Starting phenix.real_space_refine on Sun Apr 5 08:39:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m8k_63712/04_2026/9m8k_63712.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m8k_63712/04_2026/9m8k_63712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m8k_63712/04_2026/9m8k_63712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m8k_63712/04_2026/9m8k_63712.map" model { file = "/net/cci-nas-00/data/ceres_data/9m8k_63712/04_2026/9m8k_63712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m8k_63712/04_2026/9m8k_63712.cif" } resolution = 3.0 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= -0.001 sd= 0.158 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 5752 2.51 5 N 1504 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8992 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1885 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 2, 'TRANS': 235} Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2591 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 4, 'TRANS': 334} Chain: "G" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 465 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 6, 'TRANS': 49} Chain: "N" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2226 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 7, 'TRANS': 271} Chain breaks: 1 Chain: "S" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Time building chain proxies: 2.00, per 1000 atoms: 0.22 Number of scatterers: 8992 At special positions: 0 Unit cell: (95.7, 124.3, 129.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1668 8.00 N 1504 7.00 C 5752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS N 159 " - pdb=" SG CYS N 229 " distance=2.04 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: 0.62 Conformation dependent library (CDL) restraints added in 304.6 milliseconds 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 13 sheets defined 38.8% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.903A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 4.461A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 4.119A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 211 through 216' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 271 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.287A pdb=" N ILE A 285 " --> pdb=" O HIS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.549A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.727A pdb=" N PHE A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 6 through 21 Processing helix chain 'G' and resid 26 through 41 Proline residue: G 32 - end of helix Processing helix chain 'G' and resid 49 through 54 removed outlier: 4.087A pdb=" N LEU G 52 " --> pdb=" O ASN G 49 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS G 54 " --> pdb=" O ASP G 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.694A pdb=" N SER N 31 " --> pdb=" O ALA N 28 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 53 through 56 removed outlier: 3.905A pdb=" N GLY N 56 " --> pdb=" O SER N 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 53 through 56' Processing helix chain 'N' and resid 220 through 224 removed outlier: 3.693A pdb=" N ASP N 223 " --> pdb=" O GLU N 220 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL N 224 " --> pdb=" O ALA N 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 220 through 224' Processing helix chain 'R' and resid 2 through 38 Processing helix chain 'R' and resid 42 through 72 Processing helix chain 'R' and resid 77 through 111 removed outlier: 3.661A pdb=" N LYS R 109 " --> pdb=" O LEU R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 126 removed outlier: 4.223A pdb=" N SER R 126 " --> pdb=" O LYS R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 154 Processing helix chain 'R' and resid 176 through 213 Processing helix chain 'R' and resid 222 through 251 removed outlier: 3.779A pdb=" N VAL R 226 " --> pdb=" O THR R 222 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU R 236 " --> pdb=" O MET R 232 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE R 237 " --> pdb=" O VAL R 233 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE R 240 " --> pdb=" O LEU R 236 " (cutoff:3.500A) Proline residue: R 241 - end of helix removed outlier: 3.541A pdb=" N LEU R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 269 Processing helix chain 'R' and resid 271 through 284 Processing helix chain 'R' and resid 284 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 removed outlier: 4.357A pdb=" N ILE A 56 " --> pdb=" O GLN A 188 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLN A 188 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 9.745A pdb=" N CYS A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LYS A 35 " --> pdb=" O CYS A 220 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 234 removed outlier: 3.578A pdb=" N VAL A 240 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.177A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.868A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS B 91 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.889A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TYR B 105 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N PHE B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.755A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE B 151 " --> pdb=" O ASN B 156 