (final): 0.5005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5006 r_free = 0.5006 target_work(ls_wunit_k1) = 0.236 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5006 r_free = 0.5006 target_work(ls_wunit_k1) = 0.236 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.5006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1062 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9329 Z= 0.119 Angle : 0.554 8.812 12661 Z= 0.292 Chirality : 0.041 0.147 1449 Planarity : 0.004 0.043 1598 Dihedral : 4.214 19.208 1277 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.93 % Allowed : 12.07 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.13 (0.25), residues: 1151 helix: 2.15 (0.25), residues: 420 sheet: 0.47 (0.30), residues: 272 loop : -0.36 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 49 TYR 0.019 0.001 TYR D 216 PHE 0.027 0.002 PHE B 292 TRP 0.037 0.002 TRP D 164 HIS 0.030 0.002 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 9327) covalent geometry : angle 0.55377 / 0.29 (12657) SS BOND : bond 0.00698 / 0.50 ( 2) SS BOND : angle 1.05463 / 0.87 ( 4) hydrogen bonds : bond 0.03515 / 2.31 ( 480) hydrogen bonds : angle 4.68185 / 3.42 ( 1364) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.319 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 99 SER cc_start: 0.4947 (p) cc_final: 0.4685 (p) REVERT: A 284 MET cc_start: 0.1751 (mtp) cc_final: 0.1524 (mtm) REVERT: A 312 MET cc_start: 0.2273 (mtm) cc_final: 0.0959 (mpm) REVERT: B 61 MET cc_start: -0.2199 (tpp) cc_final: -0.3595 (mtt) REVERT: B 229 ILE cc_start: 0.0893 (mm) cc_final: 0.0618 (mp) REVERT: D 200 PHE cc_start: -0.1177 (OUTLIER) cc_final: -0.3571 (m-80) outliers start: 19 outliers final: 7 residues processed: 83 average time/residue: 0.3678 time to fit residues: 33.3383 Evaluate side-chains 76 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 200 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5196 r_free = 0.5196 target = 0.261791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.5119 r_free = 0.5119 target = 0.241917 restraints weight = 47366.313| |-----------------------------------------------------------------------------| r_work (start): 0.5002 rms_B_bonded: 5.02 r_work (final): 0.5002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5008 r_free = 0.5008 target_work(ls_wunit_k1) = 0.236 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5008 r_free = 0.5008 target_work(ls_wunit_k1) = 0.236 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.5008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1236 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9329 Z= 0.132 Angle : 0.581 7.715 12661 Z= 0.306 Chirality : 0.042 0.136 1449 Planarity : 0.004 0.061 1598 Dihedral : 4.317 18.757 1277 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.72 % Allowed : 12.47 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.05 (0.25), residues: 1151 helix: 2.15 (0.25), residues: 419 sheet: 0.43 (0.31), residues: 273 loop : -0.47 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 148 TYR 0.021 0.002 TYR D 216 PHE 0.026 0.002 PHE B 292 TRP 0.051 0.002 TRP D 164 HIS 0.025 0.002 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 9327) covalent geometry : angle 0.58053 / 0.31 (12657) SS BOND : bond 0.00733 / 0.52 ( 2) SS BOND : angle 1.08665 / 0.87 ( 4) hydrogen bonds : bond 0.03535 / 2.29 ( 480) hydrogen bonds : angle 4.80653 / 3.50 ( 1364) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.320 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 99 SER cc_start: 0.4497 (p) cc_final: 0.4229 (p) REVERT: A 189 ILE cc_start: 0.5876 (OUTLIER) cc_final: 0.5670 (pp) REVERT: A 284 MET cc_start: 0.1659 (mtp) cc_final: 0.1421 (mtm) REVERT: A 312 MET cc_start: 0.2258 (mtm) cc_final: 0.0966 (mpm) REVERT: B 61 MET cc_start: -0.2053 (tpp) cc_final: -0.3555 (mtt) REVERT: B 101 MET cc_start: 0.2046 (OUTLIER) cc_final: 0.0103 (ttp) REVERT: B 229 ILE cc_start: 0.0992 (mm) cc_final: 0.0737 (mp) REVERT: D 93 MET cc_start: -0.0332 (mtm) cc_final: -0.0836 (mtm) outliers start: 17 outliers final: 6 residues processed: 84 average time/residue: 0.3841 time to fit residues: 35.3960 Evaluate side-chains 77 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain C residue 44 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 76 optimal weight: 0.2980 chunk 14 optimal weight: 0.0670 chunk 58 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 101 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 240 ASN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5196 r_free = 0.5196 target = 