Starting phenix.real_space_refine on Thu Jul 2 16:17:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wq3_32698/07_2026/7wq3_32698.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wq3_32698/07_2026/7wq3_32698.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/7wq3_32698/07_2026/7wq3_32698.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wq3_32698/07_2026/7wq3_32698.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wq3_32698/07_2026/7wq3_32698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wq3_32698/07_2026/7wq3_32698.map" model { file = "/net/cci-nas-00/data/ceres_data/7wq3_32698/07_2026/7wq3_32698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wq3_32698/07_2026/7wq3_32698.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= 0.006 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 61 5.16 5 C 5915 2.51 5 N 1548 2.21 5 O 1685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 9209 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2303 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 13, 'TRANS': 275} 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: "S" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1787 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "L" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 117 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "R" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 1.85, per 1000 atoms: 0.20 Number of scatterers: 9209 At special positions: 0 Unit cell: (110.16, 125.46, 123.42, 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 61 16.00 O 1685 8.00 N 1548 7.00 C 5915 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 187 " 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: 0.71 Conformation dependent library (CDL) restraints added in 444.2 milliseconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 39.7% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'R' and resid 32 through 61 removed outlier: 4.618A pdb=" N VAL R 38 " --> pdb=" O PHE R 34 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER R 61 " --> pdb=" O VAL R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 98 removed outlier: 3.754A pdb=" N ILE R 89 " --> pdb=" O LEU R 85 " (cutoff:3.500A) Proline residue: R 90 - end of helix removed outlier: 4.257A pdb=" N THR R 94 " --> pdb=" O PRO R 90 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL R 95 " --> pdb=" O PHE R 91 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR R 96 " --> pdb=" O GLN R 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 139 removed outlier: 4.015A pdb=" N ILE R 107 " --> pdb=" O LEU R 103 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N HIS R 112 " --> pdb=" O CYS R 108 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR R 113 " --> pdb=" O LYS R 109 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR R 116 " --> pdb=" O HIS R 112 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE R 137 " --> pdb=" O ARG R 133 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS R 139 " --> pdb=" O VAL R 135 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 147 Processing helix chain 'R' and resid 148 through 167 Processing helix chain 'R' and resid 167 through 174 removed outlier: 3.656A pdb=" N ALA R 171 " --> pdb=" O ALA R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 209 removed outlier: 3.715A pdb=" N ALA R 199 " --> pdb=" O ARG R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 231 Processing helix chain 'R' and resid 235 through 260 removed outlier: 4.429A pdb=" N TRP R 260 " --> pdb=" O PHE R 256 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 272 Processing helix chain 'R' and resid 278 through 303 removed outlier: 3.780A pdb=" N SER R 296 " --> pdb=" O ALA R 292 " (cutoff:3.500A) Proline residue: R 300 - end of helix Processing helix chain 'R' and resid 307 through 318 Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 5.078A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.166A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 232 " --> pdb=" O ASP A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 232' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.543A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 removed outlier: 4.360A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.631A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) 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 24 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.631A 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 removed outlier: 3.852A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.605A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.884A 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 removed outlier: 4.184A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.789A