Starting phenix.real_space_refine on Sun May 3 14:40:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wda_65887/05_2026/9wda_65887_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wda_65887/05_2026/9wda_65887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wda_65887/05_2026/9wda_65887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wda_65887/05_2026/9wda_65887.map" model { file = "/net/cci-nas-00/data/ceres_data/9wda_65887/05_2026/9wda_65887_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wda_65887/05_2026/9wda_65887_trim.cif" } resolution = 2.35 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= 0.042 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 4314 2.51 5 N 1159 2.21 5 O 1322 1.98 5 H 6534 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13385 Number of models: 1 Model: "" Number of chains: 4 Chain: "a" Number of atoms: 6662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 6662 Classifications: {'peptide': 431} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 410} Chain breaks: 1 Chain: "b" Number of atoms: 6595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6595 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "a" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {' MG': 1, 'G2P': 1, 'TA1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.85, per 1000 atoms: 0.14 Number of scatterers: 13385 At special positions: 0 Unit cell: (74.5446, 72.6332, 113.728, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 48 16.00 P 6 15.00 Mg 2 11.99 O 1322 8.00 N 1159 7.00 C 4314 6.00 H 6534 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.05 Conformation dependent library (CDL) restraints added in 440.1 milliseconds 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 5 sheets defined 51.9% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'a' and resid 10 through 29 removed outlier: 3.604A pdb=" N ALA a 19 " --> pdb=" O GLN a 15 " (cutoff:3.500A) Processing helix chain 'a' and resid 48 through 51 Processing helix chain 'a' and resid 72 through 80 removed outlier: 3.840A pdb=" N GLU a 77 " --> pdb=" O THR a 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL a 78 " --> pdb=" O VAL a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 88 through 90 No H-bonds generated for 'chain 'a' and resid 88 through 90' Processing helix chain 'a' and resid 102 through 108 Processing helix chain 'a' and resid 109 through 128 removed outlier: 4.011A pdb=" N GLU a 113 " --> pdb=" O THR a 109 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE a 114 " --> pdb=" O ILE a 110 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASP a 116 " --> pdb=" O LYS a 112 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU a 117 " --> pdb=" O GLU a 113 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN a 128 " --> pdb=" O LYS a 124 " (cutoff:3.500A) Processing helix chain 'a' and resid 147 through 161 removed outlier: 3.566A pdb=" N SER a 151 " --> pdb=" O SER a 147 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL a 159 " --> pdb=" O GLU a 155 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP a 160 " --> pdb=" O ARG a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 182 through 190 Processing helix chain 'a' and resid 190 through 197 Processing helix chain 'a' and resid 206 through 216 Processing helix chain 'a' and resid 223 through 239 removed outlier: 3.576A pdb=" N LEU a 230 " --> pdb=" O ASN a 226 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE a 234 " --> pdb=" O LEU a 230 " (cutoff:3.500A) Processing helix chain 'a' and resid 240 through 243 Processing helix chain 'a' and resid 251 through 258 removed outlier: 3.764A pdb=" N ASN a 258 " --> pdb=" O GLU a 254 " (cutoff:3.500A) Processing helix chain 'a' and resid 289 through 296 removed outlier: 3.607A pdb=" N PHE a 296 " --> pdb=" O THR a 292 " (cutoff:3.500A) Processing helix chain 'a' and resid 297 through 301 removed outlier: 3.875A pdb=" N GLN a 301 " --> pdb=" O PRO a 298 " (cutoff:3.500A) Processing helix chain 'a' and resid 306 through 310 Processing helix chain 'a' and resid 324 through 337 Processing helix chain 'a' and resid 384 through 401 removed outlier: 3.742A pdb=" N TRP a 388 " --> pdb=" O ILE a 384 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU a 391 " --> pdb=" O ALA a 387 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS a 394 " --> pdb=" O ARG a 390 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS a 401 " --> pdb=" O LEU a 397 " (cutoff:3.500A) Processing helix chain 'a' and resid 404 through 410 removed outlier: 4.115A pdb=" N TYR a 408 " --> pdb=" O PHE a 404 " (cutoff:3.500A) Processing helix chain 'a' and resid 415 through 435 removed outlier: 3.830A pdb=" N SER a 419 " --> pdb=" O GLU a 415 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU a 433 " --> pdb=" O GLU a 429 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 29 Processing helix chain 'b' and resid 40 through 45 removed outlier: 4.340A pdb=" N LEU b 44 " --> pdb=" O SER b 40 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU b 45 " --> pdb=" O ASP b 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 40 through 45' Processing helix chain 'b' and resid 46 through 49 Processing helix chain 'b' and resid 70 through 79 removed outlier: 3.736A pdb=" N SER b 75 " --> pdb=" O GLY b 71 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL b 76 " --> pdb=" O THR b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 86 through 88 No H-bonds generated for 'chain 'b' and resid 86 through 88' Processing helix chain 'b' and resid 100 through 106 removed outlier: 3.534A pdb=" N GLY b 104 " --> pdb=" O ASN b 100 " (cutoff:3.500A) Processing