0.261364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.241432 restraints weight = 46702.197| |-----------------------------------------------------------------------------| r_work (start): 0.5001 rms_B_bonded: 4.99 r_work (final): 0.5001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5011 r_free = 0.5011 target_work(ls_wunit_k1) = 0.237 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5011 r_free = 0.5011 target_work(ls_wunit_k1) = 0.237 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.5011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1174 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9329 Z= 0.113 Angle : 0.567 8.163 12661 Z= 0.295 Chirality : 0.041 0.196 1449 Planarity : 0.005 0.078 1598 Dihedral : 4.241 17.902 1277 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.62 % Allowed : 13.39 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.10 (0.25), residues: 1151 helix: 2.19 (0.25), residues: 419 sheet: 0.50 (0.31), residues: 274 loop : -0.48 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 60 TYR 0.018 0.001 TYR D 216 PHE 0.027 0.002 PHE B 292 TRP 0.060 0.002 TRP D 164 HIS 0.011 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 9327) covalent geometry : angle 0.56724 / 0.29 (12657) SS BOND : bond 0.00663 / 0.47 ( 2) SS BOND : angle 1.09862 / 0.84 ( 4) hydrogen bonds : bond 0.03417 / 2.24 ( 480) hydrogen bonds : angle 4.69679 / 3.43 ( 1364) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.338 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 99 SER cc_start: 0.4494 (p) cc_final: 0.4025 (p) REVERT: R 249 MET cc_start: -0.4662 (ttt) cc_final: -0.4948 (mmm) REVERT: A 60 ARG cc_start: 0.6722 (mmm160) cc_final: 0.5207 (mmt180) REVERT: A 189 ILE cc_start: 0.5938 (OUTLIER) cc_final: 0.5737 (pp) REVERT: A 284 MET cc_start: 0.1757 (mtp) cc_final: 0.1507 (mtm) REVERT: B 61 MET cc_start: -0.1740 (tpp) cc_final: -0.3529 (mtt) REVERT: B 101 MET cc_start: 0.1892 (OUTLIER) cc_final: -0.0002 (ttp) REVERT: B 229 ILE cc_start: 0.0978 (mm) cc_final: 0.0709 (mp) outliers start: 16 outliers final: 8 residues processed: 81 average time/residue: 0.3782 time to fit residues: 33.7452 Evaluate side-chains 79 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 200 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 70 optimal weight: 0.9980 chunk 95 optimal weight: 0.3980 chunk 17 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 104 HIS R 320 HIS ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN C 44 HIS D 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5192 r_free = 0.5192 target = 0.260428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5134 r_free = 0.5134 target = 0.244423 restraints weight = 30318.152| |-----------------------------------------------------------------------------| r_work (start): 0.5038 rms_B_bonded: 3.36 r_work: 0.4978 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.4978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4959 r_free = 0.4959 target_work(ls_wunit_k1) = 0.231 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4959 r_free = 0.4959 target_work(ls_wunit_k1) = 0.231 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.4959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1566 moved from start: 0.6938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9329 Z= 0.183 Angle : 0.705 8.524 12661 Z= 0.373 Chirality : 0.045 0.220 1449 Planarity : 0.005 0.052 1598 Dihedral : 4.915 21.539 1277 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.93 % Allowed : 12.68 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.58 (0.25), residues: 1151 helix: 1.77 (0.25), residues: 417 sheet: 0.34 (0.31), residues: 274 loop : -0.85 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 60 TYR 0.023 0.002 TYR D 216 PHE 0.042 0.003 PHE R 205 TRP 0.066 0.003 TRP D 164 HIS 0.027 0.002 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 9327) covalent geometry : angle 0.70533 / 0.37 (12657) SS BOND : bond 0.00751 / 0.53 ( 2) SS BOND : angle 0.98905 / 0.79 ( 4) hydrogen bonds : bond 0.04093 / 2.69 ( 480) hydrogen bonds : angle 5.38722 / 3.91 ( 1364) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.346 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 99 SER cc_start: 0.4766 (p) cc_final: 0.4520 (p) REVERT: A 24 MET cc_start: 0.2138 (mmm) cc_final: 0.1401 (mtt) REVERT: A 284 MET cc_start: 0.2250 (mtp) cc_final: 0.1942 (mtm) REVERT: B 101 MET cc_start: 0.0853 (OUTLIER) cc_final: 0.0594 (ttp) REVERT: B 313 ASN cc_start: 0.5361 (OUTLIER) cc_final: 0.5076 (t0) outliers start: 19 outliers final: 10 residues processed: 83 average time/residue: 