Starting phenix.real_space_refine on Thu Feb 5 10:59:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8irt_35685/02_2026/8irt_35685_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8irt_35685/02_2026/8irt_35685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8irt_35685/02_2026/8irt_35685_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8irt_35685/02_2026/8irt_35685_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8irt_35685/02_2026/8irt_35685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8irt_35685/02_2026/8irt_35685.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 69 5.16 5 C 5571 2.51 5 N 1485 2.21 5 O 1643 1.98 5 H 8669 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17437 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3572 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 2 Chain: "B" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5108 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "E" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3503 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 885 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 4341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 4341 Classifications: {'peptide': 273} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 262} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Unusual residues: {'R5F': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 2.51, per 1000 atoms: 0.14 Number of scatterers: 17437 At special positions: 0 Unit cell: (112.86, 132.715, 108.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 69 16.00 O 1643 8.00 N 1485 7.00 C 5571 6.00 H 8669 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 103 " - pdb=" SG CYS R 181 " distance=2.04 Simple disulfide: pdb=" SG CYS R 355 " - pdb=" SG CYS R 358 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 486.2 milliseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 13 sheets defined 40.6% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.766A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.863A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 232 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.875A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.211A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.560A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'R' and resid 32 through 57 Processing helix chain 'R' and resid 58 through 61 Processing helix chain 'R' and resid 62 through 81 removed outlier: 3.627A pdb=" N LEU R 67 " --> pdb=" O THR R 63 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL R 68 " --> pdb=" O THR R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 92 removed outlier: 4.522A pdb=" N TRP R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 134 removed outlier: 3.694A pdb=" N VAL R 132 " --> pdb=" O ARG R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 139 Processing helix chain 'R' and resid 143 through 166 Processing helix chain 'R' and resid 167 through 170 Processing helix chain 'R' and resid 185 through 197 removed outlier: 4.827A pdb=" N TYR R 191 " --> pdb=" O ASP R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 223 Processing helix chain 'R' and resid 322 through 354 Proline residue: R 344 - end of helix Processing helix chain 'R' and resid 361 through 384 removed outlier: 3.800A pdb=" N ASN R 375 " --> pdb=" O LEU R 371 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER R 376 " --> pdb=" O GLY R 372 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA R 377 " --> pdb=" O TYR R 373 " (cutoff:3.500A) Proline residue: R 380 - end of helix Processing helix chain 'R' and resid 387 through 400 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.706A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.532A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.836A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.940A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.568A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.743A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.451A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.625A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.694A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.525A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.043A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1326 