helix chain 'b' and resid 107 through 126 removed outlier: 4.086A pdb=" N GLU b 111 " --> pdb=" O THR b 107 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASP b 114 " --> pdb=" O ALA b 110 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N SER b 115 " --> pdb=" O GLU b 111 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN b 126 " --> pdb=" O LYS b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 159 removed outlier: 3.781A pdb=" N GLU b 157 " --> pdb=" O SER b 153 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU b 158 " --> pdb=" O LYS b 154 " (cutoff:3.500A) Processing helix chain 'b' and resid 180 through 188 removed outlier: 3.577A pdb=" N ASN b 184 " --> pdb=" O VAL b 180 " (cutoff:3.500A) Processing helix chain 'b' and resid 188 through 196 removed outlier: 3.563A pdb=" N THR b 196 " --> pdb=" O LEU b 192 " (cutoff:3.500A) Processing helix chain 'b' and resid 203 through 214 Processing helix chain 'b' and resid 221 through 237 removed outlier: 3.511A pdb=" N LEU b 228 " --> pdb=" O ASP b 224 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR b 237 " --> pdb=" O MET b 233 " (cutoff:3.500A) Processing helix chain 'b' and resid 238 through 241 Processing helix chain 'b' and resid 249 through 256 Processing helix chain 'b' and resid 277 through 282 removed outlier: 4.035A pdb=" N GLN b 280 " --> pdb=" O GLY b 277 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG b 282 " --> pdb=" O GLN b 279 " (cutoff:3.500A) Processing helix chain 'b' and resid 285 through 295 Processing helix chain 'b' and resid 296 through 299 removed outlier: 3.915A pdb=" N MET b 299 " --> pdb=" O ALA b 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 296 through 299' Processing helix chain 'b' and resid 304 through 308 Processing helix chain 'b' and resid 322 through 337 removed outlier: 4.012A pdb=" N GLN b 334 " --> pdb=" O MET b 330 " (cutoff:3.500A) Processing helix chain 'b' and resid 338 through 341 removed outlier: 3.685A pdb=" N PHE b 341 " --> pdb=" O SER b 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 338 through 341' Processing helix chain 'b' and resid 374 through 391 removed outlier: 3.736A pdb=" N PHE b 378 " --> pdb=" O ILE b 374 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE b 381 " --> pdb=" O LEU b 377 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG b 391 " --> pdb=" O ALA b 387 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 400 Processing helix chain 'b' and resid 405 through 416 removed outlier: 3.714A pdb=" N THR b 409 " --> pdb=" O GLU b 405 " (cutoff:3.500A) Processing helix chain 'b' and resid 420 through 425 removed outlier: 4.427A pdb=" N TYR b 425 " --> pdb=" O GLU b 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 92 through 94 removed outlier: 8.258A pdb=" N ILE a 93 " --> pdb=" O ALA a 65 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE a 67 " --> pdb=" O ILE a 93 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VAL a 66 " --> pdb=" O CYS a 4 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER a 6 " --> pdb=" O VAL a 66 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N VAL a 68 " --> pdb=" O SER a 6 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N HIS a 8 " --> pdb=" O VAL a 68 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N SER a 140 " --> pdb=" O VAL a 9 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N PHE a 135 " --> pdb=" O LEU a 167 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE a 169 " --> pdb=" O PHE a 135 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL a 137 " --> pdb=" O PHE a 169 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE a 171 " --> pdb=" O VAL a 137 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N HIS a 139 " --> pdb=" O ILE a 171 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS a 200 " --> pdb=" O LYS a 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'a' and resid 268 through 273 removed outlier: 6.806A pdb=" N ALA a 374 " --> pdb=" O TYR a 319 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR a 319 " --> pdb=" O ALA a 374 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N CYS a 376 " --> pdb=" O LEU a 317 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU a 317 " --> pdb=" O CYS a 376 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU a 378 " --> pdb=" O CYS a 315 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS a 315 " --> pdb=" O LEU a 378 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN a 380 " --> pdb=" O MET a 313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 90 through 92 removed outlier: 8.349A pdb=" N ILE b 91 " --> pdb=" O ALA b 63 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU b 65 " --> pdb=" O ILE b 91 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL b 5 " --> pdb=" O GLN b 134 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N THR b 136 " --> pdb=" O VAL b 5 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE b 7 " --> pdb=" O THR b 136 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N SER b 138 " --> pdb=" O ILE b 7 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ALA b 9 " --> pdb=" O SER b 138 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N PHE b 133 " --> pdb=" O ASN b 165 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE b 167 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU b 135 " --> pdb=" O PHE b 167 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL b 169 " --> pdb=" O LEU b 135 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N HIS b 137 " --> pdb=" O VAL b 169 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N MET b 164 " --> pdb=" O GLU b 198 