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.750A 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: 6.552A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU B 190 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU B 198 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.494A pdb=" N CYS B 250 " --> pdb=" O CYS B 263 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N CYS B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.833A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.933A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N TYR N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N MET N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 146 through 148 removed outlier: 3.842A pdb=" N GLU N 246 " --> pdb=" O VAL N 147 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY N 225 " --> pdb=" O LEU N 245 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU N 174 " --> pdb=" O TYR N 190 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR N 190 " --> pdb=" O LEU N 174 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP N 176 " --> pdb=" O LEU N 188 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR N 190 " --> pdb=" O ASN N 194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 155 through 160 removed outlier: 4.209A pdb=" N ALA N 211 " --> pdb=" O SER N 208 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1305 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: 1.37 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2855 1.35 - 1.47: 2290 1.47 - 1.59: 3938 1.59 - 1.71: 0 1.71 - 1.83: 100 Bond restraints: 9183 Sorted by residual: bond pdb=" CA VAL G 6 " pdb=" CB VAL G 6 " ideal model delta sigma weight residual 1.534 1.543 -0.009 6.80e-03 2.16e+04 1.60e+00 bond pdb=" CB ILE R 21 " pdb=" CG2 ILE R 21 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.50e+00 bond pdb=" CA ASP B 254 " pdb=" CB ASP B 254 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.55e-02 4.16e+03 1.47e+00 bond pdb=" CB ASP B 212 " pdb=" CG ASP B 212 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.04e+00 bond pdb=" CG LEU R 181 " pdb=" CD2 LEU R 181 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.01e+00 ... (remaining 9178 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 12236 2.36 - 4.73: 152 4.73 - 7.09: 22 7.09 - 9.46: 5 9.46 - 11.82: 2 Bond angle restraints: 12417 Sorted by residual: angle pdb=" C THR G 30 " pdb=" N ILE G 31 " pdb=" CA ILE G 31 " ideal model delta sigma weight residual 120.33 123.44 -3.11 8.00e-01 1.56e+00 1.51e+01 angle pdb=" N ARG N 202 " pdb=" CA ARG N 202 " pdb=" C ARG N 202 " ideal model delta sigma weight residual 113.97 109.46 4.51 1.28e+00 6.10e-01 1.24e+01 angle pdb=" CB MET A 232 " pdb=" CG MET A 232 " pdb=" SD MET A 232 " ideal model delta sigma weight residual 112.70 122.92 -10.22 3.00e+00 1.11e-01 1.16e+01 angle pdb=" CA LEU R 181 " pdb=" CB LEU R 181 " pdb=" CG LEU R 181 " ideal model delta sigma weight residual 116.30 128.12 -11.82 3.50e+00 8.16e-02 1.14e+01 angle pdb=" CG MET B 300 " pdb=" SD MET B 300 " pdb=" CE MET B 300 " ideal model delta sigma weight residual 100.90 107.91 -7.01 2.20e+00 2.07e-01 1.02e+01 ... (remaining 12412 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 4720 16.06 - 32.11: 501 32.11 - 48.17: 177 48.17 - 64.23: 30 64.23 - 80.29: 5 Dihedral angle restraints: 5433 sinusoidal: 2119 harmonic: 3314 Sorted by residual: dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual -180.00 -151.86 -28.14 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 162.80 17.20 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA LEU B 79 " pdb=" C LEU B 79 " pdb=" N ILE B 80 " pdb=" CA ILE B 80 " ideal model delta harmonic sigma weight residual -180.00 -163.85 -16.15 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 5430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 865 0.030 - 0.060: 342 0.060 - 0.089: 122 0.089 - 0.119: 70 0.119 - 0.149: 13 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CB THR A 340 " pdb=" CA THR A 340 " pdb=" OG1 THR A 340 " pdb=" CG2 THR A 340 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA VAL A 218 " pdb=" N VAL A 218 " pdb=" C VAL A 218 " pdb=" CB VAL A 218 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA MET N 192 " pdb=" N MET N 192 " pdb=" C MET N 192 " pdb=" CB MET N 192 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 1409 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 212 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C ASP B 212 " -0.024 2.00e-02 2.50e+03 pdb=" O ASP B 212 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL B 213 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO B 236 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 254 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.53e+00 pdb=" CG ASP B 254 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASP B 254 " 0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP B 254 " 0.007 2.00e-02 2.50e+03 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 230 2.71 - 3.26: 8318 3.26 - 3.80: 13642 3.80 - 4.35: 16252 4.35 - 4.90: 29276 Nonbonded interactions: 67718 Sorted by model distance: nonbonded pdb=" OG1 THR A 181 " pdb=" O THR B 143 " model vdw 2.162 3.040 nonbonded pdb=" NH2 ARG B 49 " pdb=" O TRP G 58 " model vdw 2.195 3.120 nonbonded pdb=" O SER R 13 " pdb=" ND2 ASN R 17 " model vdw 2.215 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.240 3.040 nonbonded pdb=" O PHE N 32 " pdb=" NH2 ARG N 72 " model vdw 2.297 3.120 ... (remaining 67713 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.100 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:10.