Starting phenix.real_space_refine on Wed Sep 17 13:52:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6b3j_7039/09_2025/6b3j_7039.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b3j_7039/09_2025/6b3j_7039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6b3j_7039/09_2025/6b3j_7039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b3j_7039/09_2025/6b3j_7039.map" model { file = "/net/cci-nas-00/data/ceres_data/6b3j_7039/09_2025/6b3j_7039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b3j_7039/09_2025/6b3j_7039.cif" } resolution = 3.3 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= 0.008 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 54 5.16 5 C 5758 2.51 5 N 1560 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9034 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3134 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 364} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "P" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 254 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "A" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1654 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain breaks: 4 Chain: "B" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2595 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Time building chain proxies: 2.02, per 1000 atoms: 0.22 Number of scatterers: 9034 At special positions: 0 Unit cell: (82.68, 177.02, 98.58, 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 54 16.00 O 1662 8.00 N 1560 7.00 C 5758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.02 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.02 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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: 0.85 Conformation dependent library (CDL) restraints added in 275.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 44.3% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'R' and resid 31 through 53 Processing helix chain 'R' and resid 91 through 95 removed outlier: 3.577A pdb=" N SER R 94 " --> pdb=" O TRP R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 170 removed outlier: 4.006A pdb=" N ARG R 170 " --> pdb=" O LEU R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 205 removed outlier: 3.535A pdb=" N TYR R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 211 Processing helix chain 'R' and resid 213 through 223 Processing helix chain 'R' and resid 225 through 257 removed outlier: 3.722A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU R 231 " --> pdb=" O ARG R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 292 Proline residue: R 277 - end of helix Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 296 through 300 removed outlier: 3.785A pdb=" N ARG R 299 " --> pdb=" O CYS R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 337 removed outlier: 3.640A pdb=" N TRP R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 361 through 370 Processing helix chain 'R' and resid 372 through 376 removed outlier: 3.612A pdb=" N ARG R 376 " --> pdb=" O GLU R 373 " (cutoff:3.500A) Processing helix chain 'R' and resid 379 through 405 removed outlier: 4.307A pdb=" N LYS R 383 " --> pdb=" O LEU R 379 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR R 402 " --> pdb=" O VAL R 398 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 423 Processing helix chain 'P' and resid 2 through 31 Processing helix chain 'A' and resid 12 through 39 Processing helix chain 'A' and resid 231 through 236 removed outlier: 4.126A pdb=" N GLN A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 4.112A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.832A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.987A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.734A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.632A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.759A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.532A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.584A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 83 through 84 removed outlier: 4.107A pdb=" N VAL R 83 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL R 100 " --> pdb=" O VAL R 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.602A pdb=" N VAL A 217 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.715A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.608A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.960A 