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N TYR b 200 " --> pdb=" O MET b 164 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR b 166 " --> pdb=" O TYR b 200 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE b 202 " --> pdb=" O THR b 166 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER b 168 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR b 199 " --> pdb=" O PHE b 266 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N CYS b 201 " --> pdb=" O PRO b 268 " (cutoff:3.500A) removed outlier: 10.981A pdb=" N PHE b 270 " --> pdb=" O CYS b 201 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE b 265 " --> pdb=" O SER b 371 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER b 371 " --> pdb=" O PHE b 265 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER b 364 " --> pdb=" O PHE b 317 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE b 317 " --> pdb=" O SER b 364 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR b 366 " --> pdb=" O THR b 315 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR b 315 " --> pdb=" O THR b 366 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE b 368 " --> pdb=" O VAL b 313 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL b 313 " --> pdb=" O ILE b 368 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN b 370 " --> pdb=" O LEU b 311 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 51 through 54 removed outlier: 3.663A pdb=" N LYS b 58 " --> pdb=" O ALA b 54 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 798 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: 2.89 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.07: 6514 1.07 - 1.29: 1170 1.29 - 1.52: 3913 1.52 - 1.75: 1869 1.75 - 1.98: 79 Bond restraints: 13545 Sorted by residual: bond pdb=" O5' G2P b 503 " pdb=" PA G2P b 503 " ideal model delta sigma weight residual 1.656 1.880 -0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" O3B G2P b 503 " pdb=" PG G2P b 503 " ideal model delta sigma weight residual 1.716 1.845 -0.129 2.00e-02 2.50e+03 4.15e+01 bond pdb=" C3A G2P b 503 " pdb=" PB G2P b 503 " ideal model delta sigma weight residual 1.850 1.977 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C3A G2P b 503 " pdb=" PA G2P b 503 " ideal model delta sigma weight residual 1.818 1.695 0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C1' G2P b 503 " pdb=" N9 G2P b 503 " ideal model delta sigma weight residual 1.448 1.544 -0.096 2.00e-02 2.50e+03 2.29e+01 ... (remaining 13540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 24303 3.86 - 7.71: 41 7.71 - 11.57: 13 11.57 - 15.43: 3 15.43 - 19.28: 4 Bond angle restraints: 24364 Sorted by residual: angle pdb=" O2A G2P b 503 " pdb=" PA G2P b 503 " pdb=" O5' G2P b 503 " ideal model delta sigma weight residual 107.71 88.43 19.28 3.00e+00 1.11e-01 4.13e+01 angle pdb=" O1A G2P b 503 " pdb=" PA G2P b 503 " pdb=" O5' G2P b 503 " ideal model delta sigma weight residual 109.23 90.68 18.55 3.00e+00 1.11e-01 3.83e+01 angle pdb=" C3A G2P b 503 " pdb=" PB G2P b 503 " pdb=" O3B G2P b 503 " ideal model delta sigma weight residual 99.71 116.57 -16.86 3.00e+00 1.11e-01 3.16e+01 angle pdb=" C14 TA1 b 501 " pdb=" C11 TA1 b 501 " pdb=" O04 TA1 b 501 " ideal model delta sigma weight residual 119.42 103.94 15.48 3.00e+00 1.11e-01 2.66e+01 angle pdb=" PA GTP a 502 " pdb=" O3A GTP a 502 " pdb=" PB GTP a 502 " ideal model delta sigma weight residual 120.50 134.89 -14.39 3.00e+00 1.11e-01 2.30e+01 ... (remaining 24359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.70: 6019 27.70 - 55.39: 404 55.39 - 83.09: 66 83.09 - 110.78: 13 110.78 - 138.48: 18 Dihedral angle restraints: 6520 sinusoidal: 3578 harmonic: 2942 Sorted by residual: dihedral pdb=" C8 GTP a 502 " pdb=" C1' GTP a 502 " pdb=" N9 GTP a 502 " pdb=" O4' GTP a 502 " ideal model delta sinusoidal sigma weight residual 104.59 -31.13 135.73 1 2.00e+01 2.50e-03 4.12e+01 dihedral pdb=" C5' GTP a 502 " pdb=" O5' GTP a 502 " pdb=" PA GTP a 502 " pdb=" O3A GTP a 502 " ideal model delta sinusoidal sigma weight residual 69.27 -161.37 -129.36 1 2.00e+01 2.50e-03 3.92e+01 dihedral pdb=" O3B GTP a 502 " pdb=" O3A GTP a 502 " pdb=" PB GTP a 502 " pdb=" PA GTP a 502 " ideal model delta sinusoidal sigma weight residual 291.08 171.12 119.96 1 2.00e+01 2.50e-03 3.60e+01 ... (remaining 6517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 976 0.095 - 0.190: 60 0.190 - 0.285: 1 0.285 - 0.380: 2 0.380 - 0.475: 1 Chirality restraints: 1040 Sorted by residual: chirality pdb=" C18 TA1 b 501 " pdb=" C10 TA1 b 501 " pdb=" C17 TA1 b 501 " pdb=" C20 TA1 b 501 " both_signs ideal model delta sigma weight residual False -3.16 -2.69 -0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" C2' G2P b 503 " pdb=" C1' G2P b 503 " pdb=" C3' G2P b 503 " pdb=" O2' G2P b 503 " both_signs ideal model delta sigma weight residual False -2.48 -2.82 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C4' G2P b 503 " pdb=" C3' G2P b 503 " pdb=" C5' G2P b 503 " pdb=" O4' G2P b 503 " both_signs ideal model delta sigma weight residual False -2.49 -2.80 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 1037 not shown) Planarity restraints: 2049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C29 TA1 b 501 " -0.018 2.00e-02 2.50e+03 1.57e-02 3.10e+00 pdb=" C30 TA1 b 501 " 0.015 2.00e-02 2.50e+03 pdb=" C31 TA1 b 501 " -0.017 2.00e-02 2.50e+03 pdb=" N01 TA1 b 501 " 0.020 2.00e-02 2.50e+03 pdb=" O14 TA1 b 501 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL a 324 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO a 325 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO a 325 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO a 