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 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 : 0.003 0.040 9184 Z= 0.159 Angle : 0.706 11.819 12419 Z= 0.394 Chirality : 0.042 0.149 1412 Planarity : 0.004 0.038 1552 Dihedral : 15.164 80.285 3292 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.09 % Favored : 96.82 % Rotamer: Outliers : 2.10 % Allowed : 22.78 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.44 (0.25), residues: 1131 helix: 2.88 (0.25), residues: 413 sheet: -0.38 (0.30), residues: 288 loop : -1.92 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.015 0.001 TYR N 190 PHE 0.021 0.002 PHE R 49 TRP 0.017 0.002 TRP B 211 HIS 0.005 0.001 HIS N 35 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9183) covalent geometry : angle 0.70549 (12417) SS BOND : bond 0.00534 ( 1) SS BOND : angle 1.34376 ( 2) hydrogen bonds : bond 0.14251 ( 454) hydrogen bonds : angle 4.95399 ( 1305) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7089 (tp30) cc_final: 0.6762 (mt-10) REVERT: A 29 LYS cc_start: 0.7274 (tttt) cc_final: 0.6724 (tptt) REVERT: A 198 MET cc_start: 0.7739 (ttp) cc_final: 0.7379 (tpp) REVERT: A 200 ASP cc_start: 0.7805 (t0) cc_final: 0.7426 (m-30) REVERT: A 224 CYS cc_start: 0.8409 (p) cc_final: 0.7964 (t) REVERT: B 4 MET cc_start: 0.6547 (mpp) cc_final: 0.5546 (mmm) REVERT: B 44 GLN cc_start: 0.7138 (mt0) cc_final: 0.6828 (tt0) REVERT: B 45 MET cc_start: 0.7228 (mtt) cc_final: 0.3854 (pp-130) REVERT: B 52 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6673 (mtt-85) REVERT: B 68 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.6543 (tttm) REVERT: B 75 GLN cc_start: 0.4810 (mm-40) cc_final: 0.4512 (mm-40) REVERT: B 96 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6977 (ttp80) REVERT: B 101 MET cc_start: 0.7594 (mtp) cc_final: 0.7363 (mtm) REVERT: B 112 VAL cc_start: 0.7477 (t) cc_final: 0.7228 (p) REVERT: B 127 LYS cc_start: 0.6702 (mttt) cc_final: 0.6135 (mmpt) REVERT: B 134 LYS cc_start: 0.6742 (mttt) cc_final: 0.6001 (mmmt) REVERT: B 188 MET cc_start: 0.7641 (mtp) cc_final: 0.7440 (mtp) REVERT: B 227 SER cc_start: 0.9142 (m) cc_final: 0.8815 (t) REVERT: B 300 MET cc_start: 0.7646 (tpt) cc_final: 0.7354 (mmm) REVERT: B 327 VAL cc_start: 0.6724 (OUTLIER) cc_final: 0.6279 (t) REVERT: G 9 MET cc_start: 0.5398 (mmm) cc_final: 0.4823 (mpm) REVERT: G 26 MET cc_start: 0.7648 (mmp) cc_final: 0.6349 (tmm) REVERT: N 17 SER cc_start: 0.8041 (m) cc_final: 0.7466 (t) REVERT: N 34 MET cc_start: 0.8774 (mmm) cc_final: 0.8560 (mmt) REVERT: N 46 GLU cc_start: 0.7548 (pt0) cc_final: 0.7167 (pm20) REVERT: R 55 ARG cc_start: 0.6596 (mmm-85) cc_final: 0.6276 (mtt90) REVERT: R 66 THR cc_start: 0.7008 (m) cc_final: 0.6773 (p) REVERT: R 89 MET cc_start: 0.6934 (ttm) cc_final: 0.6671 (mtp) REVERT: R 257 MET cc_start: 0.5826 (mmm) cc_final: 0.5560 (mmp) outliers start: 21 outliers final: 1 residues processed: 183 average time/residue: 0.4675 time to fit residues: 92.2973 Evaluate side-chains 121 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 237 ASN B 266 HIS B 340 ASN N 167 HIS N 169 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.248827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.196942 restraints weight = 8659.448| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 1.89 r_work: 0.3788 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9184 Z= 0.146 Angle : 0.614 7.925 12419 Z= 0.313 Chirality : 0.043 0.237 1412 Planarity : 0.004 0.033 1552 Dihedral : 5.371 58.220 1238 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.45 % Favored : 96.46 % Rotamer: Outliers : 5.69 % Allowed : 20.78 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.61 (0.25), residues: 1131 helix: 3.04 (0.25), residues: 419 sheet: -0.38 (0.30), residues: 289 loop : -1.84 (0.26), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 40 TYR 0.018 0.002 TYR N 190 PHE 0.017 0.002 PHE N 32 TRP 0.019 0.002 TRP B 211 HIS 0.006 0.002 HIS N 232 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9183) covalent geometry : angle 0.61331 (12417) SS BOND : bond 0.00773 ( 1) SS BOND : angle 1.97715 ( 2) hydrogen bonds : bond 0.04557 ( 454) hydrogen bonds : angle 3.96263 ( 1305) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 119 time to evaluate : 0.271 Fit side-chains REVERT: A 198 MET cc_start: 0.7980 (ttp) cc_final: 0.7746 (tpp) REVERT: A 200 ASP cc_start: 0.7966 (t0) cc_final: 0.7367 (m-30) REVERT: A 224 CYS cc_start: 0.8599 (p) cc_final: 0.8164 (t) REVERT: B 4 MET cc_start: 0.6361 (mpp) cc_final: 0.5610 (mmm) REVERT: B 44 GLN cc_start: 0.7100 (mt0) cc_final: 0.6847 (tt0) REVERT: B 46 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6711 (mmt180) REVERT: B 65 THR cc_start: 0.7415 (m) cc_final: 0.7185 (p) REVERT: B 68 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7782 (tttm) REVERT: B 134 LYS cc_start: 0.6635 (mttt) cc_final: 0.6221 (mmmt) REVERT: B 154 ASP cc_start: 0.7251 (m-30) cc_final: 0.6628 (m-30) REVERT: B 227 SER cc_start: 0.9236 (m) cc_final: 0.8934 (t) REVERT: B 300 MET cc_start: 0.8070 (tpt) cc_final: 0.7710 (mmm) REVERT: B 314 ARG cc_start: 0.7583 (ttm170) cc_final: 0.6509 (ttp80) REVERT: B 327 