pdb=" N ASP S 223 " --> pdb=" O GLU S 220 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 220 through 224' Processing helix chain 'L' and resid 3 through 12 Processing sheet with id=AA1, first strand: chain 'R' and resid 175 through 177 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.299A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.973A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.033A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.010A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.495A 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 151 removed outlier: 3.789A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.177A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.457A 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: 4.121A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.620A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.292A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.292A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.928A pdb=" N THR S 141 " --> pdb=" O ARG S 160 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG S 160 " --> pdb=" O THR S 141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 4.028A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG S 191 " --> pdb=" O ASN S 194 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1311 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: 1.29 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2915 1.34 - 1.46: 2281 1.46 - 1.58: 4113 1.58 - 1.70: 25 1.70 - 1.81: 91 Bond restraints: 9425 Sorted by residual: bond pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " ideal model delta sigma weight residual 1.332 1.652 -0.320 2.00e-02 2.50e+03 2.56e+02 bond pdb=" C5 CLR R 402 " pdb=" C6 CLR R 402 " ideal model delta sigma weight residual 1.332 1.651 -0.319 2.00e-02 2.50e+03 2.54e+02 bond pdb=" C5 CLR R 405 " pdb=" C6 CLR R 405 " ideal model delta sigma weight residual 1.332 1.651 -0.319 2.00e-02 2.50e+03 2.54e+02 bond pdb=" C5 CLR R 403 " pdb=" C6 CLR R 403 " ideal model delta sigma weight residual 1.332 1.651 -0.319 2.00e-02 2.50e+03 2.54e+02 bond pdb=" C5 CLR R 404 " pdb=" C6 CLR R 404 " ideal model delta sigma weight residual 1.332 1.650 -0.318 2.00e-02 2.50e+03 2.53e+02 ... (remaining 9420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 12667 2.66 - 5.32: 91 5.32 - 7.98: 19 7.98 - 10.64: 10 10.64 - 13.30: 10 Bond angle restraints: 12797 Sorted by residual: angle pdb=" C5 CLR R 405 " pdb=" C6 CLR R 405 " pdb=" C7 CLR R 405 " ideal model delta sigma weight residual 125.11 111.81 13.30 3.00e+00 1.11e-01 1.97e+01 angle pdb=" C5 CLR R 403 " pdb=" C6 CLR R 403 " pdb=" C7 CLR R 403 " ideal model delta sigma weight residual 125.11 111.81 13.30 3.00e+00 1.11e-01 1.97e+01 angle pdb=" C5 CLR R 402 " pdb=" C6 CLR R 402 " pdb=" C7 CLR R 402 " ideal model delta sigma weight residual 125.11 111.81 13.30 3.00e+00 1.11e-01 1.96e+01 angle pdb=" C5 CLR R 404 " pdb=" C6 CLR R 404 " pdb=" C7 CLR R 404 " ideal model delta sigma weight residual 125.11 111.82 13.29 3.00e+00 1.11e-01 1.96e+01 angle pdb=" C4 CLR R 401 " pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " ideal model delta sigma weight residual 120.33 107.93 12.40 3.00e+00 1.11e-01 1.71e+01 ... (remaining 12792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.56: 5341 15.56 - 31.12: 150 31.12 - 46.68: 23 46.68 - 62.24: 13 62.24 - 77.79: 1 Dihedral angle restraints: 5528 sinusoidal: 2163 harmonic: 3365 Sorted by residual: dihedral pdb=" N ARG S 191 " pdb=" CA ARG S 191 " pdb=" CB ARG S 191 " pdb=" CG ARG S 191 " ideal model delta sinusoidal sigma weight residual -60.00 -119.85 59.85 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N PHE B 234 " pdb=" CA PHE B 234 " pdb=" CB PHE B 234 " pdb=" CG PHE B 234 " ideal model delta sinusoidal sigma weight residual -180.00 -122.95 -57.05 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" N PHE R 114 " pdb=" CA PHE R 114 " pdb=" CB PHE R 114 " pdb=" CG PHE R 114 " ideal model delta sinusoidal sigma weight residual -60.00 -113.13 53.13 3 1.50e+01 4.44e-03 9.18e+00 ... (remaining 5525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1408 0.112 - 0.223: 29 0.223 - 0.335: 11 0.335 - 0.446: 4 0.446 - 0.558: 5 Chirality restraints: 1457 Sorted by residual: chirality pdb=" C13 CLR R 405 " pdb=" C12 CLR R 405 " pdb=" C14 CLR R 405 " pdb=" C17 CLR R 405 " both_signs ideal model delta sigma weight residual False -2.93 -2.37 -0.56 2.00e-01 2.50e+01 7.78e+00 chirality pdb=" C13 CLR R 404 " pdb=" C12 CLR R 404 " pdb=" C14 CLR R 404 " pdb=" C17 CLR R 404 " both_signs ideal model delta sigma weight residual False -2.93 -2.38 -0.56 2.00e-01 2.50e+01 7.74e+00 chirality pdb=" C13 CLR R 401 " pdb=" C12 CLR R 401 " pdb=" C14 CLR R 401 " pdb=" C17 