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: 3.64 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 8637 1.13 - 1.30: 1520 1.30 - 1.47: 3462 1.47 - 1.65: 3898 1.65 - 1.82: 98 Bond restraints: 17615 Sorted by residual: bond pdb=" NE2 GLN R 356 " pdb="HE22 GLN R 356 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE3 TRP E 36 " pdb=" HE3 TRP E 36 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASN R 97 " pdb=" H ASN R 97 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ILE B 58 " pdb=" H ILE B 58 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NH1 ARG B 283 " pdb="HH11 ARG B 283 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 17610 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 27020 2.76 - 5.51: 3647 5.51 - 8.27: 960 8.27 - 11.02: 37 11.02 - 13.78: 28 Bond angle restraints: 31692 Sorted by residual: angle pdb=" C TYR B 105 " pdb=" CA TYR B 105 " pdb=" CB TYR B 105 " ideal model delta sigma weight residual 109.71 122.47 -12.76 1.83e+00 2.99e-01 4.86e+01 angle pdb=" N ASN A 269 " pdb=" CA ASN A 269 " pdb=" C ASN A 269 " ideal model delta sigma weight residual 113.18 121.46 -8.28 1.21e+00 6.83e-01 4.68e+01 angle pdb=" N ARG B 52 " pdb=" CA ARG B 52 " pdb=" C ARG B 52 " ideal model delta sigma weight residual 112.90 121.78 -8.88 1.31e+00 5.83e-01 4.59e+01 angle pdb=" C LEU B 51 " pdb=" CA LEU B 51 " pdb=" CB LEU B 51 " ideal model delta sigma weight residual 111.77 121.44 -9.67 1.52e+00 4.33e-01 4.05e+01 angle pdb=" CA ASP B 228 " pdb=" CB ASP B 228 " pdb=" CG ASP B 228 " ideal model delta sigma weight residual 112.60 118.66 -6.06 1.00e+00 1.00e+00 3.67e+01 ... (remaining 31687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7617 17.95 - 35.91: 447 35.91 - 53.86: 145 53.86 - 71.81: 126 71.81 - 89.77: 8 Dihedral angle restraints: 8343 sinusoidal: 4468 harmonic: 3875 Sorted by residual: dihedral pdb=" CA ASN A 311 " pdb=" C ASN A 311 " pdb=" N LYS A 312 " pdb=" CA LYS A 312 " ideal model delta harmonic sigma weight residual 180.00 150.13 29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA TYR R 138 " pdb=" C TYR R 138 " pdb=" N GLN R 139 " pdb=" CA GLN R 139 " ideal model delta harmonic sigma weight residual -180.00 -150.27 -29.73 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA TYR B 289 " pdb=" C TYR B 289 " pdb=" N ASP B 290 " pdb=" CA ASP B 290 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 8340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 889 0.086 - 0.173: 379 0.173 - 0.259: 90 0.259 - 0.345: 26 0.345 - 0.431: 5 Chirality restraints: 1389 Sorted by residual: chirality pdb=" CA SER B 334 " pdb=" N SER B 334 " pdb=" C SER B 334 " pdb=" CB SER B 334 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CA THR R 357 " pdb=" N THR R 357 " pdb=" C THR R 357 " pdb=" CB THR R 357 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA ASP B 228 " pdb=" N ASP B 228 " pdb=" C ASP B 228 " pdb=" CB ASP B 228 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 1386 not shown) Planarity restraints: 2610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.404 2.00e-02 2.50e+03 1.59e-01 7.54e+02 pdb=" CG TYR B 105 " -0.228 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " -0.085 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " -0.169 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.062 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " 0.176 2.00e-02 2.50e+03 pdb=" HD1 TYR B 105 " 0.005 2.00e-02 2.50e+03 pdb=" HD2 TYR B 105 " -0.090 2.00e-02 2.50e+03 pdb=" HE1 TYR B 105 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 TYR B 105 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 175 " -0.293 2.00e-02 2.50e+03 1.22e-01 4.45e+02 pdb=" CG TYR E 175 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR E 175 " 0.089 2.00e-02 2.50e+03 pdb=" CD2 TYR E 175 " 0.067 2.00e-02 2.50e+03 pdb=" CE1 TYR E 175 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR E 175 " 0.060 2.00e-02 2.50e+03 pdb=" CZ TYR E 175 " -0.038 2.00e-02 2.50e+03 pdb=" OH TYR E 175 " -0.202 2.00e-02 2.50e+03 pdb=" HD1 TYR E 175 " 0.149 2.00e-02 2.50e+03 pdb=" HD2 TYR E 175 " 