325 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE a 267 " -0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO a 268 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO a 268 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO a 268 " -0.018 5.00e-02 4.00e+02 ... (remaining 2046 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 4175 2.35 - 2.92: 29450 2.92 - 3.48: 33848 3.48 - 4.04: 47503 4.04 - 4.60: 70901 Nonbonded interactions: 185877 Sorted by model distance: nonbonded pdb=" H LYS a 163 " pdb=" HD3 LYS a 163 " model vdw 1.792 2.270 nonbonded pdb=" HG1 THR a 292 " pdb=" HH TYR a 319 " model vdw 1.887 2.100 nonbonded pdb=" H THR a 150 " pdb="HG22 THR a 150 " model vdw 1.910 2.270 nonbonded pdb=" H THR a 73 " pdb=" HG1 THR a 73 " model vdw 1.921 2.100 nonbonded pdb=" H THR b 386 " pdb=" HG1 THR b 386 " model vdw 1.921 2.100 ... (remaining 185872 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: 13.320 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: 0.070 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.020 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 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 : 0.005 0.224 7011 Z= 0.267 Angle : 0.821 19.283 9534 Z= 0.331 Chirality : 0.046 0.475 1040 Planarity : 0.004 0.040 1234 Dihedral : 21.379 138.475 2666 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.55 % Allowed : 23.87 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.63 (0.28), residues: 851 helix: 0.03 (0.28), residues: 351 sheet: -0.62 (0.43), residues: 161 loop : -0.59 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG b 276 TYR 0.009 0.001 TYR a 24 PHE 0.008 0.001 PHE a 49 TRP 0.007 0.001 TRP b 21 HIS 0.004 0.001 HIS a 283 Details of bonding type rmsd covalent geometry : bond 0.00542 ( 7011) covalent geometry : angle 0.82122 ( 9534) hydrogen bonds : bond 0.28106 ( 276) hydrogen bonds : angle 7.81494 ( 798) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.295 Fit side-chains REVERT: a 1 MET cc_start: 0.5666 (tpp) cc_final: 0.5189 (tpp) REVERT: a 49 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.5763 (t80) REVERT: a 55 GLU cc_start: 0.7318 (tt0) cc_final: 0.6785 (mm-30) REVERT: a 96 LYS cc_start: 0.8453 (mttp) cc_final: 0.7733 (mmmt) REVERT: a 120 ASP cc_start: 0.8507 (t0) cc_final: 0.8091 (m-30) REVERT: a 300 ASN cc_start: 0.8076 (t0) cc_final: 0.7749 (t160) REVERT: a 342 GLN cc_start: 0.8177 (mm110) cc_final: 0.7894 (mm110) REVERT: b 197 ASP cc_start: 0.8847 (m-30) cc_final: 0.8590 (m-30) REVERT: b 359 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7716 (mtp-110) REVERT: b 390 ARG cc_start: 0.8244 (ptp-170) cc_final: 0.7855 (ptt90) REVERT: b 425 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7875 (m-80) outliers start: 4 outliers final: 2 residues processed: 109 average time/residue: 1.2814 time to fit residues: 146.3507 Evaluate side-chains 103 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 PHE Chi-restraints excluded: chain a residue 367 ASP Chi-restraints excluded: chain b residue 170 VAL Chi-restraints excluded: chain b residue 425 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.0670 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.117679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.097544 restraints weight = 23225.625| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.25 r_work: 0.3321 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7011 Z= 0.144 Angle : 0.569 8.919 9534 Z= 0.293 Chirality : 0.043 0.189 1040 Planarity : 0.004 0.036 1234 Dihedral : 15.027 141.808 1091 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.33 % Allowed : 22.63 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.07 (0.29), residues: 851 helix: 1.02 (0.28), residues: 357 sheet: -0.42 (0.43), residues: 158 loop : -0.67 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG b 380 TYR 0.008 0.001 TYR a 224 PHE 0.007 0.001 PHE a 418 TRP 0.012 0.002 TRP a 21 HIS 0.004 0.001 HIS b 6 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7011) covalent geometry : angle 0.56869 ( 9534) hydrogen bonds : bond 0.08028 ( 276) hydrogen bonds : angle 5.36145 ( 798) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.342 Fit side-chains REVERT: a 1 MET cc_start: 0.5514 (tpp) cc_final: 0.4988 (tpp) REVERT: a 49 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.5626 (t80) REVERT: a 55 GLU cc_start: 0.7262 (tt0) cc_final: 0.6649 (mm-30) REVERT: a 96 LYS cc_start: 0.8311 (mttp) cc_final: 0.7506 (mmmt) REVERT: a 120 ASP cc_start: 0.8115 (t0) cc_final: 0.7557 (m-30) REVERT: a 300 ASN cc_start: 0.7932 (t0) cc_final: 0.7543 (t160) REVERT: a 342 GLN cc_start: 0.8025 (mm110) cc_final: 0.7582 (mm110) REVERT: b 157 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: b 158 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7066 (tm-30) REVERT: b 197 ASP cc_start: 0.8751 (m-30) cc_final: 0.8416 (m-30) REVERT: b 323 MET cc_start: 0.8090 (mmm) cc_final: 0.7867 (mmm) REVERT: b 359 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7716 (mtp-110) REVERT: b 388 MET cc_start: 0.8487 (ttm) cc_final: 0.8170 (ttm) REVERT: b 390 ARG cc_start: 0.8132 (ptp-170) cc_final: 0.7733 (ptt90) outliers start: 17 outliers final: 7 residues processed: 107 average time/residue: 1.1938 time to fit residues: 134.5545 Evaluate side-chains 103 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 PHE Chi-restraints excluded: chain a residue 158 SER Chi-restraints excluded: chain a residue 305 CYS Chi-restraints excluded: chain a residue 437 VAL Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 124 CYS Chi-restraints excluded: chain b residue 157 GLU Chi-restraints excluded: chain b