Starting phenix.real_space_refine on Tue Mar 3 23:27:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wq3_32698/03_2026/7wq3_32698.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wq3_32698/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wq3_32698/03_2026/7wq3_32698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wq3_32698/03_2026/7wq3_32698.map" model { file = "/net/cci-nas-00/data/ceres_data/7wq3_32698/03_2026/7wq3_32698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wq3_32698/03_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 2.10, per 1000 atoms: 0.23 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: 0.67 Conformation dependent library (CDL) restraints added in 341.2 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: 0.32 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: 1.16 Time building geometry restraints manager: 0.88 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: 5564 15.56 - 31.12: 165 31.12 - 46.68: 53 46.68 - 62.24: 23 62.24 - 77.79: 3 Dihedral angle restraints: 5808 sinusoidal: 2443 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 5805 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.940 Find NCS groups from input model: 0.040 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:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4588 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 : 9.420 77.794 3633 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 covalent geometry : bond 0.01071 ( 9425) covalent geometry : angle 0.72428 (12797) SS BOND : bond 0.00054 ( 1) SS BOND : angle 0.37252 ( 2) hydrogen bonds : bond 0.14093 ( 460) hydrogen bonds : angle 4.96401 ( 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 : 0.235 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: 0.4757 time to fit residues: 118.3545 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 : 0.269 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: R 71 ASN R 173 HIS R 190 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.193411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.162132 restraints weight = 11020.608| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.97 r_work: 0.3732 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.6538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9426 Z= 0.205 Angle : 0.765 12.058 12799 Z= 0.388 Chirality : 0.047 0.200 1457 Planarity : 0.005 0.045 1586 Dihedral : 7.295 58.210 1574 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.44 % Allowed : 10.93 % Favored : 85.63 % 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: -0.28 (0.24), residues: 1144 helix: 1.19 (0.27), residues: 392 sheet: -0.45 (0.29), residues: 282 loop : -1.14 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 208 TYR 0.015 0.002 TYR R 84 PHE 0.043 0.003 PHE R 91 TRP 0.015 0.002 TRP R 101 HIS 0.015 0.003 HIS R 173 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9425) covalent geometry : angle 0.76447 (12797) SS BOND : bond 0.00580 ( 1) SS BOND : angle 2.83298 ( 2) hydrogen bonds : bond 0.04585 ( 460) hydrogen bonds : angle 4.51359 ( 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 230 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7829 (mttt) cc_final: 0.7484 (mtmt) REVERT: A 28 GLU cc_start: 0.7355 (tt0) cc_final: 0.6943 (mt-10) REVERT: A 248 LYS cc_start: 0.7891 (ttmm) cc_final: 0.7667 (tmmm) REVERT: A 308 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6625 (mp0) REVERT: A 314 LYS cc_start: 0.6932 (mttt) cc_final: 0.6725 (tppt) REVERT: B 55 LEU cc_start: 0.8314 (mt) cc_final: 0.8029 (mt) REVERT: B 98 SER cc_start: 0.8746 (m) cc_final: 0.8290 (t) REVERT: B 134 ARG cc_start: 0.8299 (mtp180) cc_final: 0.7570 (mtp-110) REVERT: B 138 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8245 (mt-10) REVERT: B 293 ASN cc_start: 0.7840 (p0) cc_final: 0.7320 (m-40) REVERT: G 38 MET cc_start: 0.6479 (OUTLIER) cc_final: 0.6126 (mmm) REVERT: S 3 GLN cc_start: 0.8007 (tm-30) cc_final: 0.7731 (tt0) REVERT: S 46 GLU cc_start: 0.8333 (pt0) cc_final: 0.7857 (pt0) REVERT: S 83 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8311 (ptp) REVERT: S 93 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7264 (tpp) REVERT: S 115 THR cc_start: 0.7120 (t) cc_final: 0.6771 (t) REVERT: S 171 ASN cc_start: 0.6901 (m-40) cc_final: 0.6664 (m110) outliers start: 34 outliers final: 10 residues processed: 