0.079 2.00e-02 2.50e+03 pdb=" HE1 TYR E 175 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR E 175 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 47 " 0.026 2.00e-02 2.50e+03 1.05e-01 4.38e+02 pdb=" CG TRP E 47 " -0.098 2.00e-02 2.50e+03 pdb=" CD1 TRP E 47 " -0.079 2.00e-02 2.50e+03 pdb=" CD2 TRP E 47 " -0.086 2.00e-02 2.50e+03 pdb=" NE1 TRP E 47 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TRP E 47 " -0.098 2.00e-02 2.50e+03 pdb=" CE3 TRP E 47 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 47 " -0.074 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 47 " 0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP E 47 " -0.036 2.00e-02 2.50e+03 pdb=" HD1 TRP E 47 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 TRP E 47 " 0.328 2.00e-02 2.50e+03 pdb=" HE3 TRP E 47 " 0.069 2.00e-02 2.50e+03 pdb=" HZ2 TRP E 47 " -0.063 2.00e-02 2.50e+03 pdb=" HZ3 TRP E 47 " 0.130 2.00e-02 2.50e+03 pdb=" HH2 TRP E 47 " -0.019 2.00e-02 2.50e+03 ... (remaining 2607 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1074 2.16 - 2.77: 30730 2.77 - 3.38: 52633 3.38 - 3.99: 71035 3.99 - 4.60: 103637 Nonbonded interactions: 259109 Sorted by model distance: nonbonded pdb=" HG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 1.550 2.450 nonbonded pdb=" HG1 THR B 274 " pdb=" O VAL B 315 " model vdw 1.557 2.450 nonbonded pdb=" HG SER B 147 " pdb=" O VAL B 187 " model vdw 1.560 2.450 nonbonded pdb=" OE2 GLU A 8 " pdb=" HH TYR E 175 " model vdw 1.577 2.450 nonbonded pdb=" OD2 ASP B 170 " pdb=" HG1 THR B 173 " model vdw 1.596 2.450 ... (remaining 259104 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.040 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.012 0.082 8950 Z= 0.748 Angle : 1.886 12.762 12134 Z= 1.252 Chirality : 0.103 0.431 1389 Planarity : 0.019 0.274 1527 Dihedral : 13.032 89.767 3208 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 3.33 % 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: -0.67 (0.24), residues: 1104 helix: -0.47 (0.22), residues: 388 sheet: -0.17 (0.31), residues: 264 loop : -0.36 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG R 222 TYR 0.377 0.025 TYR B 105 PHE 0.105 0.018 PHE R 345 TRP 0.121 0.025 TRP B 82 HIS 0.022 0.005 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.01219 ( 8946) covalent geometry : angle 1.88561 (12126) SS BOND : bond 0.00616 ( 4) SS BOND : angle 1.96859 ( 8) hydrogen bonds : bond 0.14465 ( 472) hydrogen bonds : angle 7.30597 ( 1326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8139 (m-40) cc_final: 0.7931 (m-40) REVERT: A 26 ASP cc_start: 0.7501 (m-30) cc_final: 0.7208 (m-30) REVERT: A 207 GLU cc_start: 0.7262 (tt0) cc_final: 0.6857 (tt0) REVERT: B 214 ARG cc_start: 0.6868 (mmp80) cc_final: 0.6569 (mmp-170) REVERT: B 325 MET cc_start: 0.8139 (mmt) cc_final: 0.7476 (mmm) REVERT: G 14 LYS cc_start: 0.7418 (tptp) cc_final: 0.7069 (tttt) REVERT: R 170 PHE cc_start: 0.6066 (p90) cc_final: 0.5835 (p90) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 1.2791 time to fit residues: 281.1425 Evaluate side-chains 156 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 213 HIS A 294 ASN A 322 HIS B 35 ASN B 340 ASN E 171 ASN G 24 ASN R 47 ASN R 352 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.173637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.134711 restraints weight = 25066.652| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.82 r_work: 0.3232 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8950 Z= 0.166 Angle : 0.655 7.526 12134 Z= 0.360 Chirality : 0.044 0.155 1389 Planarity : 0.005 0.089 1527 Dihedral : 7.602 79.913 1236 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.66 % Allowed : 7.18 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.27 (0.25), residues: 1104 helix: 1.27 (0.25), residues: 385 sheet: -0.33 (0.30), residues: 268 loop : -0.32 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 67 TYR 0.048 0.002 TYR B 105 PHE 0.027 0.002 PHE R 345 TRP 0.016 0.002 TRP B 99 HIS 0.003 0.001 HIS R 137 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8946) covalent geometry : angle 0.65504 (12126) SS BOND : bond 0.00240 ( 4) SS BOND : angle 1.11708 ( 8) hydrogen bonds : bond 0.05007 ( 472) hydrogen bonds : angle 5.61724 ( 1326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8546 (m-40) cc_final: 0.8333 (m110) REVERT: A 26 ASP cc_start: 0.7943 (m-30) cc_final: 0.7640 (m-30) REVERT: A 242 ARG cc_start: 0.7287 (mtt180) cc_final: 0.7074 (mtt180) REVERT: A 345 LYS cc_start: 0.8573 (mttt) cc_final: 0.8234 (mttm) REVERT: B 175 GLN cc_start: 0.8329 (tp40) cc_final: 0.8125 (mp10) REVERT: B 197 ARG cc_start: 0.8235 (mmp-170) cc_final: 0.7840 (mmm-85) REVERT: B 312 ASP cc_start: 0.7697 (m-30) cc_final: 0.7489 (m-30) REVERT: E 160 ARG cc_start: 0.7701 (ttm170) cc_final: 0.6979 (ttm-80) REVERT: E 244 LYS cc_start: 0.7694 (ptmm) cc_final: 0.7457 (ptmt) REVERT: G 20 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.6505 (tttm) REVERT: R 113 MET cc_start: 0.7548 (mmt) cc_final: 0.7222 (mmt) REVERT: R 216 LYS cc_start: 0.6839 (ttpp) cc_final: 0.6608 (mptt) REVERT: R 387 ASN cc_start: 0.6533 (t0) cc_final: 0.6067 (t0) outliers start: 16 outliers final: 7 residues processed: 192 average time/residue: 1.3971 time to fit residues: 283.9220 Evaluate side-chains 167 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 333 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 61 optimal weight: 0.3980 chunk 43 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.0170 chunk 79 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 overall best weight: 1.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 331 ASN A 333 GLN B 266 HIS R 137 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.173884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.134638 restraints weight = 25304.959| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.86 r_work: 0.3229 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8950 Z= 0.149 Angle : 0.574 5.601 12134 Z= 0.312 Chirality : 0.042 0.148 1389 Planarity : 0.004 0.059 1527 Dihedral : 6.896 70.809 1236 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.56 % Allowed : 11.34 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.59 (0.25), residues: 1104 helix: 1.86 (0.26), residues: 388 sheet: -0.42 (0.30), residues: 271 loop : -0.29 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 129 TYR 0.029 0.002 TYR B 105 PHE 0.017 0.002 PHE R 345 TRP 0.016 0.002 TRP B 339 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8946) covalent geometry : angle 0.57414 (12126) SS BOND : bond 0.00213 ( 4) SS BOND : angle 0.69181 ( 8) hydrogen bonds : bond 0.04241 ( 472) hydrogen bonds : angle 5.28073 ( 1326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8474 (m-40) cc_final: 0.8262 (m110) REVERT: A 26 ASP cc_start: 0.8051 (m-30) cc_final: 0.7771 (m-30) REVERT: A 318 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7797 (tt0) REVERT: B 312 ASP cc_start: 0.7658 (m-30) cc_final: 0.7451 (m-30) REVERT: E 116 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8462 (m) REVERT: E 160 ARG cc_start: 0.7681 (ttm170) cc_final: 0.6931 (ttm-80) REVERT: G 14 LYS cc_start: 0.6910 (tptp) cc_final: 0.6484 (tttt) REVERT: G 20 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.6697 (tttm) REVERT: R 113 MET cc_start: 0.7546 (mmt) cc_final: 0.7317 (mmt) REVERT: R 170 PHE cc_start: 0.5976 (OUTLIER) cc_final: 0.5280 (p90) REVERT: R 216 LYS cc_start: 0.6794 (ttpp) cc_final: 0.6569 (mptt) REVERT: R 389 GLU cc_start: 0.7147 (mp0) cc_final: 0.6918 (mp0) outliers start: 15 outliers final: 7 residues processed: 174 average time/residue: 1.3499 time to fit residues: 249.6472 Evaluate side-chains 161 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 14 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.170628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.123980 restraints weight = 25314.495| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.64 r_work: 0.3170 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8950 Z= 0.201 Angle : 0.584 5.578 12134 Z= 0.316 Chirality : 0.042 0.148 1389 Planarity : 0.004 0.067 1527 Dihedral : 6.457 58.873 1236 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.39 % Allowed : 11.76 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.25), residues: 1104 helix: 2.02 (0.26), residues: 389 sheet: -0.55 (0.31), residues: 281 loop : -0.31 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 129 