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: 6.354A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG 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: 3.724A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.135A 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: 3.892A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.414A 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: 3.583A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.792A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 8 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11 removed outlier: 7.111A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1380 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: 1.51 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2888 1.34 - 1.46: 2116 1.46 - 1.58: 4163 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 9240 Sorted by residual: bond pdb=" CB TRP B 169 " pdb=" CG TRP B 169 " ideal model delta sigma weight residual 1.498 1.442 0.056 3.10e-02 1.04e+03 3.30e+00 bond pdb=" C VAL R 276 " pdb=" N PRO R 277 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.36e-02 5.41e+03 3.30e+00 bond pdb=" N LYS R 113 " pdb=" CA LYS R 113 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.16e+00 bond pdb=" N ILE R 357 " pdb=" CA ILE R 357 " ideal model delta sigma weight residual 1.464 1.484 -0.020 1.23e-02 6.61e+03 2.53e+00 bond pdb=" CB MET P 15 " pdb=" CG MET P 15 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.35e+00 ... (remaining 9235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 12250 2.80 - 5.59: 242 5.59 - 8.39: 19 8.39 - 11.18: 12 11.18 - 13.98: 1 Bond angle restraints: 12524 Sorted by residual: angle pdb=" C LYS N 76 " pdb=" N ASN N 77 " pdb=" CA ASN N 77 " ideal model delta sigma weight residual 121.54 132.25 -10.71 1.91e+00 2.74e-01 3.14e+01 angle pdb=" C ASP B 66 " pdb=" N SER B 67 " pdb=" CA SER B 67 " ideal model delta sigma weight residual 121.54 130.29 -8.75 1.91e+00 2.74e-01 2.10e+01 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 129.75 -8.21 1.91e+00 2.74e-01 1.85e+01 angle pdb=" C GLU A 330 " pdb=" N ASP A 331 " pdb=" CA ASP A 331 " ideal model delta sigma weight residual 121.59 135.57 -13.98 3.54e+00 7.98e-02 1.56e+01 angle pdb=" N GLY R 168 " pdb=" CA GLY R 168 " pdb=" C GLY R 168 " ideal model delta sigma weight residual 112.73 117.15 -4.42 1.20e+00 6.94e-01 1.35e+01 ... (remaining 12519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 5186 15.66 - 31.33: 216 31.33 - 46.99: 52 46.99 - 62.65: 3 62.65 - 78.32: 7 Dihedral angle restraints: 5464 sinusoidal: 2178 harmonic: 3286 Sorted by residual: dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 171.32 -78.32 1 1.00e+01 1.00e-02 7.66e+01 dihedral pdb=" CA ALA R 57 " pdb=" C ALA R 57 " pdb=" N THR R 58 " pdb=" CA THR R 58 " ideal model delta harmonic sigma weight residual 180.00 144.49 35.51 0 5.00e+00 4.00e-02 5.04e+01 dihedral pdb=" CA SER R 261 " pdb=" C SER R 261 " pdb=" N GLU R 262 " pdb=" CA GLU R 262 " ideal model delta harmonic sigma weight residual -180.00 -155.28 -24.72 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 5461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1068 0.069 - 0.138: 264 0.138 - 0.207: 37 0.207 - 0.276: 5 0.276 - 0.345: 2 Chirality restraints: 1376 Sorted by residual: chirality pdb=" CB VAL R 276 " pdb=" CA VAL R 276 " pdb=" CG1 VAL R 276 " pdb=" CG2 VAL R 276 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB ILE R 317 " pdb=" CA ILE R 317 " pdb=" CG1 ILE R 317 " pdb=" CG2 ILE R 317 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1373 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 272 " 0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C ILE R 272 " -0.069 2.00e-02 2.50e+03 pdb=" O ILE R 272 " 0.026 2.00e-02 2.50e+03 pdb=" N GLY R 273 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 360 " -0.059 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO A 361 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.025 2.00e-02 2.50e+03 1.96e-02 7.65e+00 pdb=" CG TYR B 105 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " 0.001 2.00e-02 2.50e+03 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1328 2.76 - 3.30: 8363 3.30 - 3.83: 14711 3.83 - 4.37: 16344 4.37 - 4.90: 29559 Nonbonded interactions: 70305 Sorted by model distance: nonbonded pdb=" OG1 