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.93 -2.38 -0.55 2.00e-01 2.50e+01 7.69e+00 ... (remaining 1454 not shown) Planarity restraints: 1586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 299 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO R 300 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 300 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 300 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA S 40 " -0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO S 41 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO S 41 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO S 41 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO B 236 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.016 5.00e-02 4.00e+02 ... (remaining 1583 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 435 2.73 - 3.27: 9049 3.27 - 3.82: 14930 3.82 - 4.36: 17758 4.36 - 4.90: 31232 Nonbonded interactions: 73404 Sorted by model distance: nonbonded pdb=" O LYS A 248 " pdb=" OD1 ASP A 251 " model vdw 2.189 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR A 230 " pdb=" OG SER A 281 " model vdw 2.248 3.040 nonbonded pdb=" O PHE S 29 " pdb=" NH2 ARG S 72 " model vdw 2.263 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.269 3.040 ... (remaining 73399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.670 Find NCS groups from input model: 0.050 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:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4746 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 : 0.011 0.320 9426 Z= 0.539 Angle : 0.724 13.301 12799 Z= 0.335 Chirality : 0.061 0.558 1457 Planarity : 0.003 0.032 1586 Dihedral : 8.044 77.794 3353 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.40 % Allowed : 2.43 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.23), residues: 1144 helix: 0.07 (0.25), residues: 408 sheet: -1.00 (0.27), residues: 292 loop : -1.59 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.006 0.001 TYR S 102 PHE 0.008 0.001 PHE A 274 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.000 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.01071 / 0.54 ( 9425) covalent geometry : angle 0.72428 / 0.33 (12797) SS BOND : bond 0.00054 / 0.03 ( 1) SS BOND : angle 0.37252 / 0.20 ( 2) hydrogen bonds : bond 0.14093 / 9.20 ( 460) hydrogen bonds : angle 4.96401 / 3.44 ( 1311) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 227 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: R 71 ASN cc_start: 0.6883 (m110) cc_final: 0.6622 (m110) REVERT: R 244 LYS cc_start: 0.6246 (mttt) cc_final: 0.5999 (mtmm) REVERT: A 248 LYS cc_start: 0.6669 (ttmm) cc_final: 0.6377 (tmmm) REVERT: A 266 LEU cc_start: 0.5029 (tp) cc_final: 0.4807 (tm) REVERT: A 276 GLU cc_start: 0.7628 (mp0) cc_final: 0.7292 (mp0) REVERT: A 305 CYS cc_start: 0.6720 (m) cc_final: 0.6438 (m) REVERT: A 314 LYS cc_start: 0.6025 (mttt) cc_final: 0.5625 (tppt) REVERT: A 342 VAL cc_start: 0.6855 (t) cc_final: 0.6526 (m) REVERT: G 20 LYS cc_start: 0.7013 (ptpp) cc_final: 0.6256 (pttm) REVERT: G 60 PRO cc_start: 0.6335 (Cg_endo) cc_final: 0.6097 (Cg_exo) REVERT: S 53 SER cc_start: 0.6534 (t) cc_final: 0.6274 (p) outliers start: 4 outliers final: 0 residues processed: 231 average time/residue: 0.4331 time to fit residues: 107.8307 Evaluate side-chains 136 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.0010 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 71 ASN R 173 HIS R 190 GLN R 228 HIS A 204 GLN B 91 HIS B 142 HIS B 176 GLN G 18 GLN S 39 GLN S 194 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.192565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.161567 restraints weight = 11001.807| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.91 r_work: 0.3723 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.6410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9426 Z= 0.197 Angle : 0.749 11.311 12799 Z= 0.382 Chirality : 0.046 0.195 1457 Planarity : 0.005 0.045 1586 Dihedral : 5.775 57.036 1294 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.54 % Allowed : 10.93 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.32 (0.24), residues: 1144 helix: 1.15 (0.27), residues: 396 sheet: -0.41 (0.29), residues: 278 loop : -1.22 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 208 TYR 0.016 0.002 TYR R 84 PHE 0.045 0.003 PHE R 91 TRP 0.016 0.002 TRP R 101 HIS 0.014 0.002 HIS R 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 ( 9425) covalent geometry : angle 0.74824 / 0.38 (12797) SS BOND : bond 0.00447 / 0.24 ( 1) SS BOND : angle 2.54761 / 1.40 ( 2) hydrogen bonds : bond 0.04469 / 2.95 ( 460) hydrogen bonds : angle 4.46063 / 3.19 ( 1311) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7786 (mttt) cc_final: 0.7448 (mtmt) REVERT: A 28 GLU cc_start: 0.7330 (tt0) cc_final: 0.6912 (mt-10) REVERT: A 248 LYS cc_start: 0.7923 (ttmm) cc_final: 0.7709 (tmmm) REVERT: A 276 GLU cc_start: 0.7800 (mp0) cc_final: 0.7595 (mp0) REVERT: A 308 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6614 (mp0) REVERT: A 314 LYS cc_start: 0.6931 (mttt) cc_final: 0.6713 (tppt) REVERT: B 55 LEU cc_start: 0.8264 (mt) cc_final: 0.8005 (mt) REVERT: B 98 SER cc_start: 0.8723 (m) cc_final: 0.8264 (t) REVERT: B 134 ARG cc_start: 0.8291 (mtp180) cc_final: 0.7563 (mtp-110) REVERT: B 293 ASN cc_start: 0.7842 (p0) cc_final: 0.7339 (m-40) REVERT: G 38 MET cc_start: 0.6398 (OUTLIER) cc_final: 0.5367 (tmm) REVERT: S 3 GLN cc_start: 0.8048 (tm-30) cc_final: 0.7747 (tt0) REVERT: S 46 GLU cc_start: 0.8256 (pt0) cc_final: 0.7806 (pt0) REVERT: S 93 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7236 (tpp) outliers start: 35 outliers final: 8 residues processed: 211 average time/residue: 0.4458 time to fit residues: 101.6211 Evaluate side-chains 144 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 164 SER Chi-restraints excluded: chain L residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 105 optimal weight: 0.0970 chunk 106 optimal weight: 0.0770 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 190 GLN R 299 ASN A 204 GLN B 32 GLN B 156 GLN S 179 GLN L 5 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.183853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.150420 restraints weight = 10731.866| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.01 r_work: 0.3574 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.7377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9426 Z= 0.105 Angle : 0.497 7.834 12799 Z= 0.258 Chirality : 0.040 0.140 1457 Planarity : 0.003 0.039 1586 Dihedral : 4.734 58.876 1294 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.24 % Allowed : 15.69 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.50 (0.25), residues: 1144 helix: 1.99 (0.27), residues: 396 sheet: -0.03 (0.29), residues: 286 loop : -0.86 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 191 TYR 0.010 0.001 TYR S 173 PHE 0.010 0.001 PHE S 27 TRP 0.012 0.001 TRP S 47 HIS 0.006 0.001 HIS R 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 ( 9425) covalent geometry : angle 0.49723 / 0.26 (12797) SS BOND : bond 0.00233 / 0.12 ( 1) SS BOND : angle 1.28066 / 0.71 ( 2) hydrogen bonds : bond 0.03328 / 2.17 ( 460) hydrogen bonds : angle 3.87783 / 2.76 ( 1311) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7897 (mttt) cc_final: 0.7605 (mtmt) REVERT: A 22 ASN cc_start: 0.7684 (m-40) cc_final: 0.7473 (m110) REVERT: A 24 ARG cc_start: 0.7323 (ttp-110) cc_final: 0.6766 (ttm110) REVERT: A 25 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6547 (tm-30) REVERT: A 28 GLU cc_start: 0.7741 (tt0) cc_final: 0.7165 (mt-10) REVERT: A 209 LYS cc_start: 0.7847 (tmmt) cc_final: 0.7448 (mptt) REVERT: A 276 GLU cc_start: 0.7945 (mp0) cc_final: 0.7678 (mp0) REVERT: B 98 SER cc_start: 0.8801 (m) cc_final: 0.8470 (t) REVERT: B 134 ARG cc_start: 0.8325 (mtp180) cc_final: 0.7727 (mtp-110) REVERT: B 215 GLU cc_start: 0.7958 (mp0) cc_final: 0.7603 (mt-10) REVERT: B 268 ASN cc_start: 0.7460 (t0) cc_final: 0.7127 (m-40) REVERT: S 46 GLU cc_start: 0.8478 (pt0) cc_final: 0.8164 (pt0) REVERT: S 183 GLN cc_start: 0.5910 (mm110) cc_final: 0.5657 (mp-120) REVERT: S 191 ARG cc_start: 0.2902 (OUTLIER) cc_final: 0.2009 (tpp80) outliers start: 32 outliers final: 10 residues processed: 176 average time/residue: 0.4880 time to fit residues: 92.3546 Evaluate side-chains 141 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 191 ARG Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 101 optimal weight: 0.0370 chunk 61 optimal weight: 3.9990 chunk 103 optimal weight: 0.2980 chunk 39 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 190 GLN A 204 GLN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.178186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.146032 restraints weight = 11506.432| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.91 r_work: 0.3567 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.9194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9426 Z= 0.132 Angle : 0.553 5.841 12799 Z= 0.291 Chirality : 0.042 0.183 1457 Planarity : 0.004 0.047 1586 Dihedral : 5.078 56.299 1294 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.15 % Allowed : 16.30 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.85 (0.25), residues: 1144 helix: 2.28 (0.28), residues: 392 sheet: 0.23 (0.29), residues: 291 loop : -0.69 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 160 TYR 0.012 0.001 TYR S 95 PHE 0.024 0.002 PHE R 110 TRP 0.009 0.001 TRP B 211 HIS 0.005 0.001 HIS R 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9425) covalent