TYR 0.032 0.002 TYR B 105 PHE 0.018 0.002 PHE R 345 TRP 0.014 0.002 TRP B 99 HIS 0.007 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 8946) covalent geometry : angle 0.58360 (12126) SS BOND : bond 0.00153 ( 4) SS BOND : angle 1.16940 ( 8) hydrogen bonds : bond 0.04149 ( 472) hydrogen bonds : angle 5.25455 ( 1326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.6159 (OUTLIER) cc_final: 0.5751 (mt0) REVERT: A 318 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7645 (tt0) REVERT: A 345 LYS cc_start: 0.8566 (mttt) cc_final: 0.8079 (mmtm) REVERT: B 197 ARG cc_start: 0.8205 (mmp-170) cc_final: 0.7779 (mmm-85) REVERT: B 219 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7443 (mmm-85) REVERT: B 290 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7413 (p0) REVERT: E 116 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8463 (m) REVERT: E 160 ARG cc_start: 0.7645 (ttm170) cc_final: 0.6819 (ttm-80) REVERT: G 14 LYS cc_start: 0.6886 (tptp) cc_final: 0.6469 (tttt) REVERT: G 20 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.6629 (tttm) REVERT: R 170 PHE cc_start: 0.6093 (OUTLIER) cc_final: 0.5017 (p90) REVERT: R 216 LYS cc_start: 0.6760 (ttpp) cc_final: 0.6472 (mmtt) REVERT: R 330 MET cc_start: 0.7504 (mmm) cc_final: 0.7276 (mmm) REVERT: R 389 GLU cc_start: 0.7120 (mp0) cc_final: 0.6839 (mp0) outliers start: 23 outliers final: 8 residues processed: 171 average time/residue: 1.4422 time to fit residues: 261.7942 Evaluate side-chains 163 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 195 HIS B 266 HIS B 268 ASN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.169702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.131339 restraints weight = 25185.850| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.83 r_work: 0.3214 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8950 Z= 0.179 Angle : 0.562 5.252 12134 Z= 0.303 Chirality : 0.042 0.148 1389 Planarity : 0.004 0.055 1527 Dihedral : 6.193 53.432 1236 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.91 % Allowed : 12.07 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.66 (0.26), residues: 1104 helix: 2.19 (0.26), residues: 389 sheet: -0.66 (0.30), residues: 282 loop : -0.32 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 129 TYR 0.022 0.002 TYR B 105 PHE 0.017 0.002 PHE R 345 TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 8946) covalent geometry : angle 0.56188 (12126) SS BOND : bond 0.00165 ( 4) SS BOND : angle 1.09642 ( 8) hydrogen bonds : bond 0.03936 ( 472) hydrogen bonds : angle 5.12497 ( 1326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.6166 (OUTLIER) cc_final: 0.5805 (mt0) REVERT: A 313 ARG cc_start: 0.6329 (OUTLIER) cc_final: 0.6082 (mtt90) REVERT: A 318 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7673 (tt0) REVERT: A 345 LYS cc_start: 0.8497 (mttt) cc_final: 0.8269 (mttm) REVERT: B 215 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: B 219 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7497 (mmm-85) REVERT: B 290 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7444 (p0) REVERT: E 160 ARG cc_start: 0.7740 (ttm170) cc_final: 0.6989 (ttm-80) REVERT: G 14 LYS cc_start: 0.6943 (tptp) cc_final: 0.6532 (tttt) REVERT: G 20 LYS cc_start: 0.7761 (ttpt) cc_final: 0.6675 (tttm) REVERT: R 170 PHE cc_start: 0.6165 (OUTLIER) cc_final: 0.5092 (p90) REVERT: R 216 LYS cc_start: 0.6703 (ttpp) cc_final: 0.6464 (mmtt) REVERT: R 389 GLU cc_start: 0.7191 (mp0) cc_final: 0.6945 (mp0) outliers start: 28 outliers final: 13 residues processed: 166 average time/residue: 1.4178 time to fit residues: 249.2519 Evaluate side-chains 164 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Chi-restraints excluded: chain R residue 352 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 56 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 73 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 91 HIS B 340 ASN G 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.172804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.135027 restraints weight = 25148.701| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.77 r_work: 0.3246 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8950 Z= 0.122 Angle : 0.519 5.144 