residue 158 GLU Chi-restraints excluded: chain b residue 164 MET Chi-restraints excluded: chain b residue 221 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 77 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 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 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.117504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.097032 restraints weight = 23530.413| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.29 r_work: 0.3306 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7011 Z= 0.149 Angle : 0.531 5.578 9534 Z= 0.275 Chirality : 0.044 0.302 1040 Planarity : 0.004 0.039 1234 Dihedral : 12.548 172.620 1086 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.61 % Allowed : 22.36 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.18 (0.29), residues: 851 helix: 1.16 (0.28), residues: 365 sheet: -0.25 (0.43), residues: 153 loop : -0.78 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG b 2 TYR 0.008 0.001 TYR b 59 PHE 0.008 0.001 PHE b 317 TRP 0.011 0.002 TRP a 21 HIS 0.004 0.001 HIS b 6 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7011) covalent geometry : angle 0.53102 ( 9534) hydrogen bonds : bond 0.06722 ( 276) hydrogen bonds : angle 4.94485 ( 798) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.338 Fit side-chains REVERT: a 1 MET cc_start: 0.5504 (tpp) cc_final: 0.4957 (tpp) REVERT: a 49 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.5701 (t80) REVERT: a 96 LYS cc_start: 0.8331 (mttp) cc_final: 0.7549 (mmmt) REVERT: a 120 ASP cc_start: 0.8207 (t0) cc_final: 0.7666 (m-30) REVERT: a 300 ASN cc_start: 0.7953 (t0) cc_final: 0.7567 (t160) REVERT: a 342 GLN cc_start: 0.8079 (mm110) cc_final: 0.7644 (mm110) REVERT: b 147 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.6370 (tmt) REVERT: b 157 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: b 197 ASP cc_start: 0.8737 (m-30) cc_final: 0.8395 (m-30) REVERT: b 359 ARG cc_start: 0.8180 (mtp85) cc_final: 0.7815 (mtp-110) REVERT: b 388 MET cc_start: 0.8585 (ttm) cc_final: 0.8357 (ttm) REVERT: b 390 ARG cc_start: 0.8080 (ptp-170) cc_final: 0.7761 (ptt180) outliers start: 19 outliers final: 9 residues processed: 110 average time/residue: 1.1234 time to fit residues: 130.5625 Evaluate side-chains 102 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 PHE Chi-restraints excluded: chain a residue 158 SER Chi-restraints excluded: chain a residue 194 THR Chi-restraints excluded: chain a residue 367 ASP Chi-restraints excluded: chain a residue 437 VAL Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 124 CYS Chi-restraints excluded: chain b residue 147 MET Chi-restraints excluded: chain b residue 157 GLU Chi-restraints excluded: chain b residue 164 MET Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 335 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 32 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.118175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.097898 restraints weight = 23307.786| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.26 r_work: 0.3319 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7011 Z= 0.131 Angle : 0.505 5.630 9534 Z= 0.264 Chirality : 0.042 0.144 1040 Planarity : 0.004 0.039 1234 Dihedral : 11.985 179.293 1086 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.74 % Allowed : 22.50 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.34 (0.29), residues: 851 helix: 1.32 (0.28), residues: 366 sheet: -0.24 (0.43), residues: 153 loop : -0.70 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG a 121 TYR 0.007 0.001 TYR b 59 PHE 0.008 0.001 PHE b 317 TRP 0.011 0.001 TRP a 21 HIS 0.004 0.001 HIS b 6 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7011) covalent geometry : angle 0.50540 ( 9534) hydrogen bonds : bond 0.05858 ( 276) hydrogen bonds : angle 4.70644 ( 798) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.355 Fit side-chains REVERT: a 1 MET cc_start: 0.5451 (tpp) cc_final: 0.4969 (tpp) REVERT: a 49 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.5660 (t80) REVERT: a 96 LYS cc_start: 0.8340 (mttp) cc_final: 0.7516 (mmmt) REVERT: a 120 ASP cc_start: 0.8203 (t70) cc_final: 0.7666 (m-30) REVERT: a 166 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8142 (ttpt) REVERT: a 286 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8204 (pp) REVERT: a 300 ASN cc_start: 0.7909 (t0) cc_final: 0.7510 (t160) REVERT: a 342 GLN cc_start: 0.8043 (mm110) cc_final: 0.7606 (mm110) REVERT: b 147 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.6324 (tmt) REVERT: b 197 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8361 (m-30) REVERT: b 323 MET cc_start: 0.8098 (mmm) cc_final: 0.7849 (mmm) REVERT: b 359 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7768 (mtp-110) REVERT: b 390 ARG cc_start: 0.8011 (ptp-170) cc_final: 0.7698 (ptt90) outliers start: 20 outliers final: 8 residues processed: 107 average time/residue: 1.1845 time to fit residues: 133.5740 Evaluate side-chains 106 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 PHE Chi-restraints excluded: chain a residue 158 SER Chi-restraints excluded: chain a residue 166 LYS Chi-restraints excluded: chain a residue 286 LEU Chi-restraints excluded: chain a residue 367 ASP Chi-restraints excluded: chain a residue 437 VAL Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 124 CYS Chi-restraints excluded: chain b residue 147 MET Chi-restraints excluded: chain b residue 164 MET Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 335 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 60 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.115971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.095821 