0.3882 time to fit residues: 35.6522 Evaluate side-chains 80 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 218 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 23 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 88 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 256 ASN R 343 HIS A 209 GLN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5177 r_free = 0.5177 target = 0.257906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5117 r_free = 0.5117 target = 0.242288 restraints weight = 30779.291| |-----------------------------------------------------------------------------| r_work (start): 0.5033 rms_B_bonded: 3.58 r_work: 0.4967 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.4967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4948 r_free = 0.4948 target_work(ls_wunit_k1) = 0.229 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4948 r_free = 0.4948 target_work(ls_wunit_k1) = 0.229 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.4948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1892 moved from start: 0.8146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 9329 Z= 0.250 Angle : 0.862 11.251 12661 Z= 0.452 Chirality : 0.050 0.327 1449 Planarity : 0.006 0.061 1598 Dihedral : 5.874 28.464 1277 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.13 % Favored : 94.78 % Rotamer: Outliers : 1.42 % Allowed : 13.49 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.29 (0.24), residues: 1151 helix: 1.14 (0.25), residues: 415 sheet: -0.05 (0.33), residues: 238 loop : -1.41 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 322 TYR 0.030 0.003 TYR D 216 PHE 0.042 0.004 PHE A 341 TRP 0.064 0.004 TRP D 164 HIS 0.018 0.002 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.25 ( 9327) covalent geometry : angle 0.86184 / 0.45 (12657) SS BOND : bond 0.00783 / 0.56 ( 2) SS BOND : angle 1.16895 / 0.81 ( 4) hydrogen bonds : bond 0.04997 / 3.30 ( 480) hydrogen bonds : angle 6.15414 / 4.46 ( 1364) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.327 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: R 99 SER cc_start: 0.4821 (p) cc_final: 0.4576 (p) REVERT: R 163 SER cc_start: 0.5448 (t) cc_final: 0.5207 (m) REVERT: A 24 MET cc_start: 0.2250 (mmm) cc_final: 0.1548 (mtt) REVERT: A 189 ILE cc_start: 0.6826 (OUTLIER) cc_final: 0.6375 (pp) REVERT: A 284 MET cc_start: 0.2919 (mtp) cc_final: 0.2640 (mtm) REVERT: B 101 MET cc_start: 0.1076 (OUTLIER) cc_final: 0.0840 (tpt) outliers start: 14 outliers final: 8 residues processed: 85 average time/residue: 0.3475 time to fit residues: 32.8816 Evaluate side-chains 82 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 200 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 79 optimal weight: 0.4980 chunk 74 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 50.0000 chunk 47 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 131 HIS R 343 HIS ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5182 r_free = 0.5182 target = 0.258456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.5113 r_free = 0.5113 target = 0.238302 restraints weight = 62869.512| |-----------------------------------------------------------------------------| r_work (start): 0.4990 rms_B_bonded: 6.24 r_work (final): 0.4990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4990 r_free = 0.4990 target_work(ls_wunit_k1) = 0.233 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4990 r_free = 0.4990 target_work(ls_wunit_k1) = 0.233 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.4990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1580 moved from start: 0.8093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9329 Z= 0.136 Angle : 0.678 10.716 12661 Z= 0.347 Chirality : 0.044 0.319 1449 Planarity : 0.005 0.038 1598 Dihedral : 5.031 22.073 1277 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.12 % Allowed : 14.50 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.14 (0.24), residues: 1151 helix: 1.42 (0.25), residues: 420 sheet: 0.06 (0.31), residues: 267 loop : -1.09 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 60 TYR 0.020 0.001 TYR D 216 PHE 0.038 0.002 PHE R 205 TRP 0.066 0.003 TRP D 164 HIS 0.008 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 9327) covalent geometry : angle 0.67777 / 0.35 (12657) SS BOND : bond 0.00625 / 0.44 ( 2) SS BOND : angle 1.19734 / 0.85 ( 4) hydrogen bonds : bond 0.03858 / 2.52 ( 480) hydrogen bonds : angle 5.45901 / 4.01 ( 1364) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4365.84 seconds wall clock time: 74 minutes 57.26 seconds (4497.26 seconds total)