THR N 91 " pdb=" O VAL N 124 " model vdw 2.229 3.040 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.272 3.040 nonbonded pdb=" OG1 THR R 105 " pdb=" O LEU R 109 " model vdw 2.276 3.040 nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.300 3.040 ... (remaining 70300 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.300 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 : 0.007 0.075 9246 Z= 0.310 Angle : 1.005 13.976 12536 Z= 0.569 Chirality : 0.061 0.345 1376 Planarity : 0.007 0.089 1597 Dihedral : 9.888 77.618 3320 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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 aren not related in a simple way. whole: 0.60 (0.24), residues: 1105 helix: 2.60 (0.22), residues: 451 sheet: 0.58 (0.37), residues: 196 loop : -2.12 (0.24), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 64 TYR 0.048 0.004 TYR B 105 PHE 0.026 0.003 PHE R 367 TRP 0.031 0.004 TRP R 72 HIS 0.010 0.002 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00692 ( 9240) covalent geometry : angle 1.00377 (12524) SS BOND : bond 0.00582 ( 6) SS BOND : angle 2.08567 ( 12) hydrogen bonds : bond 0.15739 ( 477) hydrogen bonds : angle 6.42273 ( 1380) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: R 67 ASP cc_start: 0.4130 (p0) cc_final: 0.3885 (m-30) REVERT: R 123 LEU cc_start: 0.4851 (pp) cc_final: 0.4611 (tp) REVERT: R 127 GLU cc_start: 0.6915 (tp30) cc_final: 0.6556 (mt-10) REVERT: R 182 ASN cc_start: 0.8973 (m-40) cc_final: 0.8718 (m110) REVERT: R 211 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7910 (tt0) REVERT: R 242 TYR cc_start: 0.8440 (m-80) cc_final: 0.8026 (m-80) REVERT: R 305 TYR cc_start: 0.7486 (m-10) cc_final: 0.7153 (m-10) REVERT: R 351 LYS cc_start: 0.8633 (tttt) cc_final: 0.8249 (mmtt) REVERT: R 393 PHE cc_start: 0.8134 (m-10) cc_final: 0.7760 (m-10) REVERT: R 404 PHE cc_start: 0.4434 (t80) cc_final: 0.3359 (m-80) REVERT: R 408 GLU cc_start: 0.8503 (pt0) cc_final: 0.8123 (pt0) REVERT: P 21 ARG cc_start: 0.8405 (mtt180) cc_final: 0.8191 (mmm-85) REVERT: A 286 SER cc_start: 0.9165 (m) cc_final: 0.8717 (p) REVERT: B 23 LYS cc_start: 0.8236 (tttp) cc_final: 0.7512 (mmtt) REVERT: B 46 ARG cc_start: 0.7053 (tpt-90) cc_final: 0.6555 (mtp-110) REVERT: B 71 VAL cc_start: 0.8702 (t) cc_final: 0.8436 (p) REVERT: B 82 TRP cc_start: 0.8855 (m100) cc_final: 0.8630 (m100) REVERT: B 154 ASP cc_start: 0.7964 (m-30) cc_final: 0.7642 (t0) REVERT: B 189 SER cc_start: 0.9163 (t) cc_final: 0.8883 (p) REVERT: B 217 MET cc_start: 0.7812 (ptp) cc_final: 0.7322 (tpt) REVERT: G 14 LYS cc_start: 0.7804 (mmmt) cc_final: 0.7309 (tttp) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1324 time to fit residues: 42.0805 Evaluate side-chains 122 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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: 4.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 115 ASN R 263 GLN R 407 ASN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 155 ASN B 266 HIS G 24 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.116067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.101527 restraints weight = 23322.012| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.81 r_work: 0.3615 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9246 Z= 0.168 Angle : 0.659 8.883 12536 Z= 0.354 Chirality : 0.043 0.153 1376 Planarity : 0.005 0.053 1597 Dihedral : 5.612 50.584 1233 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.16 % Allowed : 8.65 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % 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 aren not related in a simple way. whole: 0.91 (0.25), residues: 1105 helix: 2.84 (0.23), residues: 451 sheet: 0.53 (0.36), residues: 194 loop : -1.81 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 299 TYR 0.021 0.002 TYR R 402 PHE 0.029 0.002 PHE R 230 TRP 0.018 0.002 TRP R 33 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9240) covalent geometry : angle 0.64897 (12524) SS BOND : bond 0.00662 ( 6) SS BOND : angle 3.76950 ( 12) hydrogen bonds : bond 0.04642 ( 477) hydrogen bonds : angle 5.06886 ( 1380) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.401 Fit side-chains REVERT: R 67 ASP cc_start: 0.4934 (p0) cc_final: 0.4026 (m-30) REVERT: R 267 ARG cc_start: 0.7024 (mmm-85) cc_final: 0.6745 (mtp180) REVERT: R 269 TYR cc_start: 0.8196 (m-80) cc_final: 0.7653 (m-80) REVERT: R 305 TYR cc_start: 0.7586 (m-10) cc_final: 0.7357 (m-10) REVERT: R 354 LEU cc_start: 0.8295 (mt) cc_final: 0.8017 (tt) REVERT: R 404 PHE cc_start: 0.4567 (t80) cc_final: 0.3733 (m-80) REVERT: A 318 TYR cc_start: 0.5969 (t80) cc_final: 0.5435 (t80) REVERT: B 23 LYS cc_start: 0.8379 (tttp) cc_final: 0.7722 (mmtt) REVERT: B 46 ARG cc_start: 0.7179 (tpt-90) cc_final: 0.6850 (mmm160) REVERT: B 82 TRP cc_start: 0.8832 (m100) cc_final: 0.8580 (m100) REVERT: B 154 ASP cc_start: 0.7761 (m-30) cc_final: 0.7507 (t0) REVERT: B 189 SER cc_start: 0.9068 (t) cc_final: 0.8867 (p) REVERT: G 14 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7543 (tttp) outliers start: 21 outliers final: 14 residues processed: 152 average time/residue: 0.0906 time to fit residues: 19.4351 Evaluate side-chains 128 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 5 ASN ** A 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 = 0.3954 r_free = 0.3954 target = 0.117092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.103388 restraints weight = 23103.022| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.44 r_work: 0.3655 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9246 Z= 0.121 Angle : 0.565 7.634 12536 Z= 0.303 Chirality : 0.041 0.154 1376 Planarity : 0.004 0.056 1597 Dihedral : 5.102 42.960 1233 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.88 % Allowed : 10.20 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % 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 aren not related in a simple way. whole: 1.07 (0.25), residues: 1105 helix: 2.93 (0.24), residues: 448 sheet: 0.39 (0.36), residues: 195 loop : -1.52 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 62 TYR 0.020 0.001 TYR N 60 PHE 0.028 0.001 PHE R 385 TRP 0.017 0.001 TRP R 33 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9240) covalent geometry : angle 0.55829 (12524) SS BOND : bond 0.00318 ( 6) SS BOND : angle 2.82885 ( 12) hydrogen bonds : bond 0.04016 ( 477) hydrogen bonds : angle 4.59100 ( 1380) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: R 67 ASP cc_start: 0.4927 (p0) cc_final: 0.4177 (m-30) REVERT: R 139 GLU cc_start: 0.6963 (tt0) cc_final: 0.6295 (pm20) REVERT: R 298 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.7887 (t) REVERT: R 404 PHE cc_start: 0.4638 (t80) cc_final: 0.3846 (m-80) REVERT: A 318 TYR cc_start: 0.6001 (t80) cc_final: 0.5483 (t80) REVERT: B 23 LYS cc_start: 0.8280 (tttp) cc_final: 0.7757 (mmtt) REVERT: B 46 ARG cc_start: 0.7190 (tpt-90) cc_final: 0.6947 (mmm160) REVERT: B 82 TRP cc_start: 0.8699 (m100) cc_final: 0.8460 (m100) REVERT: B 270 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8334 (pp) REVERT: G 14 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7609 (tttp) outliers start: 28 outliers final: 17 residues processed: 157 average time/residue: 0.0906 time to fit residues: 20.1832 Evaluate side-chains 130 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 21 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.114832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.100519 restraints weight = 23708.125| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.86 r_work: 0.3591 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9246 Z= 0.163 Angle : 0.584 7.933 12536 Z= 0.312 Chirality : 0.042 0.164 1376 Planarity : 0.004 0.051 1597 Dihedral : 5.069 39.959 1233 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.40 % Allowed : 11.02 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % 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 aren not related in a simple way. whole: 1.03 (0.25), residues: 1105 helix: 2.94 (0.24), residues: 444 sheet: 0.16 (0.36), residues: 201 loop : -1.46 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 62 TYR 0.017 0.002 TYR B 105 PHE 0.021 0.002 PHE R 385 TRP 0.017 0.001 TRP R 120 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 9240) covalent geometry : angle 0.57818 (12524) SS BOND : bond 0.00277 ( 6) SS BOND : angle 2.63874 ( 12) hydrogen bonds : bond 0.04032 ( 477) hydrogen bonds : angle 4.55037 ( 1380) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: R 67 ASP cc_start: 0.4653 (p0) cc_final: 0.4099 (m-30) REVERT: R 120 TRP cc_start: 0.5984 (t60) cc_final: 0.5779 (t60) REVERT: R 139 GLU cc_start: 0.7037 (tt0) cc_final: 0.6390 (pm20) REVERT: R 247 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8036 (tp30) REVERT: R 269 TYR cc_start: 0.8130 (m-80) cc_final: 0.7813 (m-80) REVERT: R 298 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.8036 (t) REVERT: R 404 PHE cc_start: 0.4491 (t80) cc_final: 0.3675 (m-80) REVERT: A 318 TYR cc_start: 0.5996 (t80) cc_final: 0.5471 (t80) REVERT: B 23 LYS cc_start: 0.8438 (tttp) cc_final: 0.7752 (mmtt) REVERT: B 45 MET cc_start: 0.8381 (mtp) cc_final: 0.7996 (mtp) REVERT: B 46 ARG cc_start: 0.7334 (tpt-90) cc_final: 0.7026 (mmm-85) REVERT: B 82 TRP cc_start: 0.8821 (m100) cc_final: 0.8570 (m100) REVERT: B 270 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8449 (pp) REVERT: G 14 LYS cc_start: 0.7964 (mmmt) cc_final: 0.7500 (tttp) outliers start: 33 outliers final: 21 residues processed: 133 average time/residue: 0.0916 time to fit residues: 17.4346 Evaluate side-chains 130 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 247 GLU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 58 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.110943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.096768 restraints weight = 24169.437| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.81 r_work: 0.3527 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9246 Z= 0.251 Angle : 0.690 10.945 12536 Z= 0.367 Chirality : 0.045 0.179 1376 Planarity : 0.005 0.047 1597 Dihedral : 5.529 40.857 1233 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.81 % Allowed : 12.36 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % 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 aren not related in a simple way. whole: 0.68 (0.25), residues: 1105 helix: 2.63 (0.23), residues: 442 sheet: -0.22 (0.33), residues: 225 loop : -1.55 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 64 TYR 0.024 0.002 TYR B 105 PHE 0.024 0.002 PHE A 246 TRP 0.026 0.002 TRP R 110 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00573 ( 9240) covalent geometry : angle 0.68438 (12524) SS BOND : bond 0.00417 ( 6) SS BOND : angle 2.91467 ( 12) hydrogen bonds : bond 0.04654 ( 477) hydrogen bonds : angle 4.84940 ( 1380) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.359 Fit side-chains REVERT: R 67 ASP cc_start: 0.4441 (p0) cc_final: 0.4123 (m-30) REVERT: R 120 TRP cc_start: 0.6044 (t60) cc_final: 0.5687 (t60) REVERT: R 139 GLU cc_start: 0.7125 (tt0) cc_final: 0.6431 (pm20) REVERT: R 247 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8156 (tp30) REVERT: R 354 LEU cc_start: 0.8415 (mt) cc_final: 0.8185 (tt) REVERT: R 404 PHE cc_start: 0.4437 (t80) cc_final: 0.3656 (m-80) REVERT: A 27 GLU cc_start: 0.7746 (pp20) cc_final: 0.7535 (pp20) REVERT: A 318 TYR cc_start: 0.6059 (t80) cc_final: 0.5537 (t80) REVERT: B 23 LYS cc_start: 0.8684 (tttp) cc_final: 0.7915 (mmtt) REVERT: B 46 ARG cc_start: 0.7330 (tpt-90) cc_final: 0.7023 (mmm-85) REVERT: B 234 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.7390 (t80) REVERT: B 270 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8415 (pp) REVERT: G 14 LYS cc_start: 0.7949 (mmmt) cc_final: 0.7506 (tttp) REVERT: G 51 LEU cc_start: 0.7395 (tp) cc_final: 0.7135 (mt) outliers start: 37 outliers final: 28 residues processed: 140 average time/residue: 0.0904 time to fit residues: 18.2190 Evaluate side-chains 130 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 247 GLU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 30 optimal weight: 10.0000 chunk 17 optimal weight: 0.0980 chunk 66 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 63 optimal weight: 0.1980 chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 5 ASN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** 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 = 0.3908 r_free = 0.3908 target = 0.114695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.100290 restraints weight = 23724.613| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.85 r_work: 0.3584 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9246 Z= 0.115 Angle : 0.547 6.732 12536 Z= 0.293 Chirality : 0.041 0.157 1376 Planarity : 0.004 0.048 1597 Dihedral : 4.991 38.075 1233 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.68 % Allowed : 14.21 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % 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 aren not related in a simple way. whole: 0.90 (0.26), residues: 1105 helix: 2.87 (0.24), residues: 445 sheet: -0.19 (0.34), residues: 218 loop : -1.47 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 389 TYR 0.016 0.001 TYR R 69 PHE 0.021 0.001 PHE R 385 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 9240) covalent geometry : angle 0.54169 (12524) SS BOND : bond 0.00275 ( 6) SS BOND : angle 2.41132 ( 12) hydrogen bonds : bond 0.03802 ( 477) hydrogen bonds : angle 4.42556 ( 1380) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.366 Fit side-chains REVERT: R 67 ASP cc_start: 0.4361 (p0) cc_final: 0.4084 (m-30) REVERT: R 120 TRP cc_start: 0.5991 (t60) cc_final: 0.5645 (t60) REVERT: R 139 GLU cc_start: 0.7124 (tt0) cc_final: 0.6463 (pm20) REVERT: R 247 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: R 354 LEU cc_start: 0.8342 (mt) cc_final: 0.8074 (tt) REVERT: R 404 PHE cc_start: 0.4445 (t80) cc_final: 0.3767 (m-80) REVERT: A 27 GLU cc_start: 0.7775 (pp20) cc_final: 0.7528 (pp20) REVERT: A 318 TYR cc_start: 0.5800 (t80) cc_final: 0.5416 (t80) REVERT: A 358 TYR cc_start: 0.8311 (m-80) cc_final: 0.7735 (m-80) REVERT: B 23 LYS cc_start: 0.8533 (tttp) cc_final: 0.7805 (mmtt) REVERT: B 45 MET cc_start: 0.8366 (mtp) cc_final: 0.8053 (mtp) REVERT: B 46 ARG cc_start: 0.7404 (tpt-90) cc_final: 0.7158 (mtp-110) REVERT: B 170 ASP cc_start: 0.7365 (t0) cc_final: 0.7165 (t0) REVERT: B 270 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8458 (pp) REVERT: G 14 LYS cc_start: 0.7890 (mmmt) cc_final: 0.7458 (tttp) outliers start: 26 outliers final: 19 residues processed: 132 average time/residue: 0.0948 time to fit residues: 17.8045 Evaluate side-chains 125 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 247 GLU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 54 optimal weight: 0.0030 chunk 3 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 5 ASN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** 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 = 0.3894 r_free = 0.3894 target = 0.113820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.099345 restraints weight = 23915.803| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.87 r_work: 0.3569 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9246 Z= 0.144 Angle : 0.572 7.115 12536 Z= 0.303 Chirality : 0.041 0.164 1376 Planarity : 0.004 0.048 1597 Dihedral : 4.951 37.191 1233 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.30 % Allowed : 14.73 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % 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 aren not related in a simple way. whole: 0.82 (0.26), residues: 1105 helix: 2.67 (0.24), residues: 451 sheet: -0.21 (0.34), residues: 219 loop : -1.42 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 64 TYR 0.015 0.002 TYR R 69 PHE 0.019 0.002 PHE R 385 TRP 0.018 0.001 TRP R 39 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9240) covalent geometry : angle 0.56670 (12524) SS BOND : bond 0.00290 ( 6) SS BOND : angle 2.52411 ( 12) hydrogen bonds : bond 0.03846 ( 477) hydrogen bonds : angle 4.43319 ( 1380) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.389 Fit side-chains REVERT: R 67 ASP cc_start: 0.4421 (p0) cc_final: 0.4059 (m-30) REVERT: R 120 TRP cc_start: 0.6060 (t60) cc_final: 0.5685 (t60) REVERT: R 139 GLU cc_start: 0.7173 (tt0) cc_final: 0.6491 (pm20) REVERT: R 247 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8141 (tp30) REVERT: R 269 TYR cc_start: 0.8421 (m-10) cc_final: 0.8215 (m-80) REVERT: R 354 LEU cc_start: 0.8361 (mt) cc_final: 0.8095 (tt) REVERT: R 404 PHE cc_start: 0.4519 (t80) cc_final: 0.3822 (m-80) REVERT: A 27 GLU cc_start: 0.7728 (pp20) cc_final: 0.7471 (pp20) REVERT: A 318 TYR cc_start: 0.5866 (t80) cc_final: 0.5489 (t80) REVERT: B 23 LYS cc_start: 0.8579 (tttp) cc_final: 0.7821 (mmtt) REVERT: B 45 MET cc_start: 0.8315 (mtp) cc_final: 0.8006 (mtp) REVERT: B 46 ARG cc_start: 0.7382 (tpt-90) cc_final: 0.7138 (mtp-110) REVERT: B 170 ASP cc_start: 0.7522 (t0) cc_final: 0.7319 (t0) REVERT: B 234 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7345 (t80) REVERT: B 270 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8364 (pp) REVERT: G 14 LYS cc_start: 0.7903 (mmmt) cc_final: 0.7470 (tttp) outliers start: 32 outliers final: 26 residues processed: 130 average time/residue: 0.0855 time to fit residues: 16.3638 Evaluate side-chains 132 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 247 GLU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 400 