restraints weight = 22895.905| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.22 r_work: 0.3267 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7011 Z= 0.136 Angle : 0.504 5.660 9534 Z= 0.264 Chirality : 0.042 0.138 1040 Planarity : 0.004 0.039 1234 Dihedral : 11.782 179.426 1086 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.61 % Allowed : 22.77 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.38 (0.29), residues: 851 helix: 1.35 (0.28), residues: 367 sheet: -0.24 (0.43), residues: 153 loop : -0.68 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG b 2 TYR 0.008 0.001 TYR b 59 PHE 0.010 0.001 PHE b 317 TRP 0.010 0.001 TRP a 21 HIS 0.004 0.001 HIS b 6 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7011) covalent geometry : angle 0.50447 ( 9534) hydrogen bonds : bond 0.05827 ( 276) hydrogen bonds : angle 4.63226 ( 798) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.387 Fit side-chains REVERT: a 1 MET cc_start: 0.5406 (tpp) cc_final: 0.4901 (tpp) REVERT: a 49 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.5637 (t80) REVERT: a 96 LYS cc_start: 0.8295 (mttp) cc_final: 0.7425 (mmmt) REVERT: a 120 ASP cc_start: 0.8099 (t70) cc_final: 0.7511 (m-30) REVERT: a 166 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8045 (ttpt) REVERT: a 286 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8157 (pp) REVERT: a 300 ASN cc_start: 0.7844 (t0) cc_final: 0.7448 (t160) REVERT: a 342 GLN cc_start: 0.7943 (mm110) cc_final: 0.7493 (mm110) REVERT: b 147 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.6344 (tmt) REVERT: b 197 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8272 (m-30) REVERT: b 323 MET cc_start: 0.7985 (mmm) cc_final: 0.7734 (mmm) REVERT: b 359 ARG cc_start: 0.8071 (mtp85) cc_final: 0.7690 (mtp-110) REVERT: b 390 ARG cc_start: 0.7878 (ptp-170) cc_final: 0.7579 (ptt90) outliers start: 19 outliers final: 8 residues processed: 108 average time/residue: 1.1985 time to fit residues: 136.0886 Evaluate side-chains 108 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 PHE Chi-restraints excluded: chain a residue 158 SER Chi-restraints excluded: chain a residue 166 LYS Chi-restraints excluded: chain a residue 194 THR Chi-restraints excluded: chain a residue 286 LEU Chi-restraints excluded: chain a residue 367 ASP Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 124 CYS Chi-restraints excluded: chain b residue 147 MET Chi-restraints excluded: chain b residue 164 MET Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 335 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 15 GLN a 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.116399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.096249 restraints weight = 22667.040| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.21 r_work: 0.3273 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7011 Z= 0.128 Angle : 0.500 5.692 9534 Z= 0.261 Chirality : 0.042 0.137 1040 Planarity : 0.004 0.039 1234 Dihedral : 11.697 179.022 1086 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.88 % Allowed : 22.50 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.46 (0.29), residues: 851 helix: 1.42 (0.28), residues: 369 sheet: -0.23 (0.43), residues: 153 loop : -0.63 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG b 2 TYR 0.007 0.001 TYR b 59 PHE 0.009 0.001 PHE b 317 TRP 0.010 0.001 TRP a 21 HIS 0.004 0.001 HIS a 266 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7011) covalent geometry : angle 0.50030 ( 9534) hydrogen bonds : bond 0.05567 ( 276) hydrogen bonds : angle 4.55410 ( 798) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: a 1 MET cc_start: 0.5398 (tpp) cc_final: 0.4493 (tpp) REVERT: a 49 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.5709 (t80) REVERT: a 96 LYS cc_start: 0.8291 (mttp) cc_final: 0.7433 (mmmt) REVERT: a 120 ASP cc_start: 0.8067 (t70) cc_final: 0.7482 (m-30) REVERT: a 166 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8006 (ttpt) REVERT: a 286 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8176 (pp) REVERT: a 300 ASN cc_start: 0.7782 (t0) cc_final: 0.7393 (t160) REVERT: a 342 GLN cc_start: 0.7941 (mm110) cc_final: 0.7496 (mm110) REVERT: b 147 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.6332 (tmt) REVERT: b 197 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8267 (m-30) REVERT: b 359 ARG cc_start: 0.8056 (mtp85) cc_final: 0.7677 (mtp-110) REVERT: b 390 ARG cc_start: 0.7871 (ptp-170) cc_final: 0.7595 (ptt90) outliers start: 21 outliers final: 10 residues processed: 110 average time/residue: 1.2180 time to fit residues: 140.9922 Evaluate side-chains 108 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 PHE Chi-restraints excluded: chain a residue 158 SER Chi-restraints excluded: chain a residue 166 LYS Chi-restraints excluded: chain a residue 194 THR Chi-restraints excluded: chain a residue 286 LEU Chi-restraints excluded: chain a residue 287 SER Chi-restraints excluded: chain a residue 367 ASP Chi-restraints excluded: chain a residue 437 VAL Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 124 CYS Chi-restraints excluded: chain b residue 147 MET Chi-restraints excluded: chain b residue 164 MET Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 335 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 28 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.117776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.097468 restraints weight = 22733.484| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.23 r_work: 0.3290 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7011 Z= 0.106 Angle : 0.484 5.632 9534 Z= 0.251 