VAL cc_start: 0.7700 (OUTLIER) cc_final: 0.6957 (t) REVERT: G 9 MET cc_start: 0.5461 (mmm) cc_final: 0.5014 (mpm) REVERT: G 26 MET cc_start: 0.7326 (mmp) cc_final: 0.5835 (tmm) REVERT: N 17 SER cc_start: 0.7810 (m) cc_final: 0.7391 (t) REVERT: N 46 GLU cc_start: 0.7525 (pt0) cc_final: 0.7243 (pm20) REVERT: N 103 TYR cc_start: 0.8185 (t80) cc_final: 0.7714 (t80) REVERT: R 18 PHE cc_start: 0.4366 (t80) cc_final: 0.3812 (t80) outliers start: 57 outliers final: 23 residues processed: 167 average time/residue: 0.4875 time to fit residues: 87.4063 Evaluate side-chains 132 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 215 THR Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 233 VAL Chi-restraints excluded: chain R residue 264 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 3 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 82 optimal weight: 0.0770 chunk 60 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 75 GLN N 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.246106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.194869 restraints weight = 8634.224| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 1.82 r_work: 0.3779 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9184 Z= 0.140 Angle : 0.583 8.068 12419 Z= 0.299 Chirality : 0.042 0.165 1412 Planarity : 0.004 0.035 1552 Dihedral : 4.720 55.792 1230 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.64 % Rotamer: Outliers : 5.59 % Allowed : 21.48 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.72 (0.25), residues: 1131 helix: 3.09 (0.24), residues: 420 sheet: -0.25 (0.30), residues: 285 loop : -1.79 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.021 0.002 TYR N 190 PHE 0.015 0.002 PHE R 49 TRP 0.018 0.002 TRP B 211 HIS 0.005 0.001 HIS R 284 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9183) covalent geometry : angle 0.58237 (12417) SS BOND : bond 0.00552 ( 1) SS BOND : angle 1.45725 ( 2) hydrogen bonds : bond 0.04185 ( 454) hydrogen bonds : angle 3.87915 ( 1305) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 119 time to evaluate : 0.326 Fit side-chains REVERT: A 53 MET cc_start: 0.5388 (pmm) cc_final: 0.3050 (mmm) REVERT: A 198 MET cc_start: 0.8047 (ttp) cc_final: 0.7810 (tpp) REVERT: A 200 ASP cc_start: 0.8208 (t0) cc_final: 0.7294 (m-30) REVERT: A 216 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5665 (tm-30) REVERT: A 224 CYS cc_start: 0.8640 (p) cc_final: 0.8101 (t) REVERT: B 4 MET cc_start: 0.6583 (mpp) cc_final: 0.5816 (mmm) REVERT: B 44 GLN cc_start: 0.7028 (mt0) cc_final: 0.6809 (tt0) REVERT: B 46 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6759 (mmt180) REVERT: B 52 ARG cc_start: 0.7880 (ptp-110) cc_final: 0.7551 (ptp-110) REVERT: B 68 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7821 (tttm) REVERT: B 114 CYS cc_start: 0.8516 (OUTLIER) cc_final: 0.7995 (t) REVERT: B 117 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7734 (tt) REVERT: B 134 LYS cc_start: 0.6656 (mttt) cc_final: 0.6240 (mmmt) REVERT: B 154 ASP cc_start: 0.7376 (m-30) cc_final: 0.6787 (m-30) REVERT: B 227 SER cc_start: 0.9241 (m) cc_final: 0.8930 (t) REVERT: B 314 ARG cc_start: 0.7478 (ttm170) cc_final: 0.6335 (ttp80) REVERT: B 327 VAL cc_start: 0.7653 (OUTLIER) cc_final: 0.7270 (m) REVERT: G 9 MET cc_start: 0.5347 (mmm) cc_final: 0.4964 (mpm) REVERT: G 26 MET cc_start: 0.7419 (mmp) cc_final: 0.5786 (tmm) REVERT: N 13 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8214 (mm-40) REVERT: N 17 SER cc_start: 0.8022 (m) cc_final: 0.7548 (t) REVERT: N 89 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6902 (pp20) REVERT: N 103 TYR cc_start: 0.8160 (t80) cc_final: 0.7767 (t80) REVERT: N 109 ASP cc_start: 0.7184 (p0) cc_final: 0.6978 (p0) REVERT: R 18 PHE cc_start: 0.4297 (t80) cc_final: 0.3759 (t80) REVERT: R 57 LEU cc_start: 0.5911 (OUTLIER) cc_final: 0.5598 (mt) outliers start: 56 outliers final: 24 residues processed: 167 average time/residue: 0.4541 time to fit residues: 82.0432 Evaluate side-chains 137 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 158 SER Chi-restraints excluded: chain N residue 215 THR Chi-restraints excluded: chain N residue 226 VAL Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 181 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 11 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN N 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.245386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.189515 restraints weight = 8711.767| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.06 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9184 Z= 0.119 Angle : 0.551 9.208 12419 Z= 0.283 Chirality : 0.042 0.311 1412 Planarity : 0.003 0.032 1552 Dihedral : 4.380 59.138 1228 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.36 % Favored : 96.55 % Rotamer: Outliers : 5.49 % Allowed : 22.78 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.78 (0.25), residues: 1131 helix: 3.02 (0.25), residues: 426 sheet: -0.17 (0.30), residues: 289 loop : -1.74 (0.26), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.018 0.001 TYR N 190 PHE 0.025 0.002 PHE R 88 TRP 0.018 0.001 TRP B 211 HIS 0.004 0.001 HIS R 284 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9183) covalent geometry : angle 0.55066 (12417) SS BOND : bond 0.00470 ( 1) SS BOND : angle 1.21747 ( 2) hydrogen bonds : bond 0.03730 ( 454) hydrogen