Starting phenix.real_space_refine on Thu Jul 2 18:28:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vla_32022/07_2026/7vla_32022.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vla_32022/07_2026/7vla_32022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7vla_32022/07_2026/7vla_32022.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vla_32022/07_2026/7vla_32022.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vla_32022/07_2026/7vla_32022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vla_32022/07_2026/7vla_32022.map" model { file = "/net/cci-nas-00/data/ceres_data/7vla_32022/07_2026/7vla_32022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vla_32022/07_2026/7vla_32022.cif" } resolution = 2.7 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= 0.009 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 68 5.16 5 C 6192 2.51 5 N 1625 2.21 5 O 1790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 9675 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "L" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 485 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain: "R" Number of atoms: 2505 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 302, 2493 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 10, 'TRANS': 291} Conformer: "B" Number of residues, atoms: 302, 2493 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 10, 'TRANS': 291} bond proxies already assigned to first conformer: 2550 Chain: "S" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1795 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR R 291 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR R 291 " occ=0.50 Time building chain proxies: 1.87, per 1000 atoms: 0.19 Number of scatterers: 9675 At special positions: 0 Unit cell: (109.512, 135.876, 131.82, 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 68 16.00 O 1790 8.00 N 1625 7.00 C 6192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS L 32 " - pdb=" SG CYS L 56 " distance=2.03 Simple disulfide: pdb=" SG CYS L 33 " - pdb=" SG CYS L 72 " distance=2.02 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 83 " distance=2.03 Simple disulfide: pdb=" SG CYS R 24 " - pdb=" SG CYS R 273 " distance=2.03 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 288.1 milliseconds 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2292 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 15 sheets defined 39.1% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.760A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.859A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.870A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.515A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.531A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.607A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'L' and resid 42 through 46 removed outlier: 3.831A pdb=" N MET L 46 " --> pdb=" O CYS L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 84 Processing helix chain 'L' and resid 85 through 87 No H-bonds generated for 'chain 'L' and resid 85 through 87' Processing helix chain 'R' and resid 26 through 62 removed outlier: 3.598A pdb=" N GLN R 35 " --> pdb=" O ALA R 31 " (cutoff:3.500A) Proline residue: R 38 - end of helix removed outlier: 4.187A pdb=" N LEU R 43 " --> pdb=" O PRO R 39 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR R 62 " --> pdb=" O VAL R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 97 removed outlier: 3.531A pdb=" N LEU R 87 " --> pdb=" O PHE R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 140 through 145 removed outlier: 3.613A pdb=" N ALA R 144 " --> pdb=" O PHE R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 165 Processing helix chain 'R' and resid 165 through 172 removed outlier: 3.503A pdb=" N LEU R 169 " --> pdb=" O SER R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 208 Processing helix chain 'R' and resid 208 through 227 Processing helix chain 'R' and resid 231 through 264 Proline residue: R 254 - end of helix removed outlier: 3.719A pdb=" N PHE R 264 " --> pdb=" O LEU R 260 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 269 removed outlier: 3.571A pdb=" N PHE R 269 " --> pdb=" O GLN R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 292 Processing helix chain 'R' and resid 292 through 302 Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 305 through 318 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.260A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.504A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.638A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.809A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.863A 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: 3.542A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.913A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.164A 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: 6.410A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.545A 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: 3.694A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 48 through 51 removed outlier: 3.609A pdb=" N SER L 48 " --> pdb=" O LEU L 64 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA L 73 " --> pdb=" O VAL L 61 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 173 through 177 Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.692A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.310A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148 removed outlier: 5.009A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG S 191 " --> pdb=" O ASN S 194 " (cutoff:3.500A) 507 hydrogen bonds defined for protein. 1399 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: 1.18 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2529 1.33 - 1.45: 1942 1.45 - 1.57: 5320 1.57 - 1.70: 2 1.70 - 1.82: 96 Bond restraints: 9889 Sorted by residual: bond pdb=" N CYS R 273 " pdb=" CA CYS R 273 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 7.37e+00 bond pdb=" C TYR R 170 " pdb=" N PHE R 171 " ideal model delta sigma weight residual 1.332 1.369 -0.036 1.36e-02 5.41e+03 7.17e+00 bond pdb=" C16 CLR R 401 " pdb=" C17 CLR R 401 " ideal model delta sigma weight residual 1.554 1.603 -0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" C LEU R 87 " pdb=" O LEU R 87 " ideal model delta sigma weight residual 1.244 1.221 0.023 9.80e-03 1.04e+04 5.42e+00 bond pdb=" C23 CLR R 401 " pdb=" C24 CLR R 401 " ideal model delta sigma weight residual 1.525 1.571 -0.046 2.00e-02 2.50e+03 5.40e+00 ... (remaining 9884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 12909 2.05 - 4.11: 412 4.11 - 6.16: 53 6.16 - 8.22: 15 8.22 - 10.27: 3 Bond angle restraints: 13392 Sorted by residual: angle pdb=" N GLU R 274 " pdb=" CA GLU R 274 " pdb=" C GLU R 274 " ideal model delta sigma weight residual 114.12 104.40 9.72 1.39e+00 5.18e-01 4.89e+01 angle pdb=" N SER B 245 " pdb=" CA SER B 245 " pdb=" C SER B 245 " ideal model delta sigma weight residual 109.14 119.41 -10.27 1.49e+00 4.50e-01 4.75e+01 angle pdb=" N LYS S 43 " pdb=" CA LYS S 43 " pdb=" C LYS S 43 " ideal model delta sigma weight residual 111.74 118.64 -6.90 1.35e+00 5.49e-01 2.61e+01 angle pdb=" N CYS B 250 " pdb=" CA CYS B 250 " pdb=" C CYS B 250 " ideal model delta sigma weight residual 110.17 102.28 7.89 1.61e+00 3.86e-01 2.40e+01 angle pdb=" N LYS B 209 " pdb=" CA LYS B 209 " pdb=" C LYS B 209 " ideal model delta sigma weight residual 108.34 115.74 -7.40 1.64e+00 3.72e-01 2.04e+01 ... (remaining 13387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 5390 16.67 - 33.34: 395 33.34 - 50.01: 64 50.01 - 66.67: 17 66.67 - 83.34: 10 Dihedral angle restraints: 5876 sinusoidal: 2320 harmonic: 3556 Sorted by residual: dihedral pdb=" CB CYS L 43 " pdb=" SG CYS L 43 " pdb=" SG CYS L 83 " pdb=" CB CYS L 83 " ideal model delta sinusoidal sigma weight residual -86.00 -35.13 -50.87 1 1.00e+01 1.00e-02 3.54e+01 dihedral pdb=" CA GLU R 177 " pdb=" C GLU R 177 " pdb=" N PHE R 178 " pdb=" CA PHE R 178 " ideal model delta harmonic sigma weight residual 180.00 150.94 29.06 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA PHE B 199 " pdb=" C PHE B 199 " pdb=" N VAL B 200 " pdb=" CA VAL B 200 " ideal model delta harmonic sigma weight residual 180.00 151.45 28.55 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 5873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1334 0.082 - 0.165: 158 0.165 - 0.247: 13 0.247 - 0.330: 6 0.330 - 0.412: 1 Chirality restraints: 1512 Sorted by residual: chirality pdb=" CA LYS S 43 " pdb=" N LYS S 43 " pdb=" C LYS S 43 " pdb=" CB LYS S 43 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" C17 