geometry : angle 0.55207 / 0.29 (12797) SS BOND : bond 0.00472 / 0.25 ( 1) SS BOND : angle 1.87482 / 1.03 ( 2) hydrogen bonds : bond 0.04021 / 2.67 ( 460) hydrogen bonds : angle 3.94923 / 2.85 ( 1311) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 0.346 Fit side-chains REVERT: R 91 PHE cc_start: 0.6286 (m-10) cc_final: 0.6010 (m-10) REVERT: R 234 MET cc_start: 0.7603 (mmm) cc_final: 0.7346 (mmp) REVERT: A 17 LYS cc_start: 0.8106 (mttt) cc_final: 0.7822 (mtmt) REVERT: A 24 ARG cc_start: 0.7480 (ttp-110) cc_final: 0.6982 (ttp-110) REVERT: A 25 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6974 (tm-30) REVERT: A 28 GLU cc_start: 0.7975 (tt0) cc_final: 0.7460 (mt-10) REVERT: A 209 LYS cc_start: 0.8237 (tmmt) cc_final: 0.7931 (mptt) REVERT: A 273 LEU cc_start: 0.7725 (tp) cc_final: 0.7271 (tp) REVERT: B 16 ASN cc_start: 0.6842 (m-40) cc_final: 0.6600 (m110) REVERT: B 76 ASP cc_start: 0.7589 (m-30) cc_final: 0.7205 (m-30) REVERT: B 130 GLU cc_start: 0.7612 (mt-10) cc_final: 0.6956 (mp0) REVERT: B 215 GLU cc_start: 0.8046 (mp0) cc_final: 0.7846 (mt-10) REVERT: B 312 ASP cc_start: 0.8549 (m-30) cc_final: 0.8319 (m-30) REVERT: B 325 MET cc_start: 0.8662 (tpp) cc_final: 0.8421 (mmt) REVERT: G 58 GLU cc_start: 0.7264 (mp0) cc_final: 0.6418 (tm-30) REVERT: S 46 GLU cc_start: 0.8703 (pt0) cc_final: 0.8389 (pt0) REVERT: S 83 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8252 (ptm) REVERT: S 183 GLN cc_start: 0.7062 (mm110) cc_final: 0.6816 (mp-120) REVERT: S 189 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8325 (mt) outliers start: 41 outliers final: 20 residues processed: 177 average time/residue: 0.5191 time to fit residues: 98.7727 Evaluate side-chains 150 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 197 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.1980 chunk 20 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 346 ASN B 32 GLN S 77 ASN S 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.177341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.145262 restraints weight = 11481.657| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.95 r_work: 0.3560 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.9543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9426 Z= 0.097 Angle : 0.475 6.342 12799 Z= 0.249 Chirality : 0.040 0.135 1457 Planarity : 0.004 0.056 1586 Dihedral : 4.647 55.749 1294 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.34 % Allowed : 19.43 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.26), residues: 1144 helix: 2.55 (0.28), residues: 391 sheet: 0.40 (0.30), residues: 292 loop : -0.54 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.008 0.001 TYR S 190 PHE 0.015 0.001 PHE R 110 TRP 0.015 0.001 TRP B 211 HIS 0.005 0.001 HIS R 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 ( 9425) covalent geometry : angle 0.47475 / 0.25 (12797) SS BOND : bond 0.00398 / 0.21 ( 1) SS BOND : angle 1.45151 / 0.81 ( 2) hydrogen bonds : bond 0.03264 / 2.13 ( 460) hydrogen bonds : angle 3.80120 / 2.72 ( 1311) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.350 Fit side-chains REVERT: R 82 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7802 (tp) REVERT: R 132 ASP cc_start: 0.8077 (t70) cc_final: 0.7805 (t0) REVERT: R 234 MET cc_start: 0.7691 (mmm) cc_final: 0.7404 (mmp) REVERT: A 17 LYS cc_start: 0.7950 (mttt) cc_final: 0.7670 (mtmt) REVERT: A 24 ARG cc_start: 0.7557 (ttp-110) cc_final: 0.7093 (ttp-110) REVERT: A 25 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6962 (tm-30) REVERT: A 28 GLU cc_start: 0.7925 (tt0) cc_final: 0.7443 (mt-10) REVERT: A 209 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7884 (mptt) REVERT: A 273 LEU cc_start: 0.7877 (tp) cc_final: 0.7457 (tp) REVERT: B 16 ASN cc_start: 0.6933 (m-40) cc_final: 0.6202 (m110) REVERT: B 20 ASP cc_start: 0.7747 (m-30) cc_final: 0.7438 (m-30) REVERT: B 76 ASP cc_start: 0.7638 (m-30) cc_final: 0.7377 (m-30) REVERT: B 130 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7087 (mp0) REVERT: B 215 GLU cc_start: 0.7967 (mp0) cc_final: 0.7636 (mt-10) REVERT: B 312 ASP cc_start: 0.8494 (m-30) cc_final: 0.8289 (m-30) REVERT: G 58 GLU cc_start: 0.7244 (mp0) cc_final: 0.6357 (tm-30) REVERT: S 46 GLU cc_start: 0.8731 (pt0) cc_final: 0.8431 (pt0) REVERT: S 65 LYS cc_start: 0.7594 (ttpt) cc_final: 0.7001 (tttm) REVERT: S 183 GLN cc_start: 0.7022 (mm110) cc_final: 0.6652 (mp-120) outliers start: 33 outliers final: 16 residues processed: 159 average time/residue: 0.4981 time to fit residues: 84.7289 Evaluate side-chains 150 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 10.0000 chunk 36 optimal weight: 0.3980 chunk 100 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN B 32 GLN S 77 ASN S 