214 average time/residue: 0.5175 time to fit residues: 118.8946 Evaluate side-chains 146 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU 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 83 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: 0.7980 chunk 73 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 106 optimal weight: 0.0060 chunk 21 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 20 optimal weight: 0.0770 chunk 78 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 overall best weight: 0.5154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 190 GLN R 299 ASN A 204 GLN B 32 GLN B 156 GLN B 340 ASN S 179 GLN L 5 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.183929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.150473 restraints weight = 10731.529| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.00 r_work: 0.3577 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.7370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9426 Z= 0.104 Angle : 0.493 8.078 12799 Z= 0.258 Chirality : 0.040 0.142 1457 Planarity : 0.003 0.043 1586 Dihedral : 5.762 52.104 1574 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 3.54 % Allowed : 15.79 % Favored : 80.67 % 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: 0.48 (0.25), residues: 1144 helix: 2.00 (0.28), residues: 396 sheet: -0.03 (0.29), residues: 289 loop : -0.93 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 313 TYR 0.007 0.001 TYR S 173 PHE 0.012 0.001 PHE R 115 TRP 0.014 0.001 TRP B 211 HIS 0.006 0.001 HIS R 228 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 9425) covalent geometry : angle 0.49305 (12797) SS BOND : bond 0.00386 ( 1) SS BOND : angle 1.34640 ( 2) hydrogen bonds : bond 0.03302 ( 460) hydrogen bonds : angle 3.87049 ( 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 189 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 133 ARG cc_start: 0.8163 (mtt180) cc_final: 0.7920 (mtt180) REVERT: A 17 LYS cc_start: 0.7928 (mttt) cc_final: 0.7645 (mtmt) REVERT: A 22 ASN cc_start: 0.7675 (m-40) cc_final: 0.7459 (m110) REVERT: A 24 ARG cc_start: 0.7264 (ttp-110) cc_final: 0.6734 (ttm110) REVERT: A 25 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6492 (tm-30) REVERT: A 28 GLU cc_start: 0.7626 (tt0) cc_final: 0.7110 (mt-10) REVERT: A 209 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7349 (mptt) REVERT: B 23 LYS cc_start: 0.7408 (tppp) cc_final: 0.7201 (tppt) REVERT: B 98 SER cc_start: 0.8785 (m) cc_final: 0.8484 (t) REVERT: B 134 ARG cc_start: 0.8339 (mtp180) cc_final: 0.7740 (mtp-110) REVERT: B 215 GLU cc_start: 0.8026 (mp0) cc_final: 0.7471 (mt-10) REVERT: B 219 ARG cc_start: 0.8575 (mpt90) cc_final: 0.8195 (mpt-90) REVERT: B 268 ASN cc_start: 0.7394 (t0) cc_final: 0.7054 (m-40) REVERT: S 46 GLU cc_start: 0.8507 (pt0) cc_final: 0.8183 (pt0) REVERT: S 191 ARG cc_start: 0.2886 (OUTLIER) cc_final: 0.1967 (tpp80) outliers start: 35 outliers final: 12 residues processed: 173 average time/residue: 0.5444 time to fit residues: 100.5533 Evaluate side-chains 142 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain A residue 209 LYS 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 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: 3.9990 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 101 optimal weight: 0.0170 chunk 61 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 190 GLN A 204 GLN B 32 GLN S 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.170089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.138411 restraints weight = 11498.718| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.92 r_work: 0.3485 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 1.0506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9426 Z= 0.207 Angle : 0.684 9.201 12799 Z= 0.359 Chirality : 0.046 0.208 1457 Planarity : 0.005 0.054 1586 Dihedral : 6.518 58.057 1574 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.86 % Allowed : 15.59 % 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: 0.45 (0.25), residues: 1144 helix: 1.82 (0.27), residues: 400 sheet: 0.07 (0.30), residues: 282 loop : -0.90 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 68 TYR 0.018 0.002 TYR S 95 PHE 0.031 0.002 PHE R 115 TRP 0.015 0.002 TRP R 101 HIS 0.010 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 9425) covalent geometry : angle 0.68291 (12797) SS