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C16 CLR R 401 " pdb=" C20 CLR R 401 " both_signs ideal model delta sigma weight residual False 2.55 2.88 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA ALA B 248 " pdb=" N ALA B 248 " pdb=" C ALA B 248 " pdb=" CB ALA B 248 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 1509 not shown) Planarity restraints: 1683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 176 " 0.029 2.00e-02 2.50e+03 2.52e-02 1.59e+01 pdb=" CG TRP R 176 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP R 176 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP R 176 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 176 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 176 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 176 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 176 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 176 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP R 176 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA S 40 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO S 41 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO S 41 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 41 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG G 13 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" C ARG G 13 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG G 13 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS G 14 " 0.012 2.00e-02 2.50e+03 ... (remaining 1680 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.29: 10 2.29 - 2.94: 4237 2.94 - 3.59: 13606 3.59 - 4.25: 22577 4.25 - 4.90: 38946 Nonbonded interactions: 79376 Sorted by model distance: nonbonded pdb=" OE2 GLU R 287 " pdb=" OH BTYR R 291 " model vdw 1.634 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.131 3.040 nonbonded pdb=" O ASP R 280 " pdb=" NE2 GLN R 284 " model vdw 2.230 3.120 nonbonded pdb=" O MET S 192 " pdb=" OG SER S 193 " model vdw 2.237 3.040 nonbonded pdb=" OG SER B 67 " pdb=" OD1 ASP B 323 " model vdw 2.241 3.040 ... (remaining 79371 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: 0.660 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.200 Find NCS groups from input model: 0.050 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:5.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 : 0.006 0.049 9896 Z= 0.282 Angle : 0.870 10.269 13406 Z= 0.509 Chirality : 0.057 0.412 1512 Planarity : 0.005 0.055 1683 Dihedral : 12.296 83.343 3563 Min Nonbonded Distance : 1.634 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.09 % Allowed : 0.66 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.07 (0.24), residues: 1209 helix: 1.81 (0.26), residues: 405 sheet: 1.12 (0.29), residues: 314 loop : -0.47 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 68 TYR 0.022 0.002 TYR S 103 PHE 0.023 0.003 PHE R 316 TRP 0.067 0.003 TRP R 176 HIS 0.007 0.002 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.28 ( 9889) covalent geometry : angle 0.86631 / 0.51 (13392) SS BOND : bond 0.00458 / 0.23 ( 7) SS BOND : angle 2.65347 / 1.62 ( 14) hydrogen bonds : bond 0.14244 / 9.87 ( 502) hydrogen bonds : angle 6.32154 / 4.43 ( 1399) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 195 ASP cc_start: 0.6883 (p0) cc_final: 0.6630 (p0) REVERT: B 262 MET cc_start: 0.7591 (tpp) cc_final: 0.7347 (tpp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.6024 time to fit residues: 112.1677 Evaluate side-chains 139 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0770 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 32 GLN B 176 GLN ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.184655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.151210 restraints weight = 23252.374| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 4.65 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9896 Z= 0.172 Angle : 0.642 9.182 13406 Z= 0.344 Chirality : 0.045 0.185 1512 Planarity : 0.005 0.048 1683 Dihedral : 5.035 26.602 1333 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.51 % Allowed : 8.32 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.15 (0.24), residues: 1209 helix: 2.08 (0.25), residues: 415 sheet: 0.98 (0.29), residues: 297 loop : -0.49 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 68 TYR 0.024 0.002 TYR A 296 PHE 