Chirality : 0.041 0.138 1040 Planarity : 0.004 0.037 1234 Dihedral : 11.443 178.099 1086 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.06 % Allowed : 23.87 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.29), residues: 851 helix: 1.53 (0.28), residues: 371 sheet: -0.22 (0.43), residues: 153 loop : -0.51 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG b 2 TYR 0.007 0.001 TYR a 272 PHE 0.008 0.001 PHE b 317 TRP 0.010 0.001 TRP a 21 HIS 0.003 0.001 HIS b 6 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 7011) covalent geometry : angle 0.48375 ( 9534) hydrogen bonds : bond 0.04970 ( 276) hydrogen bonds : angle 4.41939 ( 798) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: a 1 MET cc_start: 0.5374 (tpp) cc_final: 0.4473 (tpp) REVERT: a 49 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.5686 (t80) REVERT: a 96 LYS cc_start: 0.8302 (mttp) cc_final: 0.7434 (mmmt) REVERT: a 120 ASP cc_start: 0.8069 (t70) cc_final: 0.7472 (m-30) REVERT: a 286 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8116 (pp) REVERT: a 300 ASN cc_start: 0.7740 (t0) cc_final: 0.7355 (t160) REVERT: a 342 GLN cc_start: 0.7932 (mm110) cc_final: 0.7505 (mm110) REVERT: b 147 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.6127 (tmt) REVERT: b 197 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8285 (m-30) REVERT: b 323 MET cc_start: 0.7969 (mmm) cc_final: 0.7727 (mmm) REVERT: b 359 ARG cc_start: 0.7973 (mtp85) cc_final: 0.7604 (mtp-110) REVERT: b 390 ARG cc_start: 0.7859 (ptp-170) cc_final: 0.7582 (ptt90) outliers start: 15 outliers final: 8 residues processed: 102 average time/residue: 1.2218 time to fit residues: 131.0961 Evaluate side-chains 104 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 PHE Chi-restraints excluded: chain a residue 158 SER Chi-restraints excluded: chain a residue 194 THR Chi-restraints excluded: chain a residue 286 LEU Chi-restraints excluded: chain a residue 367 ASP Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 124 CYS Chi-restraints excluded: chain b residue 147 MET Chi-restraints excluded: chain b residue 164 MET Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 335 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 77 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.116937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.096732 restraints weight = 22769.457| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.22 r_work: 0.3277 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7011 Z= 0.122 Angle : 0.495 5.642 9534 Z= 0.257 Chirality : 0.042 0.137 1040 Planarity : 0.004 0.037 1234 Dihedral : 11.467 179.597 1086 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.47 % Allowed : 23.59 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.59 (0.29), residues: 851 helix: 1.52 (0.28), residues: 371 sheet: -0.23 (0.43), residues: 153 loop : -0.53 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG a 121 TYR 0.007 0.001 TYR b 59 PHE 0.009 0.001 PHE b 317 TRP 0.009 0.001 TRP a 21 HIS 0.004 0.001 HIS a 266 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7011) covalent geometry : angle 0.49473 ( 9534) hydrogen bonds : bond 0.05232 ( 276) hydrogen bonds : angle 4.42037 ( 798) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 1 MET cc_start: 0.5407 (tpp) cc_final: 0.4508 (tpp) REVERT: a 49 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.5706 (t80) REVERT: a 96 LYS cc_start: 0.8300 (mttp) cc_final: 0.7435 (mmmt) REVERT: a 120 ASP cc_start: 0.8083 (t70) cc_final: 0.7453 (m-30) REVERT: a 166 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8001 (ttpt) REVERT: a 300 ASN cc_start: 0.7790 (t0) cc_final: 0.7403 (t160) REVERT: a 342 GLN cc_start: 0.7930 (mm110) cc_final: 0.7506 (mm110) REVERT: b 147 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.6333 (tmt) REVERT: b 197 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8279 (m-30) REVERT: b 323 MET cc_start: 0.7983 (mmm) cc_final: 0.7726 (mmm) REVERT: b 359 ARG cc_start: 0.7976 (mtp85) cc_final: 0.7601 (mtp-110) REVERT: b 390 ARG cc_start: 0.7835 (ptp-170) cc_final: 0.7587 (ptt90) outliers start: 18 outliers final: 10 residues processed: 108 average time/residue: 1.2485 time to fit residues: 141.6495 Evaluate side-chains 108 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 PHE Chi-restraints excluded: chain a residue 158 SER Chi-restraints excluded: chain a residue 166 LYS Chi-restraints excluded: chain a residue 194 THR Chi-restraints excluded: chain a residue 286 LEU Chi-restraints excluded: chain a residue 367 ASP Chi-restraints excluded: chain a residue 437 VAL Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 124 CYS Chi-restraints excluded: chain b residue 147 MET Chi-restraints excluded: chain b residue 164 MET Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 335 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 83 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.117810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.097446 restraints weight = 22895.591| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.24 r_work: 0.3288 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7011 Z= 0.108 Angle : 0.484 5.658 9534 Z= 0.251 Chirality : 0.041 0.137 1040 Planarity : 0.004 0.036 1234 Dihedral : 11.286 179.448 1086 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.47 % Allowed : 23.73 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.68 (0.29), residues: 851 helix: 1.63 (0.28), residues: 371 sheet: -0.23 (0.43), residues: 153 loop : -0.50 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG b 77 TYR 0.009 0.001 TYR a 24 PHE 0.008 0.001 PHE b 317 TRP 0.009 0.001 TRP a 21 HIS 0.003 