BOND : bond 0.00968 ( 1) SS BOND : angle 2.53421 ( 2) hydrogen bonds : bond 0.05508 ( 460) hydrogen bonds : angle 4.45515 ( 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 199 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 0.367 Fit side-chains REVERT: R 42 LEU cc_start: 0.7057 (tp) cc_final: 0.6851 (mp) REVERT: A 24 ARG cc_start: 0.7481 (ttp-110) cc_final: 0.6957 (mtm-85) REVERT: A 25 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6928 (tm-30) REVERT: A 28 GLU cc_start: 0.7870 (tt0) cc_final: 0.7336 (mt-10) REVERT: A 209 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7867 (mppt) REVERT: B 42 ARG cc_start: 0.6864 (tpt170) cc_final: 0.6600 (tmt170) REVERT: B 46 ARG cc_start: 0.8143 (mmt-90) cc_final: 0.7772 (mtp-110) REVERT: B 130 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7179 (mp0) REVERT: B 134 ARG cc_start: 0.8210 (mtp180) cc_final: 0.7959 (ptp90) REVERT: B 135 VAL cc_start: 0.9053 (t) cc_final: 0.8768 (p) REVERT: B 212 ASP cc_start: 0.8441 (t70) cc_final: 0.7854 (p0) REVERT: B 312 ASP cc_start: 0.8428 (m-30) cc_final: 0.8156 (m-30) REVERT: G 58 GLU cc_start: 0.7220 (mp0) cc_final: 0.6111 (tm-30) REVERT: S 6 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8030 (mt-10) REVERT: S 46 GLU cc_start: 0.8774 (pt0) cc_final: 0.8429 (pt0) REVERT: S 78 THR cc_start: 0.8278 (t) cc_final: 0.7897 (m) REVERT: S 189 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8236 (mt) outliers start: 48 outliers final: 23 residues processed: 183 average time/residue: 0.5537 time to fit residues: 108.0551 Evaluate side-chains 150 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 258 ILE Chi-restraints excluded: chain R residue 259 SER Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 307 SER 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 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 57 THR 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 189 ILE Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 190 GLN R 225 ASN A 204 GLN B 16 ASN B 32 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.168905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.136526 restraints weight = 11318.430| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.91 r_work: 0.3479 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 1.0660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9426 Z= 0.137 Angle : 0.545 8.259 12799 Z= 0.286 Chirality : 0.042 0.136 1457 Planarity : 0.004 0.056 1586 Dihedral : 5.755 59.809 1574 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.15 % Allowed : 18.12 % Favored : 77.73 % 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: 0.81 (0.25), residues: 1144 helix: 2.29 (0.27), residues: 389 sheet: 0.25 (0.30), residues: 284 loop : -0.77 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.009 0.001 TYR S 103 PHE 0.021 0.002 PHE R 115 TRP 0.015 0.001 TRP B 211 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9425) covalent geometry : angle 0.54478 (12797) SS BOND : bond 0.00837 ( 1) SS BOND : angle 1.82260 ( 2) hydrogen bonds : bond 0.04084 ( 460) hydrogen bonds : angle 4.01115 ( 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 174 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 0.452 Fit side-chains REVERT: R 225 ASN cc_start: 0.8391 (t0) cc_final: 0.8159 (t0) REVERT: R 234 MET cc_start: 0.7604 (mmm) cc_final: 0.7353 (mmp) REVERT: A 24 ARG cc_start: 0.7641 (ttp-110) cc_final: 0.7085 (ttp-110) REVERT: A 25 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7050 (tm-30) REVERT: A 28 GLU cc_start: 0.7904 (tt0) cc_final: 0.7553 (mt-10) REVERT: A 209 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7896 (mptt) REVERT: A 306 GLN cc_start: 0.8107 (mm110) cc_final: 0.7907 (mm110) REVERT: B 42 ARG cc_start: 0.6969 (tpt170) cc_final: 0.6746 (tmt170) REVERT: B 46 ARG cc_start: 0.8155 (mmt-90) cc_final: 0.7784 (mtp-110) REVERT: B 130 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7285 (mp0) REVERT: B 134 ARG cc_start: 0.8215 (mtp180) cc_final: 0.7999 (ptp90) REVERT: B 219 ARG cc_start: 0.8417 (mpt90) cc_final: 0.8123 (mpt-90) REVERT: G 58 GLU cc_start: 0.7331 (mp0) cc_final: 0.6248 (tm-30) REVERT: S 46 GLU cc_start: 0.8715 (pt0) cc_final: 0.8438 (pt0) REVERT: S 78 THR cc_start: 0.8254 (t) cc_final: 0.7796 (m) REVERT: S 186 GLN cc_start: 0.8155 (tt0) cc_final: 0.7925 (tt0) outliers start: 41 outliers final: 21 