0.023 0.002 PHE R 85 TRP 0.030 0.002 TRP R 176 HIS 0.004 0.001 HIS R 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 9889) covalent geometry : angle 0.63806 / 0.34 (13392) SS BOND : bond 0.00527 / 0.30 ( 7) SS BOND : angle 2.23253 / 1.34 ( 14) hydrogen bonds : bond 0.05001 / 3.35 ( 502) hydrogen bonds : angle 5.12686 / 3.57 ( 1399) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 LYS cc_start: 0.7818 (mtmt) cc_final: 0.7571 (tttp) REVERT: B 262 MET cc_start: 0.7704 (tpp) cc_final: 0.7475 (tpp) REVERT: B 280 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8054 (mttt) REVERT: S 234 GLU cc_start: 0.8102 (pt0) cc_final: 0.7834 (pt0) outliers start: 16 outliers final: 5 residues processed: 144 average time/residue: 0.5477 time to fit residues: 83.5050 Evaluate side-chains 138 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain R residue 261 ILE Chi-restraints excluded: chain S residue 62 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS A 244 HIS B 32 GLN B 176 GLN B 340 ASN ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 186 HIS ** 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 = 0.4057 r_free = 0.4057 target = 0.182076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.133193 restraints weight = 18254.944| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.58 r_work: 0.3021 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9896 Z= 0.182 Angle : 0.615 7.106 13406 Z= 0.332 Chirality : 0.045 0.183 1512 Planarity : 0.005 0.046 1683 Dihedral : 4.945 26.583 1333 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.98 % Allowed : 9.17 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.12 (0.24), residues: 1209 helix: 2.17 (0.25), residues: 416 sheet: 0.84 (0.29), residues: 303 loop : -0.57 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 68 TYR 0.025 0.002 TYR A 296 PHE 0.020 0.002 PHE R 264 TRP 0.018 0.002 TRP R 176 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 ( 9889) covalent geometry : angle 0.61205 / 0.33 (13392) SS BOND : bond 0.00563 / 0.32 ( 7) SS BOND : angle 2.05844 / 1.24 ( 14) hydrogen bonds : bond 0.04992 / 3.34 ( 502) hydrogen bonds : angle 5.01585 / 3.47 ( 1399) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: A 51 LYS cc_start: 0.7883 (mttp) cc_final: 0.7649 (pptt) REVERT: A 349 LYS cc_start: 0.8109 (mtmt) cc_final: 0.7683 (tttp) REVERT: B 75 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.7730 (mm110) REVERT: B 96 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8307 (mtt-85) REVERT: B 197 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7666 (mtt90) REVERT: B 293 ASN cc_start: 0.8444 (p0) cc_final: 0.8094 (p0) outliers start: 21 outliers final: 5 residues processed: 149 average time/residue: 0.5756 time to fit residues: 91.0053 Evaluate side-chains 145 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain R residue 250 LEU Chi-restraints excluded: chain R residue 261 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 7.9990 chunk 2 optimal weight: 0.3980 chunk 74 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 65 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 176 GLN B 268 ASN B 340 ASN ** R 175 GLN ** 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 = 0.4089 r_free = 0.4089 target = 0.185157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.151686 restraints weight = 23273.005| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 4.40 r_work: 0.2844 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9896 Z= 0.130 Angle : 0.551 7.136 13406 Z= 0.297 Chirality : 0.042 0.179 1512 Planarity : 0.004 0.046 1683 Dihedral : 4.644 24.278 1333 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.70 % Allowed : 10.59 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.27 (0.24), residues: 1209 helix: 2.46 (0.26), residues: 410 sheet: 0.89 (0.29), residues: 301 loop : -0.57 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 46 TYR 0.024 0.001 TYR A 296 PHE 0.012 0.001 PHE A 189 TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS R 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 9889) covalent geometry : angle 0.54778 / 0.30 (13392) SS BOND : bond 0.00450 / 0.25 ( 7) SS BOND : angle 1.78424 / 1.07 ( 14) hydrogen bonds : bond 0.04257 / 2.83 ( 502) hydrogen bonds : angle 4.77699 / 3.30 ( 1399) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: A 51 LYS cc_start: 0.7784 (mttp) cc_final: 0.7444 (pptt) REVERT: A 349 LYS cc_start: 0.8141 (mtmt) cc_final: 0.7542 (tttp) REVERT: B 75 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7682 (mm110) REVERT: B 96 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8370 (mtt-85) REVERT: B 176 GLN cc_start: 0.9218 (tt0) cc_final: 0.9014 (tt0) REVERT: B 214 ARG cc_start: 0.7512 (mmt-90) cc_final: 0.7266 (mmt180) REVERT: G 20 LYS cc_start: 0.8362 (mtmt) cc_final: 0.8146 (mtpp) REVERT: R 239 ARG cc_start: 0.7635 (ttm170) cc_final: 0.7144 (ptp-110) outliers start: 18 outliers final: 6 residues processed: 152 average time/residue: 0.5579 time to fit residues: 89.9928 Evaluate side-chains 144 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain S residue 62 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 19 optimal weight: 0.3980 chunk 90 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 0.1980 chunk 31 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 268 ASN B 340 ASN ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.187251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.137623 restraints weight = 17218.063| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.44 r_work: 0.3121 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9896 Z= 0.105 Angle : 0.513 7.834 13406 Z= 0.275 Chirality : 0.041 0.173 1512 Planarity : 0.004 0.045 1683 Dihedral : 4.344 21.357 1333 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.17 % Allowed : 10.40 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.33 (0.24), residues: 1209 helix: 2.56 (0.26), residues: 414 sheet: 0.83 (0.29), residues: 304 loop : -0.57 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 46 TYR 0.023 0.001 TYR A 296 PHE 0.018 0.001 PHE R 101 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS R 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 9889) covalent geometry : angle 0.51077 / 0.27 (13392) SS BOND : bond 0.00388 / 0.20 ( 7) SS BOND : angle 1.61627 / 0.97 ( 14) hydrogen bonds : bond 0.03715 / 2.46 ( 502) hydrogen bonds : angle 4.58978 / 3.17 ( 1399) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.7914 (mttp) cc_final: 0.7632 (pptt) REVERT: A 252 SER cc_start: 0.8049 (OUTLIER) cc_final: 0.7820 (p) REVERT: B 42 ARG cc_start: 0.7644 (tpt170) cc_final: 0.7431 (tpp-160) REVERT: B 172 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8219 (tp30) REVERT: S 160 ARG cc_start: 0.8107 (ttm110) cc_final: 0.7659 (mtp85) REVERT: S 234 GLU cc_start: 0.8866 (pt0) cc_final: 0.8545 (pt0) outliers start: 23 outliers final: 5 residues processed: 155 average time/residue: 0.5633 time to fit residues: 92.9537 Evaluate side-chains 137 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain R residue 229 ARG Chi-restraints excluded: chain R residue 287 GLU Chi-restraints excluded: chain R residue 311 TYR Chi-restraints excluded: chain S residue 62 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS B 32 GLN B 176 GLN B 340 ASN ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.185998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.153150 restraints weight = 20339.197| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 4.33 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9896 Z= 0.123 Angle : 0.534 7.413 13406 Z= 0.285 Chirality : 0.042 0.169 1512 Planarity : 0.004 0.043 1683 Dihedral : 4.379 22.550 1333 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.08 % Allowed : 11.81 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.37 (0.24), residues: 1209 helix: 2.62 (0.25), residues: 414 sheet: 0.81 (0.29), residues: 306 loop : -0.53 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.022 0.001 TYR A 296 PHE 0.013 0.001 PHE A 189 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9889) covalent geometry : angle 0.53091 / 0.28 (13392) SS BOND : bond 0.00457 / 0.26 ( 7) SS BOND : angle 1.73235 / 1.05 ( 14) hydrogen bonds : bond 0.03944 / 2.61 ( 502) hydrogen bonds : angle 4.60720 / 3.18 ( 1399) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7159 (tt0) REVERT: R 239 ARG cc_start: 0.7449 (ttm170) cc_final: 0.7070 (ptp-110) REVERT: S 234 GLU cc_start: 0.7991 (pt0) cc_final: 0.7759 (pt0) outliers start: 22 outliers final: 7 residues processed: 141 average time/residue: 0.6168 time to fit residues: 92.2287 Evaluate side-chains 