0.001 HIS a 266 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 7011) covalent geometry : angle 0.48429 ( 9534) hydrogen bonds : bond 0.04906 ( 276) hydrogen bonds : angle 4.36064 ( 798) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 1 MET cc_start: 0.5388 (tpp) cc_final: 0.4494 (tpp) REVERT: a 49 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.5723 (t80) REVERT: a 96 LYS cc_start: 0.8302 (mttp) cc_final: 0.7439 (mmmt) REVERT: a 120 ASP cc_start: 0.8067 (t70) cc_final: 0.7465 (m-30) REVERT: a 300 ASN cc_start: 0.7742 (t0) cc_final: 0.7355 (t160) REVERT: a 342 GLN cc_start: 0.7924 (mm110) cc_final: 0.7504 (mm110) REVERT: b 147 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.6196 (tmt) REVERT: b 197 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8289 (m-30) REVERT: b 323 MET cc_start: 0.7967 (mmm) cc_final: 0.7721 (mmm) REVERT: b 359 ARG cc_start: 0.7960 (mtp85) cc_final: 0.7589 (mtp-110) REVERT: b 390 ARG cc_start: 0.7814 (ptp-170) cc_final: 0.7598 (ptt90) outliers start: 18 outliers final: 11 residues processed: 110 average time/residue: 1.2110 time to fit residues: 140.1191 Evaluate side-chains 108 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 PHE Chi-restraints excluded: chain a residue 158 SER Chi-restraints excluded: chain a residue 194 THR Chi-restraints excluded: chain a residue 286 LEU Chi-restraints excluded: chain a residue 287 SER Chi-restraints excluded: chain a residue 367 ASP Chi-restraints excluded: chain a residue 437 VAL Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 124 CYS Chi-restraints excluded: chain b residue 147 MET Chi-restraints excluded: chain b residue 164 MET Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 335 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 15 GLN a 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.116598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.096429 restraints weight = 22680.632| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.21 r_work: 0.3276 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7011 Z= 0.134 Angle : 0.508 5.743 9534 Z= 0.265 Chirality : 0.042 0.142 1040 Planarity : 0.004 0.038 1234 Dihedral : 11.415 179.825 1086 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.74 % Allowed : 23.73 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.58 (0.29), residues: 851 helix: 1.54 (0.28), residues: 370 sheet: -0.26 (0.43), residues: 153 loop : -0.57 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG a 121 TYR 0.012 0.001 TYR a 24 PHE 0.010 0.001 PHE b 317 TRP 0.008 0.001 TRP a 21 HIS 0.004 0.001 HIS b 6 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7011) covalent geometry : angle 0.50805 ( 9534) hydrogen bonds : bond 0.05417 ( 276) hydrogen bonds : angle 4.43711 ( 798) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 1 MET cc_start: 0.5412 (tpp) cc_final: 0.4516 (tpp) REVERT: a 49 PHE cc_start: 0.7295 (OUTLIER) cc_final: 0.5760 (t80) REVERT: a 96 LYS cc_start: 0.8294 (mttp) cc_final: 0.7433 (mmmt) REVERT: a 120 ASP cc_start: 0.8096 (t70) cc_final: 0.7463 (m-30) REVERT: a 166 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7960 (ttpt) REVERT: a 300 ASN cc_start: 0.7766 (t0) cc_final: 0.7377 (t160) REVERT: a 342 GLN cc_start: 0.7935 (mm110) cc_final: 0.7511 (mm110) REVERT: b 147 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.6445 (tmt) REVERT: b 197 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8275 (m-30) REVERT: b 359 ARG cc_start: 0.8035 (mtp85) cc_final: 0.7650 (mtp-110) REVERT: b 390 ARG cc_start: 0.7822 (ptp-170) cc_final: 0.7583 (ptt90) outliers start: 20 outliers final: 11 residues processed: 109 average time/residue: 1.1506 time to fit residues: 132.2953 Evaluate side-chains 109 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 PHE Chi-restraints excluded: chain a residue 158 SER Chi-restraints excluded: chain a residue 166 LYS Chi-restraints excluded: chain a residue 194 THR Chi-restraints excluded: chain a residue 286 LEU Chi-restraints excluded: chain a residue 287 SER Chi-restraints excluded: chain a residue 367 ASP Chi-restraints excluded: chain a residue 437 VAL Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 124 CYS Chi-restraints excluded: chain b residue 147 MET Chi-restraints excluded: chain b residue 164 MET Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 335 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 12 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 0.0970 chunk 13 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 46 optimal weight: 0.0970 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.119343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.099067 restraints weight = 22746.285| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.23 r_work: 0.3314 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7011 Z= 0.095 Angle : 0.481 5.766 9534 Z= 0.248 Chirality : 0.041 0.140 1040 Planarity : 0.003 0.035 1234 Dihedral : 11.009 179.391 1086 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.78 % Allowed : 24.42 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.29), residues: 851 helix: 1.76 (0.28), residues: 370 sheet: -0.11 (0.43), residues: 151 loop : -0.50 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG b 2 TYR 0.012 0.001 TYR a 24 PHE 0.008 0.001 PHE a 255 TRP 0.011 0.002 TRP a 388 HIS 0.002 0.001 HIS b 137 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 7011) covalent geometry : angle 0.48135 ( 9534) hydrogen bonds : bond 0.04405 ( 276) hydrogen bonds : angle 4.25745 ( 798) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5218.70 seconds wall clock time: 89 minutes 2.02 seconds (5342.02 seconds total)