12134 Z= 0.278 Chirality : 0.041 0.145 1389 Planarity : 0.004 0.043 1527 Dihedral : 5.719 43.638 1236 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.29 % Allowed : 13.32 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.26), residues: 1104 helix: 2.41 (0.26), residues: 391 sheet: -0.59 (0.30), residues: 273 loop : -0.27 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 129 TYR 0.013 0.001 TYR R 88 PHE 0.014 0.001 PHE R 345 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8946) covalent geometry : angle 0.51843 (12126) SS BOND : bond 0.00198 ( 4) SS BOND : angle 0.71457 ( 8) hydrogen bonds : bond 0.03602 ( 472) hydrogen bonds : angle 4.89488 ( 1326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8034 (m-30) cc_final: 0.7743 (m-30) REVERT: A 52 GLN cc_start: 0.6159 (OUTLIER) cc_final: 0.5856 (mt0) REVERT: A 313 ARG cc_start: 0.6227 (OUTLIER) cc_final: 0.6013 (mtt90) REVERT: A 318 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7603 (tt0) REVERT: A 345 LYS cc_start: 0.8572 (mttt) cc_final: 0.8225 (mttm) REVERT: B 219 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7500 (mmm-85) REVERT: B 290 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7279 (p0) REVERT: E 13 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7556 (tp-100) REVERT: E 160 ARG cc_start: 0.7760 (ttm170) cc_final: 0.7084 (ttm-80) REVERT: E 219 LEU cc_start: 0.8051 (tt) cc_final: 0.7744 (tm) REVERT: E 222 GLU cc_start: 0.6240 (tp30) cc_final: 0.6026 (tp30) REVERT: G 14 LYS cc_start: 0.6939 (tptp) cc_final: 0.6533 (tttt) REVERT: R 168 LEU cc_start: 0.7400 (mp) cc_final: 0.7014 (mp) REVERT: R 170 PHE cc_start: 0.6177 (OUTLIER) cc_final: 0.5148 (p90) REVERT: R 216 LYS cc_start: 0.6706 (ttpp) cc_final: 0.6494 (mmtt) REVERT: R 389 GLU cc_start: 0.7241 (mp0) cc_final: 0.6997 (mp0) outliers start: 22 outliers final: 9 residues processed: 174 average time/residue: 1.3057 time to fit residues: 241.6929 Evaluate side-chains 161 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 97 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN R 352 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.169725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.131884 restraints weight = 25247.922| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.85 r_work: 0.3189 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8950 Z= 0.184 Angle : 0.560 5.961 12134 Z= 0.301 Chirality : 0.042 0.144 1389 Planarity : 0.004 0.045 1527 Dihedral : 5.854 46.475 1236 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.08 % Allowed : 14.15 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.83 (0.26), residues: 1104 helix: 2.40 (0.26), residues: 392 sheet: -0.64 (0.30), residues: 281 loop : -0.25 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.014 0.002 TYR B 105 PHE 0.017 0.002 PHE R 345 TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 8946) covalent geometry : angle 0.55958 (12126) SS BOND : bond 0.00215 ( 4) SS BOND : angle 0.86430 ( 8) hydrogen bonds : bond 0.03773 ( 472) hydrogen bonds : angle 4.96919 ( 1326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.6139 (OUTLIER) cc_final: 0.5830 (mt0) REVERT: A 318 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7609 (tt0) REVERT: A 345 LYS cc_start: 0.8554 (mttt) cc_final: 0.8214 (mttm) REVERT: B 219 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7506 (mmm-85) REVERT: E 13 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7606 (tp40) REVERT: E 160 ARG cc_start: 0.7751 (ttm170) cc_final: 0.6983 (ttm-80) REVERT: G 14 LYS cc_start: 0.6918 (tptp) cc_final: 0.6495 (tttt) REVERT: R 89 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6460 (mt) REVERT: R 170 PHE cc_start: 0.6196 (OUTLIER) cc_final: 0.5211 (p90) REVERT: R 216 LYS cc_start: 0.6704 (ttpp) cc_final: 0.6472 (mmtt) REVERT: R 389 GLU cc_start: 0.7251 (mp0) cc_final: 0.6968 (mp0) outliers start: 20 outliers final: 11 residues processed: 161 average time/residue: 1.3792 time to fit residues: 235.0506 Evaluate side-chains 160 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 106 optimal weight: 0.0770 chunk 88 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN G 59 ASN R 61 GLN R 352 