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.172361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.140945 restraints weight = 11471.541| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.91 r_work: 0.3527 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 1.0197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9426 Z= 0.122 Angle : 0.518 6.392 12799 Z= 0.272 Chirality : 0.041 0.140 1457 Planarity : 0.004 0.051 1586 Dihedral : 4.838 59.028 1294 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.05 % Allowed : 19.13 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.16 (0.25), residues: 1144 helix: 2.53 (0.27), residues: 391 sheet: 0.43 (0.30), residues: 289 loop : -0.54 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.010 0.001 TYR R 303 PHE 0.021 0.001 PHE R 115 TRP 0.016 0.001 TRP B 211 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 9425) covalent geometry : angle 0.51718 / 0.27 (12797) SS BOND : bond 0.00603 / 0.32 ( 1) SS BOND : angle 1.59945 / 0.89 ( 2) hydrogen bonds : bond 0.03763 / 2.49 ( 460) hydrogen bonds : angle 3.83810 / 2.77 ( 1311) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.305 Fit side-chains REVERT: R 132 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.8017 (t0) REVERT: A 17 LYS cc_start: 0.8047 (mttt) cc_final: 0.7796 (mtmt) REVERT: A 24 ARG cc_start: 0.7612 (ttp-110) cc_final: 0.7063 (ttp-110) REVERT: A 25 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7056 (tm-30) REVERT: A 28 GLU cc_start: 0.7899 (tt0) cc_final: 0.7462 (mt-10) REVERT: A 209 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7936 (mptt) REVERT: A 273 LEU cc_start: 0.7945 (tp) cc_final: 0.7541 (tp) REVERT: B 16 ASN cc_start: 0.6943 (m-40) cc_final: 0.6300 (m110) REVERT: B 20 ASP cc_start: 0.7706 (m-30) cc_final: 0.7427 (m-30) REVERT: B 76 ASP cc_start: 0.7654 (m-30) cc_final: 0.7425 (m-30) REVERT: B 130 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7297 (mp0) REVERT: B 296 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8410 (p) REVERT: B 312 ASP cc_start: 0.8510 (m-30) cc_final: 0.8300 (m-30) REVERT: G 58 GLU cc_start: 0.7218 (mp0) cc_final: 0.6322 (tm-30) REVERT: S 46 GLU cc_start: 0.8722 (pt0) cc_final: 0.8396 (pt0) REVERT: S 65 LYS cc_start: 0.7695 (ttpt) cc_final: 0.7117 (tttm) REVERT: S 83 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8193 (ptm) REVERT: S 113 GLN cc_start: 0.8092 (mm110) cc_final: 0.7864 (mm110) REVERT: S 140 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.6902 (mmm) REVERT: S 183 GLN cc_start: 0.7508 (mm110) cc_final: 0.7054 (mp-120) outliers start: 40 outliers final: 23 residues processed: 159 average time/residue: 0.4828 time to fit residues: 82.3124 Evaluate side-chains 157 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 132 ASP Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN B 32 GLN S 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.172344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.141088 restraints weight = 11388.521| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.90 r_work: 0.3535 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 1.0516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9426 Z= 0.109 Angle : 0.496 6.785 12799 Z= 0.259 Chirality : 0.040 0.136 1457 Planarity : 0.004 0.048 1586 Dihedral : 4.768 58.510 1294 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.25 % Allowed : 19.43 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.26), residues: 1144 helix: 2.62 (0.27), residues: 393 sheet: 0.46 (0.30), residues: 279 loop : -0.44 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.009 0.001 TYR S 190 PHE 0.018 0.001 PHE R 115 TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS R 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 9425) covalent geometry : angle 0.49538 / 0.26 (12797) SS BOND : bond 0.00575 / 0.30 ( 1) SS BOND : angle 1.44859 / 0.81 ( 2) hydrogen bonds : bond 0.03467 / 2.29 ( 460) hydrogen bonds : angle 3.77894 / 2.72 ( 1311) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 0.358 Fit side-chains REVERT: A 17 LYS cc_start: 0.8002 (mttt) cc_final: 0.7731 (mtmt) REVERT: A 24 ARG cc_start: 0.7626 (ttp-110) cc_final: 0.7057 (ttp-110) REVERT: A 25 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7053 (tm-30) REVERT: A 28 GLU cc_start: 0.7940 (tt0) cc_final: 0.7573 (mt-10) REVERT: A 209 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7979 (mptt) REVERT: A 345 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8234 (mmtp) REVERT: B 16 ASN cc_start: 0.6975 (m-40) cc_final: 0.6365 (m110) REVERT: B 20 ASP cc_start: 0.7692 (m-30) cc_final: 0.7423 (m-30) REVERT: B 46 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7546 (mmt90) REVERT: B 76 ASP cc_start: 0.7642 (m-30) cc_final: 0.7425 (m-30) REVERT: B 130 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7329 (mp0) REVERT: B 296 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8403 (p) REVERT: G 46 LYS cc_start: 0.8107 (tppt) cc_final: 0.7822 (mmtm) REVERT: G 58 GLU cc_start: 0.7289 (mp0) cc_final: 0.6275 (tm-30) REVERT: S 46 GLU cc_start: 0.8753 (pt0) cc_final: 0.8466 (pt0) REVERT: S 76 LYS cc_start: 0.7691 (mtpp) cc_final: 0.7298 (ttmt) REVERT: S 83 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8189 (ptm) REVERT: S 113 GLN cc_start: 0.8070 (mm110) cc_final: 0.7851 (mm110) outliers start: 42 outliers final: 18 residues processed: 160 average time/residue: 0.4679 time to fit residues: 80.1853 Evaluate side-chains 150 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 166 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 14 optimal weight: 0.0470 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN S 77 ASN S 142 GLN S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.171780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.140746 restraints weight = 11258.196| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.88 r_work: 0.3502 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 1.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9426 Z= 0.115 Angle : 0.527 8.704 12799 Z= 0.273 Chirality : 0.040 0.137 1457 Planarity : 0.004 0.049 1586 Dihedral : 4.803 56.683 1294 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.34 % Allowed : 21.05 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.26), residues: 1144 helix: 2.56 (0.27), residues: 393 sheet: 0.45 (0.31), residues: 280 loop : -0.45 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.011 0.001 TYR R 84 PHE 0.021 0.001 PHE R 115 TRP 0.015 0.001 TRP B 211 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 9425) covalent geometry : angle 0.52661 / 0.27 (12797) SS BOND : bond 0.00616 / 0.32 ( 1) SS BOND : angle 1.50704 / 0.84 ( 2) hydrogen bonds : bond 0.03621 / 2.40 ( 460) hydrogen bonds : angle 3.80457 / 2.75 ( 1311) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.328 Fit side-chains REVERT: A 17 LYS cc_start: 0.8029 (mttt) cc_final: 0.7767 (mtmt) REVERT: A 24 ARG cc_start: 0.7608 (ttp-110) cc_final: 0.7055 (ttp-110) REVERT: A 25 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7060 (tm-30) REVERT: A 28 GLU cc_start: 0.7987 (tt0) cc_final: 0.7577 (mt-10) REVERT: B 130 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7366 (mp0) REVERT: B 135 VAL cc_start: 0.9013 (OUTLIER) cc_final: 0.8682 (p) REVERT: B 296 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8446 (p) REVERT: G 46 LYS cc_start: 0.8104 (tppt) cc_final: 0.7875 (mmtm) REVERT: G 58 GLU cc_start: 0.7372 (mp0) cc_final: 0.6355 (tm-30) REVERT: S 46 GLU cc_start: 0.8722 (pt0) cc_final: 0.8454 (pt0) REVERT: S 140 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.6974 (mmm) REVERT: L 14 HIS cc_start: 0.5108 (m-70) cc_final: 0.4764 (m-70) outliers start: 33 outliers final: 19 residues processed: 152 average time/residue: 0.4307 time to fit residues: 70.4046 Evaluate side-chains 148 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 166 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 166 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 53 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 chunk 30 optimal weight: 0.0170 chunk 15 optimal weight: 0.0980 chunk 79 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN S 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.172828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.142333 restraints weight = 11320.935| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.86 r_work: 0.3525 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 1.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9426 Z= 0.101 Angle : 0.504 7.368 12799 Z= 0.261 Chirality : 0.040 0.135 1457 Planarity : 0.004 0.049 1586 Dihedral : 4.713 57.504 1294 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.04 % Allowed : 22.17 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.30 (0.26), residues: 1144 helix: 2.66 (0.27), residues: 393 sheet: 0.41 (0.30), residues: 285 loop : -0.40 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.008 0.001 TYR R 303 PHE 0.016 0.001 PHE R 115 TRP 0.016 0.001 TRP B 211 HIS 0.004 0.001 HIS R 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 9425) covalent geometry : angle 0.50361 / 0.26 (12797) SS BOND : bond 0.00490 / 0.26 ( 1) SS BOND : angle 1.43123 / 0.80 ( 2) hydrogen bonds : bond 0.03308 / 2.17 ( 460) hydrogen bonds : angle 3.72940 / 2.69 ( 1311) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.342 Fit side-chains REVERT: R 51 ASN cc_start: 0.7235 (m-40) cc_final: 0.6785 (m110) REVERT: A 17 LYS cc_start: 0.8018 (mttt) cc_final: 0.7754 (mtmt) REVERT: A 24 ARG cc_start: 0.7602 (ttp-110) cc_final: 0.7025 (ttm110) REVERT: A 25 