bonds : angle 3.70499 ( 1305) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 112 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 36 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7540 (mt) REVERT: A 53 MET cc_start: 0.5355 (pmm) cc_final: 0.4803 (mpp) REVERT: A 200 ASP cc_start: 0.7612 (t0) cc_final: 0.7305 (m-30) REVERT: A 216 GLU cc_start: 0.5708 (OUTLIER) cc_final: 0.4796 (mm-30) REVERT: A 224 CYS cc_start: 0.7437 (p) cc_final: 0.6944 (t) REVERT: B 4 MET cc_start: 0.5881 (mpp) cc_final: 0.5522 (mmm) REVERT: B 68 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7561 (tttm) REVERT: B 117 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7617 (tt) REVERT: B 146 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8434 (mp) REVERT: B 154 ASP cc_start: 0.7105 (m-30) cc_final: 0.6675 (m-30) REVERT: B 227 SER cc_start: 0.8988 (m) cc_final: 0.8617 (t) REVERT: B 314 ARG cc_start: 0.6883 (ttm170) cc_final: 0.6396 (ptt180) REVERT: B 327 VAL cc_start: 0.7589 (OUTLIER) cc_final: 0.7266 (m) REVERT: N 13 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7996 (mm-40) REVERT: N 17 SER cc_start: 0.7763 (m) cc_final: 0.7486 (t) REVERT: N 103 TYR cc_start: 0.7923 (t80) cc_final: 0.7583 (t80) REVERT: R 57 LEU cc_start: 0.6026 (OUTLIER) cc_final: 0.5722 (mt) REVERT: R 88 PHE cc_start: 0.5770 (t80) cc_final: 0.5529 (t80) outliers start: 55 outliers final: 25 residues processed: 159 average time/residue: 0.4576 time to fit residues: 78.4322 Evaluate side-chains 137 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 158 SER Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 215 THR Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 181 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 84 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.0970 chunk 76 optimal weight: 2.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.242963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.4010 r_free = 0.4010 target = 0.174802 restraints weight = 8648.424| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.62 r_work: 0.3628 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9184 Z= 0.143 Angle : 0.595 8.167 12419 Z= 0.304 Chirality : 0.043 0.177 1412 Planarity : 0.004 0.041 1552 Dihedral : 4.529 54.062 1228 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.18 % Favored : 96.73 % Rotamer: Outliers : 6.09 % Allowed : 23.28 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.80 (0.25), residues: 1131 helix: 2.98 (0.24), residues: 427 sheet: -0.15 (0.30), residues: 290 loop : -1.68 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 52 TYR 0.018 0.001 TYR N 190 PHE 0.028 0.002 PHE R 49 TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS R 284 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9183) covalent geometry : angle 0.59468 (12417) SS BOND : bond 0.00634 ( 1) SS BOND : angle 1.45246 ( 2) hydrogen bonds : bond 0.04041 ( 454) hydrogen bonds : angle 3.74831 ( 1305) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 108 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.5635 (pmm) cc_final: 0.5333 (mpp) REVERT: A 200 ASP cc_start: 0.8091 (t0) cc_final: 0.6966 (m-30) REVERT: A 216 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.5372 (mm-30) REVERT: A 224 CYS cc_start: 0.8751 (p) cc_final: 0.8146 (t) REVERT: B 4 MET cc_start: 0.6893 (mpp) cc_final: 0.6111 (mmm) REVERT: B 44 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6272 (tp40) REVERT: B 68 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7674 (tttm) REVERT: B 117 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7598 (tt) REVERT: B 146 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8450 (mp) REVERT: B 154 ASP cc_start: 0.7365 (m-30) cc_final: 0.6806 (OUTLIER) REVERT: B 227 SER cc_start: 0.9317 (m) cc_final: 0.8940 (t) REVERT: B 314 ARG cc_start: 0.7257 (ttm170) cc_final: 0.6434 (ptt180) REVERT: G 49 ASN cc_start: 0.5463 (m-40) cc_final: 0.5098 (p0) REVERT: G 53 MET cc_start: 0.4474 (mpp) cc_final: 0.2378 (tpp) REVERT: N 13 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8269 (mm-40) REVERT: N 17 SER cc_start: 0.8096 (m) cc_final: 0.7568 (t) REVERT: N 103 TYR cc_start: 0.8186 (t80) cc_final: 0.7911 (t80) REVERT: R 57 LEU cc_start: 0.5262 (OUTLIER) cc_final: 0.4940 (mt) REVERT: R 257 MET cc_start: 0.5638 (mmt) cc_final: 0.5360 (mpp) outliers start: 61 outliers final: 36 residues processed: 157 average time/residue: 0.4623 time to fit residues: 78.2736 Evaluate side-chains 142 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 158 SER Chi-restraints excluded: chain N residue 215 THR Chi-restraints excluded: chain N residue 226 VAL Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 264 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 77 optimal weight: 0.0030 chunk 60 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.242827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 119)---------------| | r_work = 0.3988 r_free = 0.3988 target = 0.173269 restraints weight = 8625.865| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.67 r_work: 0.3687 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9184 Z= 0.128 Angle : 0.565 7.872 12419 Z= 0.289 Chirality : 0.042 0.291 1412 Planarity : 0.004 0.035 1552 Dihedral : 4.440 55.833 1228 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.18 % Favored : 96.73 % Rotamer: Outliers : 5.79 % Allowed : 23.88 