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.169923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.132114 restraints weight = 25175.757| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.75 r_work: 0.3210 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8950 Z= 0.171 Angle : 0.556 6.573 12134 Z= 0.298 Chirality : 0.042 0.146 1389 Planarity : 0.004 0.046 1527 Dihedral : 5.843 47.095 1236 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.29 % Allowed : 14.57 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.83 (0.26), residues: 1104 helix: 2.41 (0.26), residues: 393 sheet: -0.63 (0.30), residues: 281 loop : -0.31 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.013 0.002 TYR R 88 PHE 0.016 0.002 PHE R 345 TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 8946) covalent geometry : angle 0.55586 (12126) SS BOND : bond 0.00239 ( 4) SS BOND : angle 0.78871 ( 8) hydrogen bonds : bond 0.03697 ( 472) hydrogen bonds : angle 4.93897 ( 1326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.6072 (OUTLIER) cc_final: 0.5783 (mt0) REVERT: A 313 ARG cc_start: 0.6354 (OUTLIER) cc_final: 0.6111 (mtt90) REVERT: A 318 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7653 (tt0) REVERT: A 345 LYS cc_start: 0.8536 (mttt) cc_final: 0.8211 (mttm) REVERT: B 219 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7521 (mmm-85) REVERT: B 234 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8524 (m-80) REVERT: E 13 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7568 (tp-100) REVERT: E 160 ARG cc_start: 0.7763 (ttm170) cc_final: 0.6974 (ttm-80) REVERT: E 191 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8272 (mtp180) REVERT: G 14 LYS cc_start: 0.6936 (tptp) cc_final: 0.6502 (tttt) REVERT: R 89 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6485 (mt) REVERT: R 170 PHE cc_start: 0.6009 (OUTLIER) cc_final: 0.5237 (p90) REVERT: R 216 LYS cc_start: 0.6712 (ttpp) cc_final: 0.6480 (mmtt) REVERT: R 389 GLU cc_start: 0.7220 (mp0) cc_final: 0.6957 (mp0) outliers start: 22 outliers final: 11 residues processed: 160 average time/residue: 1.3186 time to fit residues: 223.8923 Evaluate side-chains 160 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN R 352 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.168816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.130795 restraints weight = 25389.209| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.82 r_work: 0.3183 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8950 Z= 0.183 Angle : 0.567 6.707 12134 Z= 0.304 Chirality : 0.042 0.147 1389 Planarity : 0.005 0.091 1527 Dihedral : 5.877 47.622 1236 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.29 % Allowed : 14.88 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.86 (0.26), residues: 1104 helix: 2.38 (0.26), residues: 393 sheet: -0.58 (0.31), residues: 281 loop : -0.23 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 129 TYR 0.012 0.002 TYR R 88 PHE 0.017 0.002 PHE R 345 TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8946) covalent geometry : angle 0.56656 (12126) SS BOND : bond 0.00258 ( 4) SS BOND : angle 0.80905 ( 8) hydrogen bonds : bond 0.03728 ( 472) hydrogen bonds : angle 4.94736 ( 1326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.6046 (OUTLIER) cc_final: 0.5772 (mt0) REVERT: A 313 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.6181 (mtt90) REVERT: A 318 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7706 (tt0) REVERT: A 345 LYS cc_start: 0.8542 (mttt) cc_final: 0.8229 (mttm) REVERT: B 44 GLN cc_start: 0.8070 (mt0) cc_final: 0.7810 (mm110) REVERT: B 219 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7526 (mmm-85) REVERT: B 234 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8610 (m-80) REVERT: E 13 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7585 (tp-100) REVERT: E 160 ARG cc_start: 0.7776 (ttm170) cc_final: 0.6957 (ttm-80) REVERT: G 14 LYS cc_start: 0.6892 (tptp) cc_final: 0.6477 (tttt) REVERT: R 61 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.7372 (mt0) REVERT: R 89 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6426 (mt) REVERT: R 169 LEU cc_start: 0.7169 (mt) cc_final: 0.6929 (mt) REVERT: R 170 PHE cc_start: 0.6069 (OUTLIER) cc_final: 0.5303 (p90) REVERT: R 