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 26 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** 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 = 0.3883 r_free = 0.3883 target = 0.112802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.098474 restraints weight = 23950.773| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.87 r_work: 0.3553 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9246 Z= 0.172 Angle : 0.607 7.917 12536 Z= 0.322 Chirality : 0.042 0.167 1376 Planarity : 0.004 0.048 1597 Dihedral : 5.067 37.161 1233 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.30 % Allowed : 14.73 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % 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 aren not related in a simple way. whole: 0.76 (0.26), residues: 1105 helix: 2.61 (0.24), residues: 451 sheet: -0.29 (0.33), residues: 226 loop : -1.43 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 64 TYR 0.016 0.002 TYR R 242 PHE 0.023 0.002 PHE R 385 TRP 0.027 0.002 TRP R 39 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 9240) covalent geometry : angle 0.60153 (12524) SS BOND : bond 0.00317 ( 6) SS BOND : angle 2.59463 ( 12) hydrogen bonds : bond 0.04017 ( 477) hydrogen bonds : angle 4.49880 ( 1380) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: R 67 ASP cc_start: 0.4585 (p0) cc_final: 0.4177 (m-30) REVERT: R 120 TRP cc_start: 0.6058 (t60) cc_final: 0.5691 (t60) REVERT: R 139 GLU cc_start: 0.7197 (tt0) cc_final: 0.6481 (pm20) REVERT: R 242 TYR cc_start: 0.8638 (m-80) cc_final: 0.8294 (m-80) REVERT: R 247 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8107 (tp30) REVERT: R 354 LEU cc_start: 0.8530 (mt) cc_final: 0.8250 (tt) REVERT: R 404 PHE cc_start: 0.4631 (t80) cc_final: 0.3812 (m-80) REVERT: A 27 GLU cc_start: 0.7760 (pp20) cc_final: 0.7480 (pp20) REVERT: A 318 TYR cc_start: 0.5961 (t80) cc_final: 0.5598 (t80) REVERT: B 23 LYS cc_start: 0.8656 (tttp) cc_final: 0.7887 (mmtt) REVERT: B 46 ARG cc_start: 0.7352 (tpt-90) cc_final: 0.7106 (mtp-110) REVERT: B 234 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7372 (t80) REVERT: B 270 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8363 (pp) REVERT: G 14 LYS cc_start: 0.7930 (mmmt) cc_final: 0.7493 (tttp) outliers start: 32 outliers final: 26 residues processed: 129 average time/residue: 0.0844 time to fit residues: 16.0092 Evaluate side-chains 130 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 247 GLU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 400 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 71 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 92 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 6 optimal weight: 0.0670 chunk 69 optimal weight: 0.7980 overall best weight: 1.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** 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 = 0.3901 r_free = 0.3901 target = 0.114302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.099846 restraints weight = 23639.410| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.86 r_work: 0.3578 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9246 Z= 0.132 Angle : 0.583 7.367 12536 Z= 0.306 Chirality : 0.041 0.159 1376 Planarity : 0.004 0.047 1597 Dihedral : 4.883 36.478 1233 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.99 % Allowed : 14.83 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % 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 aren not related in a simple way. whole: 0.80 (0.26), residues: 1105 helix: 2.65 (0.24), residues: 452 sheet: -0.25 (0.34), residues: 221 loop : -1.42 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 64 TYR 0.014 0.001 TYR R 69 PHE 0.022 0.002 PHE R 385 TRP 0.024 0.001 TRP R 39 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9240) covalent geometry : angle 0.57809 (12524) SS BOND : bond 0.00298 ( 6) SS BOND : angle 2.48274 ( 12) hydrogen bonds : bond 0.03737 ( 477) hydrogen bonds : angle 4.38651 ( 1380) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: R 67 ASP cc_start: 0.4481 (p0) cc_final: 0.4102 (m-30) REVERT: R 120 TRP cc_start: 0.5996 (t60) cc_final: 0.5701 (t60) REVERT: R 139 GLU cc_start: 0.7180 (tt0) cc_final: 0.6512 (pm20) REVERT: R 354 LEU cc_start: 0.8472 (mt) cc_final: 0.8182 (tt) REVERT: R 404 PHE cc_start: 0.4774 (t80) cc_final: 0.3935 (m-80) REVERT: A 27 GLU cc_start: 0.7740 (pp20) cc_final: 