residues processed: 157 average time/residue: 0.5785 time to fit residues: 96.8600 Evaluate side-chains 145 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 254 VAL Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain A residue 209 LYS 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 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER 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 B residue 267 ASP Chi-restraints excluded: chain B residue 338 ILE 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 166 LEU Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain L residue 6 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 32 GLN B 266 HIS B 268 ASN G 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.165966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.135610 restraints weight = 11363.866| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.88 r_work: 0.3441 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 1.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9426 Z= 0.151 Angle : 0.575 8.354 12799 Z= 0.297 Chirality : 0.043 0.140 1457 Planarity : 0.004 0.055 1586 Dihedral : 5.794 58.117 1574 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.05 % Allowed : 19.23 % Favored : 76.72 % 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: 0.81 (0.25), residues: 1144 helix: 2.23 (0.27), residues: 393 sheet: 0.22 (0.30), residues: 285 loop : -0.73 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.011 0.001 TYR S 95 PHE 0.027 0.002 PHE R 115 TRP 0.017 0.001 TRP B 211 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9425) covalent geometry : angle 0.57433 (12797) SS BOND : bond 0.00901 ( 1) SS BOND : angle 1.89315 ( 2) hydrogen bonds : bond 0.04410 ( 460) hydrogen bonds : angle 4.03791 ( 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 167 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 0.278 Fit side-chains REVERT: R 225 ASN cc_start: 0.8341 (t0) cc_final: 0.8117 (t0) REVERT: A 24 ARG cc_start: 0.7549 (ttp-110) cc_final: 0.6995 (ttp-110) REVERT: A 25 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7065 (tm-30) REVERT: A 28 GLU cc_start: 0.7925 (tt0) cc_final: 0.7550 (mt-10) REVERT: A 209 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7928 (mppt) REVERT: B 46 ARG cc_start: 0.8120 (mmt-90) cc_final: 0.7814 (mtp-110) REVERT: B 130 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7423 (mp0) REVERT: B 134 ARG cc_start: 0.8209 (mtp180) cc_final: 0.7972 (ptp90) REVERT: B 219 ARG cc_start: 0.8413 (mpt90) cc_final: 0.8090 (mpt-90) REVERT: G 58 GLU cc_start: 0.7405 (mp0) cc_final: 0.6330 (tm-30) REVERT: S 46 GLU cc_start: 0.8694 (pt0) cc_final: 0.8410 (pt0) REVERT: S 78 THR cc_start: 0.8279 (t) cc_final: 0.7890 (m) REVERT: S 186 GLN cc_start: 0.8176 (tt0) cc_final: 0.7941 (tt0) outliers start: 40 outliers final: 26 residues processed: 154 average time/residue: 0.5711 time to fit residues: 93.6255 Evaluate side-chains 149 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 254 VAL Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 310 LEU 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 187 VAL Chi-restraints excluded: chain B residue 211 TRP 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 B residue 338 ILE 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 Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain L residue 6 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 106 optimal weight: 0.0170 chunk 101 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 110 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN G 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.170223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.139320 restraints weight = 11463.408| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.88 r_work: 0.3497 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 1.