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.87 (0.25), residues: 1131 helix: 2.98 (0.24), residues: 429 sheet: -0.19 (0.30), residues: 293 loop : -1.53 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.016 0.001 TYR N 190 PHE 0.024 0.002 PHE R 49 TRP 0.015 0.001 TRP B 211 HIS 0.004 0.001 HIS R 284 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9183) covalent geometry : angle 0.56489 (12417) SS BOND : bond 0.00594 ( 1) SS BOND : angle 1.44815 ( 2) hydrogen bonds : bond 0.03737 ( 454) hydrogen bonds : angle 3.68220 ( 1305) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 104 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.5570 (pmm) cc_final: 0.5319 (mpp) REVERT: A 200 ASP cc_start: 0.7982 (t0) cc_final: 0.6874 (m-30) REVERT: A 216 GLU cc_start: 0.6169 (OUTLIER) cc_final: 0.5181 (mm-30) REVERT: A 232 MET cc_start: 0.6472 (mpm) cc_final: 0.6212 (mmp) REVERT: A 309 ASP cc_start: 0.6812 (m-30) cc_final: 0.6273 (p0) REVERT: B 4 MET cc_start: 0.6848 (mpp) cc_final: 0.6071 (mmm) REVERT: B 44 GLN cc_start: 0.6798 (OUTLIER) cc_final: 0.6102 (tp40) REVERT: B 68 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7630 (tttm) REVERT: B 117 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7502 (tt) REVERT: B 146 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8396 (mp) REVERT: B 153 ASP cc_start: 0.7552 (m-30) cc_final: 0.6510 (t70) REVERT: B 154 ASP cc_start: 0.7145 (m-30) cc_final: 0.6236 (m-30) REVERT: B 227 SER cc_start: 0.9313 (m) cc_final: 0.8920 (t) REVERT: B 314 ARG cc_start: 0.7198 (ttm170) cc_final: 0.6410 (ptt180) REVERT: G 49 ASN cc_start: 0.5645 (m-40) cc_final: 0.5129 (p0) REVERT: G 53 MET cc_start: 0.4245 (mpp) cc_final: 0.2209 (tpt) REVERT: N 13 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8230 (mm-40) REVERT: N 17 SER cc_start: 0.8163 (m) cc_final: 0.7666 (t) REVERT: N 103 TYR cc_start: 0.8151 (t80) cc_final: 0.7859 (t80) REVERT: R 229 MET cc_start: 0.4713 (mmm) cc_final: 0.4451 (mmm) outliers start: 58 outliers final: 33 residues processed: 151 average time/residue: 0.4343 time to fit residues: 71.2797 Evaluate side-chains 138 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 158 SER Chi-restraints excluded: chain N residue 215 THR Chi-restraints excluded: chain N residue 226 VAL Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 181 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.240943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.180743 restraints weight = 8583.609| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 2.22 r_work: 0.3615 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9184 Z= 0.141 Angle : 0.587 8.488 12419 Z= 0.300 Chirality : 0.043 0.208 1412 Planarity : 0.004 0.041 1552 Dihedral : 4.524 53.750 1228 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.45 % Favored : 96.46 % Rotamer: Outliers : 5.49 % Allowed : 24.28 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1131 helix: 3.13 (0.24), residues: 423 sheet: -0.15 (0.31), residues: 286 loop : -1.44 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 52 TYR 0.017 0.001 TYR N 190 PHE 0.024 0.002 PHE R 49 TRP 0.016 0.002 TRP B 211 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9183) covalent geometry : angle 0.58618 (12417) SS BOND : bond 0.00668 ( 1) SS BOND : angle 1.69557 ( 2) hydrogen bonds : bond 0.03867 ( 454) hydrogen bonds : angle 3.70597 ( 1305) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 105 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.5516 (pmm) cc_final: 0.5279 (mpp) REVERT: A 200 ASP cc_start: 0.8110 (t0) cc_final: 0.6962 (m-30) REVERT: A 216 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.5482 (mm-30) REVERT: A 224 CYS cc_start: 0.8701 (p) cc_final: 0.8170 (t) REVERT: A 232 MET cc_start: 0.6589 (mpm) cc_final: 0.6286 (mmp) REVERT: A 266 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8579 (tp) REVERT: A 309 ASP cc_start: 0.6785 (m-30) cc_final: 0.6334 (p0) REVERT: B 4 MET cc_start: 0.6944 (mpp) cc_final: 0.6276 (mmm) REVERT: B 68 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7680 (tttp) REVERT: B 117 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7685 (tt) REVERT: B 146 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8510 (mp) REVERT: B 154 ASP cc_start: 0.7325 (m-30) cc_final: 0.6748 (m-30) REVERT: B 227 SER cc_start: 0.9293 (m) cc_final: 0.8909 (t) REVERT: B 314 ARG cc_start: 0.7279 (ttm170) cc_final: 0.6544 (ptt180) REVERT: G 9 MET cc_start: 0.5980 (mpm) cc_final: 0.5396 (mmm) REVERT: G 53 MET cc_start: 0.3862 (mpp) cc_final: 0.1983 (tpp) REVERT: N 13 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8257 (mm-40) REVERT: N 17 SER cc_start: 0.8182 (m) cc_final: 0.7756 (t) REVERT: R 57 LEU cc_start: 0.5492 (OUTLIER) cc_final: 0.5151 (mt) REVERT: R 89 MET cc_start: 0.6322 (ttm) cc_final: 0.6022 (mtm) REVERT: R 257 MET cc_start: 0.5411 (mmm) cc_final: 0.4983 (mmm) outliers start: 55 outliers final: 33 residues processed: 152 average time/residue: 0.4592 time to fit residues: 75.6421 Evaluate side-chains 142 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 158 SER Chi-restraints excluded: chain N residue 197 SER Chi-restraints excluded: chain N residue 215 THR Chi-restraints excluded: chain N residue 226 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 264 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 92 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 0.0000 chunk 24 optimal weight: 8.9990 chunk 1 optimal weight: 0.2980 chunk 81 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 96 optimal weight: 0.0570 chunk 3 optimal weight: 0.7980 overall best weight: 0.