216 LYS cc_start: 0.6704 (ttpp) cc_final: 0.6462 (mmtt) REVERT: R 389 GLU cc_start: 0.7256 (mp0) cc_final: 0.6971 (mp0) outliers start: 22 outliers final: 10 residues processed: 155 average time/residue: 1.4420 time to fit residues: 235.9911 Evaluate side-chains 158 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 39 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN E 77 ASN R 352 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.169758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.130253 restraints weight = 25191.169| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.90 r_work: 0.3183 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8950 Z= 0.170 Angle : 0.567 7.150 12134 Z= 0.303 Chirality : 0.041 0.147 1389 Planarity : 0.004 0.076 1527 Dihedral : 5.799 46.659 1236 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.87 % Allowed : 15.30 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.26), residues: 1104 helix: 2.39 (0.26), residues: 393 sheet: -0.55 (0.31), residues: 281 loop : -0.25 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 129 TYR 0.013 0.002 TYR R 88 PHE 0.016 0.002 PHE R 345 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8946) covalent geometry : angle 0.56672 (12126) SS BOND : bond 0.00216 ( 4) SS BOND : angle 1.05896 ( 8) hydrogen bonds : bond 0.03665 ( 472) hydrogen bonds : angle 4.92111 ( 1326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.6135 (OUTLIER) cc_final: 0.5886 (mt0) REVERT: A 313 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.6154 (mtt90) REVERT: A 318 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7729 (tt0) REVERT: A 345 LYS cc_start: 0.8575 (mttt) cc_final: 0.8293 (mttm) REVERT: B 44 GLN cc_start: 0.8201 (mt0) cc_final: 0.7939 (mm110) REVERT: B 129 ARG cc_start: 0.8280 (mmm-85) cc_final: 0.8079 (mtp85) REVERT: B 219 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7537 (mmm-85) REVERT: B 234 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8518 (m-80) REVERT: E 13 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7598 (tp-100) REVERT: E 160 ARG cc_start: 0.7791 (ttm170) cc_final: 0.6977 (ttm-80) REVERT: E 191 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8270 (mtp180) REVERT: E 195 LEU cc_start: 0.8464 (pt) cc_final: 0.8214 (tp) REVERT: G 14 LYS cc_start: 0.6899 (tptp) cc_final: 0.6486 (tttt) REVERT: R 89 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6472 (mt) REVERT: R 169 LEU cc_start: 0.7149 (mt) cc_final: 0.6922 (mt) REVERT: R 170 PHE cc_start: 0.6231 (OUTLIER) cc_final: 0.5461 (p90) REVERT: R 216 LYS cc_start: 0.6702 (ttpp) cc_final: 0.6455 (mmtt) REVERT: R 387 ASN cc_start: 0.6315 (t0) cc_final: 0.5903 (t0) outliers start: 18 outliers final: 8 residues processed: 156 average time/residue: 1.6263 time to fit residues: 267.8538 Evaluate side-chains 160 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 170 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 42 optimal weight: 0.0060 chunk 74 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN G 59 ASN R 352 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.170318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.132839 restraints weight = 25413.917| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.77 r_work: 0.3224 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8950 Z= 0.139 Angle : 0.557 6.869 12134 Z= 0.296 Chirality : 0.041 0.147 1389 Planarity : 0.004 0.081 1527 Dihedral : 5.623 43.778 1236 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.87 % Allowed : 15.61 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.26), residues: 1104 helix: 2.47 (0.26), residues: 394 sheet: -0.54 (0.31), residues: 272 loop : -0.22 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 129 TYR 0.013 0.001 TYR R 88 PHE 0.014 0.002 PHE R 345 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 349 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8946) covalent geometry : angle 0.55696 (12126) SS BOND : bond 0.00182 ( 4) SS BOND : angle 1.10692 ( 8) hydrogen bonds : bond 0.03492 ( 472) hydrogen bonds : angle 4.83854 ( 1326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7636.16 seconds wall clock time: 129 minutes 52.47 seconds (7792.47 seconds total)