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9426 Z= 0.096 Angle : 0.487 8.249 12799 Z= 0.253 Chirality : 0.040 0.129 1457 Planarity : 0.004 0.054 1586 Dihedral : 5.394 54.005 1574 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.54 % Allowed : 19.84 % Favored : 76.62 % 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: 1.09 (0.26), residues: 1144 helix: 2.55 (0.28), residues: 391 sheet: 0.39 (0.30), residues: 283 loop : -0.65 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.009 0.001 TYR R 303 PHE 0.016 0.001 PHE R 115 TRP 0.017 0.001 TRP B 211 HIS 0.004 0.001 HIS R 112 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 9425) covalent geometry : angle 0.48657 (12797) SS BOND : bond 0.00405 ( 1) SS BOND : angle 1.40990 ( 2) hydrogen bonds : bond 0.03368 ( 460) hydrogen bonds : angle 3.77762 ( 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 175 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.218 Fit side-chains REVERT: R 225 ASN cc_start: 0.8362 (t0) cc_final: 0.8151 (t0) REVERT: R 271 GLU cc_start: 0.7557 (tp30) cc_final: 0.7201 (mm-30) REVERT: A 24 ARG cc_start: 0.7591 (ttp-110) cc_final: 0.7045 (ttm110) REVERT: A 25 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7066 (tm-30) REVERT: A 28 GLU cc_start: 0.7890 (tt0) cc_final: 0.7578 (mt-10) REVERT: A 209 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8088 (mptt) REVERT: B 46 ARG cc_start: 0.8126 (mmt-90) cc_final: 0.7838 (mtp-110) REVERT: B 76 ASP cc_start: 0.7808 (m-30) cc_final: 0.7509 (m-30) REVERT: B 130 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7378 (mp0) REVERT: B 212 ASP cc_start: 0.8327 (t70) cc_final: 0.7920 (p0) REVERT: B 219 ARG cc_start: 0.8354 (mpt90) cc_final: 0.7924 (mpt-90) REVERT: G 58 GLU cc_start: 0.7427 (mp0) cc_final: 0.6368 (tm-30) REVERT: S 46 GLU cc_start: 0.8713 (pt0) cc_final: 0.8448 (pt0) REVERT: S 65 LYS cc_start: 0.7791 (ttpt) cc_final: 0.7257 (tttm) REVERT: S 78 THR cc_start: 0.8142 (t) cc_final: 0.7780 (m) REVERT: S 113 GLN cc_start: 0.8146 (mm110) cc_final: 0.7899 (mm110) REVERT: S 186 GLN cc_start: 0.8157 (tt0) cc_final: 0.7948 (tt0) REVERT: S 192 MET cc_start: 0.4780 (mpp) cc_final: 0.3435 (mpp) outliers start: 35 outliers final: 16 residues processed: 161 average time/residue: 0.5041 time to fit residues: 87.1184 Evaluate side-chains 147 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 163 SER Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 351 CYS 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 147 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR 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: 2.9990 chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 268 ASN G 18 GLN S 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.168897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.138361 restraints weight = 11239.752| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.90 r_work: 0.3478 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 1.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9426 Z= 0.119 Angle : 0.526 8.717 12799 Z= 0.273 Chirality : 0.041 0.131 1457 Planarity : 0.004 0.055 1586 Dihedral : 5.455 55.321 1574 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.83 % Allowed : 21.46 % Favored : 75.71 % 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: 1.08 (0.26), residues: 1144 helix: 2.50 (0.27), residues: 394 sheet: 0.37 (0.30), residues: 283 loop : -0.60 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.020 0.001 TYR R 293 PHE 0.021 0.001 PHE R 115 TRP 0.018 0.001 TRP B 211 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9425) covalent geometry : angle 0.52565 (12797) SS BOND : bond 0.00683 ( 1) SS BOND : angle 1.56779 ( 2) hydrogen bonds : bond 0.03826 ( 460) hydrogen bonds : angle 3.83307 ( 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 160 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.354 Fit side-chains REVERT: R 225 ASN cc_start: 0.8349 (t0) cc_final: 0.8127 (t0) REVERT: R 308 GLU cc_start: 0.7821 (mp0) cc_final: 0.7581 (mt-10) REVERT: A 24 ARG cc_start: 0.7567 (ttp-110) cc_final: 0.7006 (mtm-85) REVERT: A 25 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7054 (tm-30) REVERT: A 28 GLU cc_start: 0.7904 (tt0) cc_final: 0.7583 (mt-10) REVERT: A 209 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.8018 (mptt) REVERT: A 345 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8381 (mttp) REVERT: B 46 ARG cc_start: 0.8157 (mmt-90) cc_final: 0.7839 (mtp-110) REVERT: B 130 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7415 (mp0) REVERT: B 135 VAL cc_start: 0.8980 (t) cc_final: 0.8644 (p) REVERT: B 212 ASP cc_start: 0.8313 (t70) cc_final: 0.7820 (p0) REVERT: B 219 ARG cc_start: 0.8347 (mpt90) cc_final: 0.7937 (mpt-90) REVERT: B 296 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8480 (p) REVERT: G 58 GLU cc_start: 0.7378 (mp0) cc_final: 0.6380 (tm-30) REVERT: S 46 GLU cc_start: 0.8699 (pt0) cc_final: 0.8432 (pt0) REVERT: S 78 THR cc_start: 0.8374 (t) cc_final: 0.7967 (m) REVERT: S 186 GLN cc_start: 0.8155 (tt0) cc_final: 0.7950 (tt0) REVERT: S 192 MET cc_start: 0.4955 (mpp) cc_final: 0.3675 (mpp) outliers start: 28 outliers final: 19 residues processed: 152 average time/residue: 0.5770 time to fit residues: 93.7307 Evaluate side-chains 151 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 132 ASP Chi-restraints excluded: chain R residue 163 SER Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 351 CYS 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 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 chunk 15 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 268 ASN G 18 GLN S 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.166891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.135860 restraints weight = 11289.792| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.94 r_work: 0.3440 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 1.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9426 Z= 0.139 Angle : 0.567 9.164 12799 Z= 0.291 Chirality : 0.042 0.135 1457 Planarity : 0.004 0.055 1586 Dihedral : 5.631 55.617 1574 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.85 % Allowed : 20.55 % 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: 0.98 (0.25), residues: 1144 helix: 2.41 (0.27), residues: 394 sheet: 0.29 (0.30), residues: 283 loop : -0.64 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.020 0.002 TYR R 293 PHE 0.023 0.002 PHE R 115 TRP 0.017 0.001 TRP B 211 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9425) covalent geometry : angle 0.56628 (12797) SS BOND : bond 0.00787 ( 1) SS BOND : angle 1.75820 ( 2) hydrogen bonds : bond 0.04193 ( 460) hydrogen bonds : angle 3.91654 ( 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 172 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 0.364 Fit side-chains REVERT: R 166 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7942 (ttt) REVERT: R 225 ASN cc_start: 0.8343 (t0) cc_final: 0.8126 (t0) REVERT: R 308 GLU cc_start: 0.7893 (mp0) cc_final: 0.7596 (mt-10) REVERT: A 24 ARG cc_start: 0.7546 (ttp-110) cc_final: 0.6957 (mtm-85) REVERT: A 25 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6990 (tm-30) REVERT: A 28 GLU cc_start: 0.7912 (tt0) cc_final: 0.7552 (mt-10) REVERT: A 209 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.8040 (mptt) REVERT: A 345 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8372 (mttp) REVERT: B 46 ARG cc_start: 0.8171 (mmt-90) cc_final: 0.7818 (mtp-110) REVERT: B 130 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7319 (mp0) REVERT: B 135 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8671 (p) REVERT: B 212 ASP cc_start: 0.8446 (t70) cc_final: 0.7771 (p0) REVERT: B 219 ARG cc_start: 0.8364 (mpt90) cc_final: 0.7992 (mpt-90) REVERT: B 296 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8475 (p) REVERT: G 58 GLU cc_start: 0.7466 (mp0) cc_final: 0.6423 (tm-30) REVERT: S 46 GLU cc_start: 0.8719 (pt0) cc_final: 0.8376 (pt0) REVERT: S 65 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7337 (tttm) REVERT: S 76 LYS cc_start: 0.7757 (mtpp) cc_final: 0.7221 (ttmt) REVERT: S 78 THR cc_start: 0.8390 (t) cc_final: 0.8044 (m) REVERT: S 98 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8170 (ttp-170) REVERT: S 186 GLN cc_start: 0.8161 (tt0) cc_final: 0.7926 (tt0) REVERT: S 192 MET cc_start: 0.5083 (mpp) cc_final: 0.3932 (mpp) REVERT: S 245 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7638 (mp) outliers start: 38 outliers final: 23 residues processed: 159 average time/residue: 0.5752 time to fit residues: 97.5185 Evaluate side-chains 159 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 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 R residue 166 MET Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 351 CYS 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 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP 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 S residue 65 LYS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain L residue 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 36 ASN B 268 ASN G 18 GLN S 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.165777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135467 restraints weight = 11365.353| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.89 r_work: 0.3440 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 1.