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.243485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.172104 restraints weight = 8635.882| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.58 r_work: 0.3656 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9184 Z= 0.105 Angle : 0.532 7.778 12419 Z= 0.272 Chirality : 0.041 0.212 1412 Planarity : 0.003 0.034 1552 Dihedral : 4.266 58.333 1228 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 4.10 % Allowed : 25.97 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.25), residues: 1131 helix: 3.22 (0.24), residues: 423 sheet: 0.03 (0.31), residues: 278 loop : -1.45 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 52 TYR 0.017 0.001 TYR N 190 PHE 0.025 0.001 PHE R 49 TRP 0.019 0.001 TRP B 211 HIS 0.003 0.001 HIS N 35 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 9183) covalent geometry : angle 0.53169 (12417) SS BOND : bond 0.00418 ( 1) SS BOND : angle 1.18299 ( 2) hydrogen bonds : bond 0.03365 ( 454) hydrogen bonds : angle 3.56612 ( 1305) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.360 Fit side-chains REVERT: A 53 MET cc_start: 0.5426 (pmm) cc_final: 0.5208 (mpp) REVERT: A 200 ASP cc_start: 0.7846 (t0) cc_final: 0.6578 (m-30) REVERT: A 216 GLU cc_start: 0.5921 (OUTLIER) cc_final: 0.5262 (tm-30) REVERT: A 232 MET cc_start: 0.6489 (mpm) cc_final: 0.6235 (mmm) REVERT: A 266 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8344 (tp) REVERT: A 309 ASP cc_start: 0.6455 (m-30) cc_final: 0.6169 (p0) REVERT: B 4 MET cc_start: 0.7029 (mpp) cc_final: 0.6368 (mmm) REVERT: B 68 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7360 (tttm) REVERT: B 117 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7234 (tt) REVERT: B 146 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8250 (mp) REVERT: B 153 ASP cc_start: 0.7413 (m-30) cc_final: 0.6445 (t70) REVERT: B 154 ASP cc_start: 0.7108 (m-30) cc_final: 0.6191 (m-30) REVERT: B 227 SER cc_start: 0.9228 (m) cc_final: 0.8812 (t) REVERT: B 239 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7611 (mm-30) REVERT: B 270 ILE cc_start: 0.7083 (OUTLIER) cc_final: 0.6838 (pp) REVERT: B 314 ARG cc_start: 0.7136 (ttm170) cc_final: 0.6349 (ptt180) REVERT: B 327 VAL cc_start: 0.7275 (OUTLIER) cc_final: 0.6638 (t) REVERT: G 9 MET cc_start: 0.5783 (mpm) cc_final: 0.5209 (mmm) REVERT: G 53 MET cc_start: 0.4088 (mpp) cc_final: 0.2200 (tpp) REVERT: N 17 SER cc_start: 0.8151 (m) cc_final: 0.7666 (t) REVERT: N 103 TYR cc_start: 0.8084 (t80) cc_final: 0.7793 (t80) REVERT: R 57 LEU cc_start: 0.4775 (OUTLIER) cc_final: 0.4483 (mt) REVERT: R 89 MET cc_start: 0.5770 (ttm) cc_final: 0.5570 (mtm) REVERT: R 210 MET cc_start: 0.3606 (mmp) cc_final: 0.3270 (tpp) REVERT: R 257 MET cc_start: 0.5571 (mmm) cc_final: 0.5103 (mmm) outliers start: 41 outliers final: 18 residues processed: 144 average time/residue: 0.4819 time to fit residues: 74.9876 Evaluate side-chains 128 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 158 SER Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 181 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 12 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.240766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 119)---------------| | r_work = 0.3953 r_free = 0.3953 target = 0.170307 restraints weight = 8613.224| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.63 r_work: 0.3658 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9184 Z= 0.143 Angle : 0.592 8.696 12419 Z= 0.302 Chirality : 0.043 0.200 1412 Planarity : 0.004 0.041 1552 Dihedral : 4.445 56.847 1228 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer: Outliers : 4.20 % Allowed : 25.87 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.25), residues: 1131 helix: 3.15 (0.24), residues: 423 sheet: 0.02 (0.32), residues: 275 loop : -1.40 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 52 TYR 0.016 0.001 TYR N 190 PHE 0.027 0.002 PHE R 88 TRP 0.015 0.002 TRP B 211 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9183) covalent geometry : angle 0.59176 (12417) SS BOND : bond 0.00657 ( 1) SS BOND : angle 1.56637 ( 2) hydrogen bonds : bond 0.03832 ( 454) hydrogen bonds : angle 3.68427 ( 1305) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.5492 (pmm) cc_final: 0.5252 (mpp) REVERT: A 200 ASP cc_start: 0.7968 (t0) cc_final: 0.6781 (m-30) REVERT: A 210 LYS cc_start: 0.4192 (OUTLIER) cc_final: 0.3876 (mttp) REVERT: A 216 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.5334 (mm-30) REVERT: A 232 MET cc_start: 0.6679 (mpm) cc_final: 0.6416 (mmp) REVERT: A 266 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8507 (tp) REVERT: A 309 ASP cc_start: 0.6713 (m-30) cc_final: 0.6372 (p0) REVERT: B 4 MET cc_start: 0.6901 (mpp) cc_final: 0.6261 (mmm) REVERT: B 68 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7635 (tttm) REVERT: B 117 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7570 (tt) REVERT: B 146 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8467 (mp) REVERT: B 153 ASP cc_start: 0.7575 (m-30) cc_final: 0.6612 (t70) REVERT: B 154 ASP cc_start: 0.7234 (m-30) cc_final: 0.6427 (m-30) REVERT: B 227 SER cc_start: 