0.7471 (pp20) REVERT: A 318 TYR cc_start: 0.5829 (t80) cc_final: 0.5466 (t80) REVERT: A 358 TYR cc_start: 0.8242 (m-80) cc_final: 0.7831 (m-80) REVERT: B 23 LYS cc_start: 0.8577 (tttp) cc_final: 0.7825 (mmtt) REVERT: B 45 MET cc_start: 0.8245 (mtp) cc_final: 0.7993 (mtp) REVERT: B 46 ARG cc_start: 0.7351 (tpt-90) cc_final: 0.7117 (mtp-110) REVERT: B 234 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7316 (t80) REVERT: B 270 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8390 (pp) REVERT: G 14 LYS cc_start: 0.8005 (mmmt) cc_final: 0.7549 (tttp) outliers start: 29 outliers final: 25 residues processed: 127 average time/residue: 0.0926 time to fit residues: 16.6668 Evaluate side-chains 130 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 247 GLU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 6.9990 chunk 77 optimal weight: 0.0060 chunk 13 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 0.0770 chunk 92 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.116496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.102064 restraints weight = 23471.890| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.85 r_work: 0.3615 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9246 Z= 0.108 Angle : 0.565 8.605 12536 Z= 0.296 Chirality : 0.040 0.150 1376 Planarity : 0.004 0.048 1597 Dihedral : 4.659 35.112 1233 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.27 % Allowed : 15.65 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % 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 aren not related in a simple way. whole: 0.89 (0.26), residues: 1105 helix: 2.76 (0.24), residues: 450 sheet: -0.16 (0.34), residues: 209 loop : -1.39 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 356 TYR 0.031 0.001 TYR R 269 PHE 0.021 0.001 PHE R 385 TRP 0.022 0.001 TRP R 39 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 9240) covalent geometry : angle 0.56084 (12524) SS BOND : bond 0.00273 ( 6) SS BOND : angle 2.25697 ( 12) hydrogen bonds : bond 0.03458 ( 477) hydrogen bonds : angle 4.25171 ( 1380) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 67 ASP cc_start: 0.4435 (p0) cc_final: 0.4067 (m-30) REVERT: R 139 GLU cc_start: 0.7116 (tt0) cc_final: 0.6506 (pm20) REVERT: R 269 TYR cc_start: 0.8528 (m-80) cc_final: 0.8310 (m-80) REVERT: R 354 LEU cc_start: 0.8464 (mt) cc_final: 0.8159 (tt) REVERT: R 404 PHE cc_start: 0.4867 (t80) cc_final: 0.4051 (m-80) REVERT: A 27 GLU cc_start: 0.7745 (pp20) cc_final: 0.7485 (pp20) REVERT: A 318 TYR cc_start: 0.5865 (t80) cc_final: 0.5564 (t80) REVERT: B 23 LYS cc_start: 0.8539 (tttp) cc_final: 0.7838 (mmtt) REVERT: B 46 ARG cc_start: 0.7368 (tpt-90) cc_final: 0.7085 (mtp-110) REVERT: B 270 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8352 (pp) REVERT: G 14 LYS cc_start: 0.8063 (mmmt) cc_final: 0.7588 (tttp) outliers start: 22 outliers final: 20 residues processed: 132 average time/residue: 0.0917 time to fit residues: 17.2554 Evaluate side-chains 126 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 0.1980 chunk 48 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 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 = 0.3928 r_free = 0.3928 target = 0.115984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.101462 restraints weight = 23353.149| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.83 r_work: 0.3608 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9246 Z= 0.124 Angle : 0.585 8.108 12536 Z= 0.306 Chirality : 0.041 0.183 1376 Planarity : 0.004 0.048 1597 Dihedral : 4.671 35.393 1233 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.27 % Allowed : 16.07 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % 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 aren not related in a simple way. whole: 0.87 (0.26), residues: 1105 helix: 2.67 (0.24), residues: 454 sheet: -0.18 (0.34), residues: 214 loop : -1.36 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 46 TYR 0.028 0.002 TYR N 60 PHE 0.021 0.001 PHE R 385 TRP 0.023 0.001 TRP R 39 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9240) covalent geometry : angle 0.58046 (12524) SS BOND : bond 0.00288 ( 6) SS BOND : angle 2.33514 ( 12) hydrogen bonds : bond 0.03536 ( 477) hydrogen bonds : angle 4.25264 ( 1380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1917.38 seconds wall clock time: 33 minutes 44.17 seconds (2024.17 seconds total)