137 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain R residue 229 ARG Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 287 GLU Chi-restraints excluded: chain S residue 115 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 40 optimal weight: 4.9990 chunk 48 optimal weight: 0.0770 chunk 88 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS B 32 GLN B 176 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.181640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.148303 restraints weight = 20525.119| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 4.59 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9896 Z= 0.147 Angle : 0.571 9.777 13406 Z= 0.301 Chirality : 0.043 0.167 1512 Planarity : 0.004 0.045 1683 Dihedral : 4.496 23.984 1333 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.17 % Allowed : 12.19 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.31 (0.24), residues: 1209 helix: 2.55 (0.25), residues: 415 sheet: 0.82 (0.29), residues: 304 loop : -0.58 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.023 0.001 TYR A 296 PHE 0.018 0.001 PHE R 101 TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 9889) covalent geometry : angle 0.56849 / 0.30 (13392) SS BOND : bond 0.00534 / 0.30 ( 7) SS BOND : angle 1.83676 / 1.11 ( 14) hydrogen bonds : bond 0.04216 / 2.79 ( 502) hydrogen bonds : angle 4.67972 / 3.24 ( 1399) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7145 (tt0) REVERT: R 239 ARG cc_start: 0.7415 (ttm170) cc_final: 0.7025 (ptp-110) outliers start: 23 outliers final: 14 residues processed: 141 average time/residue: 0.6103 time to fit residues: 91.2781 Evaluate side-chains 147 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 250 LEU Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 287 GLU Chi-restraints excluded: chain R residue 311 TYR Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 162 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 110 optimal weight: 0.0980 chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 83 optimal weight: 0.0020 chunk 41 optimal weight: 1.9990 overall best weight: 1.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 340 ASN ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.182275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.129578 restraints weight = 14125.152| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.95 r_work: 0.3119 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9896 Z= 0.133 Angle : 0.555 8.785 13406 Z= 0.293 Chirality : 0.042 0.165 1512 Planarity : 0.004 0.045 1683 Dihedral : 4.443 23.464 1333 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.89 % Allowed : 12.95 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.34 (0.24), residues: 1209 helix: 2.58 (0.25), residues: 415 sheet: 0.85 (0.29), residues: 304 loop : -0.59 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.023 0.001 TYR A 296 PHE 0.013 0.001 PHE A 189 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 9889) covalent geometry : angle 0.55249 / 0.29 (13392) SS BOND : bond 0.00509 / 0.29 ( 7) SS BOND : angle 1.78356 / 1.08 ( 14) hydrogen bonds : bond 0.04061 / 2.69 ( 502) hydrogen bonds : angle 4.63800 / 3.21 ( 1399) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: A 349 LYS cc_start: 0.8181 (mttt) cc_final: 0.7694 (tttp) REVERT: R 239 ARG cc_start: 0.7681 (ttm170) cc_final: 0.7199 (ptp-110) REVERT: S 234 GLU cc_start: 0.8803 (pt0) cc_final: 0.8434 (pt0) outliers start: 20 outliers final: 10 residues processed: 143 average time/residue: 0.5545 time to fit residues: 84.1607 Evaluate side-chains 139 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 287 GLU Chi-restraints excluded: chain R residue 311 TYR Chi-restraints excluded: chain S residue 162 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 30 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.180080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.129891 restraints weight = 18214.021| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.68 r_work: 0.2992 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9896 Z= 0.182 Angle : 0.612 10.236 13406 Z= 0.322 Chirality : 0.044 0.171 1512 Planarity : 0.004 0.046 1683 Dihedral : 4.699 26.018 1333 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.70 % Allowed : 12.95 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.23 (0.24), residues: 1209 helix: 2.45 (0.25), residues: 415 sheet: 0.89 (0.29), residues: 300 loop : -0.67 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.024 0.002 TYR A 296 PHE 0.019 0.002 PHE R 101 TRP 0.007 0.002 TRP R 195 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 ( 9889) covalent geometry : angle 0.60865 / 0.32 (13392) SS BOND : bond 0.00627 / 0.36 ( 7) SS BOND : angle 1.96363 / 1.19 ( 14) hydrogen bonds : bond 0.04635 / 3.07 ( 502) hydrogen bonds : angle 4.80441 / 3.32 ( 1399) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: A 51 LYS cc_start: 0.7793 (pptt) cc_final: 0.7458 (mttp) REVERT: A 349 LYS cc_start: 0.8105 (mttt) cc_final: 0.7614 (tttp) REVERT: B 75 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.7704 (mm110) REVERT: R 239 ARG cc_start: 0.7626 (ttm170) cc_final: 0.7149 (ptp-110) outliers start: 18 outliers final: 13 residues processed: 139 average time/residue: 0.5715 time to fit residues: 84.3604 Evaluate side-chains 145 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 250 LEU Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 287 GLU Chi-restraints excluded: chain R residue 311 TYR Chi-restraints excluded: chain S residue 162 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 69 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 175 GLN ** 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 = 0.4049 r_free = 0.4049 target = 0.181212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.129445 restraints weight = 15710.508| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.21 r_work: 0.3076 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9896 Z= 0.133 Angle : 0.562 9.336 13406 Z= 0.298 Chirality : 0.042 0.167 1512 Planarity : 0.004 0.045 1683 Dihedral : 4.521 24.353 1333 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.42 % Allowed : 13.42 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.31 (0.24), residues: 1209 helix: 2.55 (0.25), residues: 415 sheet: 0.92 (0.29), residues: 299 loop : -0.64 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.024 0.001 TYR A 296 PHE 0.014 0.001 PHE B 234 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 9889) covalent geometry : angle 0.55922 / 0.30 (13392) SS BOND : bond 0.00502 / 0.28 ( 7) SS BOND : angle 1.78566 / 1.08 ( 14) hydrogen bonds : bond 0.04095 / 2.71 ( 502) hydrogen bonds : angle 4.67466 / 3.23 ( 1399) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7647 (tt0) REVERT: A 51 LYS cc_start: 0.7822 (pptt) cc_final: 0.7528 (mppt) REVERT: A 349 LYS cc_start: 0.8216 (mttt) cc_final: 0.7705 (tttp) REVERT: R 239 ARG cc_start: 0.7750 (ttm170) cc_final: 0.7273 (ptp-110) REVERT: S 234 GLU cc_start: 0.8867 (pt0) cc_final: 0.8500 (pt0) outliers start: 15 outliers final: 13 residues processed: 139 average time/residue: 0.5366 time to fit residues: 79.5869 Evaluate side-chains 146 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 250 LEU Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 287 GLU Chi-restraints excluded: chain R residue 311 TYR Chi-restraints excluded: chain S residue 162 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 175 GLN ** 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 = 0.4054 r_free = 0.4054 target = 0.181518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.128809 restraints weight = 15414.904| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.31 r_work: 0.3069 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9896 Z= 0.144 Angle : 0.574 9.770 13406 Z= 0.303 Chirality : 0.042 0.167 1512 Planarity : 0.004 0.045 1683 Dihedral : 4.535 25.335 1333 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.51 % Allowed : 13.42 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.24), residues: 1209 helix: 2.53 (0.25), residues: 415 sheet: 0.90 (0.29), residues: 299 loop : -0.64 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.024 0.001 TYR A 296 PHE 0.019 0.001 PHE R 101 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 9889) covalent geometry : angle 0.57157 / 0.30 (13392) SS BOND : bond 0.00537 / 0.30 ( 7) SS BOND : angle 1.82939 / 1.11 ( 14) hydrogen bonds : bond 0.04217 / 2.80 ( 502) hydrogen bonds : angle 4.68914 / 3.24 ( 1399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3744.02 seconds wall clock time: 64 minutes 23.49 seconds (3863.49 seconds total)