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7057 (tm-30) REVERT: A 28 GLU cc_start: 0.7967 (tt0) cc_final: 0.7587 (mt-10) REVERT: B 46 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7558 (mmt90) REVERT: B 130 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7292 (mp0) REVERT: B 296 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8443 (p) REVERT: G 42 GLU cc_start: 0.7572 (tm-30) cc_final: 0.6376 (mm-30) REVERT: G 46 LYS cc_start: 0.8101 (tppt) cc_final: 0.7855 (mmtm) REVERT: G 58 GLU cc_start: 0.7313 (mp0) cc_final: 0.6339 (tm-30) REVERT: S 46 GLU cc_start: 0.8758 (pt0) cc_final: 0.8496 (pt0) REVERT: S 65 LYS cc_start: 0.7707 (ttpt) cc_final: 0.7238 (tttp) REVERT: S 192 MET cc_start: 0.4550 (mpp) cc_final: 0.2453 (mtm) outliers start: 30 outliers final: 22 residues processed: 158 average time/residue: 0.4741 time to fit residues: 80.4948 Evaluate side-chains 158 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN B 32 GLN S 77 ASN S 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.170754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.139866 restraints weight = 11372.604| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.89 r_work: 0.3491 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 1.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9426 Z= 0.116 Angle : 0.530 8.700 12799 Z= 0.273 Chirality : 0.041 0.134 1457 Planarity : 0.004 0.064 1586 Dihedral : 4.802 59.620 1294 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.04 % Allowed : 22.17 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.26), residues: 1144 helix: 2.56 (0.27), residues: 393 sheet: 0.38 (0.30), residues: 292 loop : -0.42 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.011 0.001 TYR S 190 PHE 0.021 0.001 PHE R 115 TRP 0.016 0.001 TRP B 211 HIS 0.004 0.001 HIS R 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 9425) covalent geometry : angle 0.52982 / 0.27 (12797) SS BOND : bond 0.00639 / 0.34 ( 1) SS BOND : angle 1.52328 / 0.84 ( 2) hydrogen bonds : bond 0.03645 / 2.41 ( 460) hydrogen bonds : angle 3.79381 / 2.74 ( 1311) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.295 Fit side-chains REVERT: R 51 ASN cc_start: 0.7379 (m-40) cc_final: 0.6857 (m110) REVERT: R 308 GLU cc_start: 0.7884 (mp0) cc_final: 0.7444 (mt-10) REVERT: A 17 LYS cc_start: 0.8039 (mttt) cc_final: 0.7769 (mtmt) REVERT: A 24 ARG cc_start: 0.7586 (ttp-110) cc_final: 0.7030 (ttp-110) REVERT: A 25 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7040 (tm-30) REVERT: A 28 GLU cc_start: 0.7938 (tt0) cc_final: 0.7595 (mt-10) REVERT: A 273 LEU cc_start: 0.8003 (tp) cc_final: 0.7785 (tp) REVERT: B 46 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7570 (mmt90) REVERT: B 130 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7310 (mp0) REVERT: B 135 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8702 (p) REVERT: B 215 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7954 (mt-10) REVERT: B 296 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8435 (p) REVERT: G 42 GLU cc_start: 0.7636 (tm-30) cc_final: 0.6382 (mm-30) REVERT: G 46 LYS cc_start: 0.8127 (tppt) cc_final: 0.7889 (mmtm) REVERT: G 58 GLU cc_start: 0.7347 (mp0) cc_final: 0.6360 (tm-30) REVERT: S 46 GLU cc_start: 0.8692 (pt0) cc_final: 0.8357 (pt0) REVERT: S 192 MET cc_start: 0.4638 (mpp) cc_final: 0.2725 (mtm) outliers start: 30 outliers final: 20 residues processed: 159 average time/residue: 0.5044 time to fit residues: 85.9864 Evaluate side-chains 159 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN B 32 GLN G 18 GLN S 77 ASN S 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.170925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.140244 restraints weight = 11238.678| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.88 r_work: 0.3504 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 1.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9426 Z= 0.110 Angle : 0.524 8.981 12799 Z= 0.268 Chirality : 0.040 0.133 1457 Planarity : 0.004 0.063 1586 Dihedral : 4.722 56.323 1294 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.94 % Allowed : 22.57 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.26), residues: 1144 helix: 2.60 (0.27), residues: 391 sheet: 0.41 (0.30), residues: 292 loop : -0.40 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.010 0.001 TYR S 190 PHE 0.020 0.001 PHE R 115 TRP 0.016 0.001 TRP B 211 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 9425) covalent geometry : angle 0.52363 / 0.27 (12797) SS BOND : bond 0.00618 / 0.33 ( 1) SS BOND : angle 1.52388 / 0.85 ( 2) hydrogen bonds : bond 0.03530 / 2.33 ( 460) hydrogen bonds : angle 3.77004 / 2.73 ( 1311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3439.26 seconds wall clock time: 59 minutes 18.41 seconds (3558.41 seconds total)