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9426 Z= 0.155 Angle : 0.584 9.676 12799 Z= 0.301 Chirality : 0.043 0.202 1457 Planarity : 0.004 0.056 1586 Dihedral : 5.761 56.350 1574 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.34 % Allowed : 21.46 % Favored : 75.20 % 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: 0.91 (0.25), residues: 1144 helix: 2.38 (0.27), residues: 392 sheet: 0.30 (0.30), residues: 276 loop : -0.72 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.017 0.002 TYR R 293 PHE 0.027 0.002 PHE R 115 TRP 0.017 0.001 TRP B 211 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9425) covalent geometry : angle 0.58388 (12797) SS BOND : bond 0.00845 ( 1) SS BOND : angle 1.75052 ( 2) hydrogen bonds : bond 0.04407 ( 460) hydrogen bonds : angle 3.99724 ( 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 162 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.263 Fit side-chains REVERT: R 166 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.8049 (ttt) REVERT: R 225 ASN cc_start: 0.8342 (t0) cc_final: 0.8117 (t0) REVERT: R 308 GLU cc_start: 0.7889 (mp0) cc_final: 0.7608 (mt-10) REVERT: A 24 ARG cc_start: 0.7551 (ttp-110) cc_final: 0.6978 (mtm-85) REVERT: A 25 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7024 (tm-30) REVERT: A 28 GLU cc_start: 0.7934 (tt0) cc_final: 0.7570 (mt-10) REVERT: A 209 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7972 (mppt) REVERT: A 273 LEU cc_start: 0.8072 (tp) cc_final: 0.7869 (tp) REVERT: B 46 ARG cc_start: 0.8193 (mmt-90) cc_final: 0.7844 (mtp-110) REVERT: B 130 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7334 (mp0) REVERT: B 135 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8710 (p) REVERT: B 219 ARG cc_start: 0.8342 (mpt90) cc_final: 0.8064 (mpt-90) REVERT: B 296 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8479 (p) REVERT: G 58 GLU cc_start: 0.7454 (mp0) cc_final: 0.6431 (tm-30) REVERT: S 46 GLU cc_start: 0.8715 (pt0) cc_final: 0.8377 (pt0) REVERT: S 65 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7379 (tttm) REVERT: S 76 LYS cc_start: 0.7821 (mtpp) cc_final: 0.7366 (ttmt) REVERT: S 78 THR cc_start: 0.8453 (t) cc_final: 0.8135 (m) REVERT: S 98 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8187 (ttp-170) REVERT: S 192 MET cc_start: 0.4953 (mpp) cc_final: 0.4235 (mpp) REVERT: S 245 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7676 (mp) outliers start: 33 outliers final: 23 residues processed: 150 average time/residue: 0.5620 time to fit residues: 89.8906 Evaluate side-chains 155 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 R residue 261 LEU Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 310 LEU 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 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain L residue 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 60 optimal weight: 0.0370 chunk 105 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 36 ASN G 18 GLN S 77 ASN S 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.168065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.137214 restraints weight = 11218.243| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.91 r_work: 0.3461 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 1.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9426 Z= 0.116 Angle : 0.530 9.329 12799 Z= 0.274 Chirality : 0.041 0.190 1457 Planarity : 0.004 0.055 1586 Dihedral : 5.510 57.423 1574 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.94 % Allowed : 21.76 % Favored : 75.30 % 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: 1.02 (0.26), residues: 1144 helix: 2.56 (0.27), residues: 390 sheet: 0.27 (0.30), residues: 288 loop : -0.69 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.017 0.001 TYR R 293 PHE 0.019 0.001 PHE R 115 TRP 0.018 0.001 TRP B 211 HIS 0.004 0.001 HIS R 112 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9425) covalent geometry : angle 0.52944 (12797) SS BOND : bond 0.00566 ( 1) SS BOND : angle 1.47039 ( 2) hydrogen bonds : bond 0.03784 ( 460) hydrogen bonds : angle 3.86038 ( 1311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3767.49 seconds wall clock time: 64 minutes 46.58 seconds (3886.58 seconds total)