0.9318 (m) cc_final: 0.8915 (t) REVERT: B 270 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6945 (pp) REVERT: B 314 ARG cc_start: 0.7236 (ttm170) cc_final: 0.6583 (ptt180) REVERT: B 327 VAL cc_start: 0.7484 (OUTLIER) cc_final: 0.6842 (t) REVERT: G 9 MET cc_start: 0.5947 (mpm) cc_final: 0.5366 (mmm) REVERT: G 53 MET cc_start: 0.4141 (mpp) cc_final: 0.2245 (tpp) REVERT: N 17 SER cc_start: 0.8211 (m) cc_final: 0.7789 (t) REVERT: N 103 TYR cc_start: 0.8150 (t80) cc_final: 0.7900 (t80) REVERT: R 57 LEU cc_start: 0.5157 (OUTLIER) cc_final: 0.4819 (mt) REVERT: R 89 MET cc_start: 0.6181 (ttm) cc_final: 0.5910 (mtm) outliers start: 42 outliers final: 23 residues processed: 136 average time/residue: 0.4617 time to fit residues: 67.6718 Evaluate side-chains 131 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 158 SER Chi-restraints excluded: chain N residue 162 SER Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 105 optimal weight: 2.9990 chunk 36 optimal weight: 0.0050 chunk 107 optimal weight: 8.9990 chunk 70 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.241215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.182454 restraints weight = 8662.395| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 1.94 r_work: 0.3664 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9184 Z= 0.129 Angle : 0.571 8.180 12419 Z= 0.291 Chirality : 0.042 0.197 1412 Planarity : 0.004 0.035 1552 Dihedral : 4.404 58.187 1228 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.36 % Favored : 96.55 % Rotamer: Outliers : 3.50 % Allowed : 26.57 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.25), residues: 1131 helix: 3.16 (0.24), residues: 423 sheet: 0.05 (0.32), residues: 275 loop : -1.39 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 52 TYR 0.018 0.001 TYR N 190 PHE 0.025 0.002 PHE R 49 TRP 0.017 0.001 TRP B 211 HIS 0.004 0.001 HIS N 35 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9183) covalent geometry : angle 0.57108 (12417) SS BOND : bond 0.00551 ( 1) SS BOND : angle 1.37025 ( 2) hydrogen bonds : bond 0.03659 ( 454) hydrogen bonds : angle 3.67320 ( 1305) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.5422 (pmm) cc_final: 0.5194 (mpp) REVERT: A 210 LYS cc_start: 0.4449 (OUTLIER) cc_final: 0.4235 (mttp) REVERT: A 216 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.5566 (tm-30) REVERT: A 232 MET cc_start: 0.6795 (mpm) cc_final: 0.6576 (mmp) REVERT: A 266 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8534 (tp) REVERT: A 309 ASP cc_start: 0.6830 (m-30) cc_final: 0.6494 (p0) REVERT: B 4 MET cc_start: 0.6814 (mpp) cc_final: 0.6185 (mmm) REVERT: B 68 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7668 (tttm) REVERT: B 146 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8511 (mp) REVERT: B 153 ASP cc_start: 0.7574 (m-30) cc_final: 0.6638 (t70) REVERT: B 154 ASP cc_start: 0.7250 (m-30) cc_final: 0.6481 (m-30) REVERT: B 227 SER cc_start: 0.9320 (m) cc_final: 0.8930 (t) REVERT: B 239 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7839 (mm-30) REVERT: B 270 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.7008 (pp) REVERT: B 314 ARG cc_start: 0.7153 (ttm170) cc_final: 0.6458 (ptt180) REVERT: B 327 VAL cc_start: 0.7531 (OUTLIER) cc_final: 0.6926 (t) REVERT: G 9 MET cc_start: 0.6127 (mpm) cc_final: 0.5557 (mmm) REVERT: G 26 MET cc_start: 0.6921 (mpp) cc_final: 0.6407 (mmt) REVERT: G 53 MET cc_start: 0.3791 (mpp) cc_final: 0.2116 (tpp) REVERT: N 17 SER cc_start: 0.8225 (m) cc_final: 0.7816 (t) REVERT: N 103 TYR cc_start: 0.8154 (t80) cc_final: 0.7901 (t80) REVERT: R 57 LEU cc_start: 0.5400 (OUTLIER) cc_final: 0.5029 (mt) REVERT: R 89 MET cc_start: 0.6256 (ttm) cc_final: 0.6006 (mtm) REVERT: R 257 MET cc_start: 0.5563 (mmm) cc_final: 0.3376 (ptp) outliers start: 35 outliers final: 23 residues processed: 131 average time/residue: 0.4943 time to fit residues: 69.7275 Evaluate side-chains 128 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 158 SER Chi-restraints excluded: chain N residue 162 SER Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 103 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 71 optimal weight: 0.0970 chunk 56 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.242082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.173819 restraints weight = 8566.173| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.73 r_work: 0.3646 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9184 Z= 0.113 Angle : 0.557 8.962 12419 Z= 0.284 Chirality : 0.042 0.295 1412 Planarity : 0.003 0.033 1552 Dihedral : 4.267 57.064 1228 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.18 % Favored : 96.73 % Rotamer: Outliers : 3.60 % Allowed : 26.37 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.25), residues: 1131 helix: 3.15 (0.25), residues: 423 sheet: 0.05 (0.31), residues: 275 loop : -1.32 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 52 TYR 0.018 0.001 TYR N 190 PHE 0.025 0.001 PHE R 49 TRP 0.018 0.001 TRP B 211 HIS 0.004 0.001 HIS N 35 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9183) covalent geometry : angle 0.55674 (12417) SS BOND : bond 0.00469 ( 1) SS BOND : angle 1.27047 ( 2) hydrogen bonds : bond 0.03485 ( 454) hydrogen bonds : angle 3.62499 ( 1305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3073.60 seconds wall clock time: 53 minutes 4.20 seconds (3184.20 seconds total)