Starting phenix.real_space_refine on Fri Jul 3 05:38:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a5d_15165/07_2026/8a5d_15165_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a5d_15165/07_2026/8a5d_15165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8a5d_15165/07_2026/8a5d_15165_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a5d_15165/07_2026/8a5d_15165_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8a5d_15165/07_2026/8a5d_15165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a5d_15165/07_2026/8a5d_15165.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 64 5.16 5 C 7719 2.51 5 N 2139 2.21 5 O 2288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12222 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 729 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "U" Number of atoms: 4876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4876 Classifications: {'peptide': 600} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 571} Chain breaks: 2 Chain: "V" Number of atoms: 2831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2831 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Chain: "W" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3377 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 31, 'TRANS': 400} Chain breaks: 1 Chain: "X" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 313 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 5, 'TRANS': 32} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.94, per 1000 atoms: 0.24 Number of scatterers: 12222 At special positions: 0 Unit cell: (85.779, 105.9, 160.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 64 16.00 P 9 15.00 Mg 3 11.99 O 2288 8.00 N 2139 7.00 C 7719 6.00 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: 0.81 Conformation dependent library (CDL) restraints added in 621.6 milliseconds 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2846 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 19 sheets defined 48.3% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'G' and resid 724 through 741 Processing helix chain 'G' and resid 741 through 775 removed outlier: 3.564A pdb=" N LYS G 773 " --> pdb=" O SER G 769 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TRP G 775 " --> pdb=" O GLU G 771 " (cutoff:3.500A) Processing helix chain 'G' and resid 779 through 808 removed outlier: 3.955A pdb=" N ARG G 806 " --> pdb=" O LYS G 802 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 14 Processing helix chain 'U' and resid 45 through 48 Processing helix chain 'U' and resid 49 through 64 Processing helix chain 'U' and resid 102 through 104 No H-bonds generated for 'chain 'U' and resid 102 through 104' Processing helix chain 'U' and resid 157 through 163 Processing helix chain 'U' and resid 163 through 184 Processing helix chain 'U' and resid 191 through 202 Processing helix chain 'U' and resid 237 through 242 Processing helix chain 'U' and resid 264 through 267 Processing helix chain 'U' and resid 269 through 288 Processing helix chain 'U' and resid 293 through 300 removed outlier: 4.292A pdb=" N LYS U 298 " --> pdb=" O ALA U 295 " (cutoff:3.500A) Processing helix chain 'U' and resid 311 through 325 Processing helix chain 'U' and resid 336 through 345 Processing helix chain 'U' and resid 371 through 374 removed outlier: 3.845A pdb=" N ARG U 374 " --> pdb=" O GLU U 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 371 through 374' Processing helix chain 'U' and resid 380 through 395 removed outlier: 3.542A pdb=" N VAL U 384 " --> pdb=" O GLY U 380 " (cutoff:3.500A) Processing helix chain 'U' and resid 406 through 421 Processing helix chain 'U' and resid 424 through 428 Processing helix chain 'U' and resid 453 through 461 Proline residue: U 459 - end of helix Processing helix chain 'U' and resid 462 through 468 Proline residue: U 465 - end of helix Processing helix chain 'U' and resid 498 through 509 removed outlier: 3.509A pdb=" N VAL U 508 " --> pdb=" O ILE U 504 " (cutoff:3.500A) Processing helix chain 'U' and resid 620 through 629 Processing helix chain 'U' and resid 636 through 650 Processing helix chain 'U' and resid 652 through 661 Processing helix chain 'U' and resid 667 through 672 removed outlier: 4.035A pdb=" N ILE U 672 " --> pdb=" O GLY U 669 " (cutoff:3.500A) Processing helix chain 'U' and resid 674 through 687 Processing helix chain 'U' and resid 707 through 719 Processing helix chain 'U' and resid 728 through 735 Processing helix chain 'U' and resid 736 through 743 removed outlier: 4.057A pdb=" N TYR U 740 " --> pdb=" O SER U 736 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET U 741 " --> pdb=" O ARG U 737 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 61 Processing helix chain 'V' and resid 78 through 92 Processing helix chain 'V' and resid 97 through 101 Processing helix chain 'V' and resid 112 through 126 removed outlier: 3.604A pdb=" N ARG V 116 " --> pdb=" O PRO V 112 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE V 124 " --> pdb=" O THR V 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 137 through 145 Processing helix chain 'V' and resid 172 through 175 Processing helix chain 'V' and resid 181 through 196 Processing helix chain 'V' and resid 202 through 217 removed outlier: 3.546A pdb=" N CYS V 217 " --> pdb=" O LYS V 213 " (cutoff:3.500A) Processing helix chain 'V' and resid 222 through 230 Processing helix chain 'V' and resid 252 through 260 Proline residue: V 258 - end of helix Processing helix chain 'V' and resid 261 through 262 No H-bonds generated for 'chain 'V' and resid 261 through 262' Processing helix chain 'V' and resid 263 through 268 Processing helix chain 'V' and resid 273 through 283 Processing helix chain 'V' and resid 289 through 295 Processing helix chain 'V' and resid 301 through 305 Processing helix chain 'V' and resid 308 through 321 removed outlier: 3.503A pdb=" N LEU V 320 " --> pdb=" O GLU V 316 " (cutoff:3.500A) Processing helix chain 'V' and resid 334 through 336 No H-bonds generated for 'chain 'V' and resid 334 through 336' Processing helix chain 'V' and resid 337 through 347 Processing helix chain 'V' and resid 348 through 355 removed outlier: 6.363A pdb=" N THR V 351 " --> pdb=" O SER V 348 " (cutoff:3.500A) Processing helix chain 'V' and resid 359 through 366 Processing helix chain 'V' and resid 368 through 374 removed outlier: 4.032A pdb=" N ARG V 372 " --> pdb=" O SER V 368 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 98 Processing helix chain 'W' and resid 155 through 171 removed outlier: 3.620A pdb=" N TRP W 170 " --> pdb=" O VAL W 166 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY W 171 " --> pdb=" O MET W 167 " (cutoff:3.500A) Processing helix chain 'W' and resid 180 through 188 Processing helix chain 'W' and resid 215 through 218 removed outlier: 3.649A pdb=" N ILE W 218 " --> pdb=" O LYS W 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 215 through 218' Processing helix chain 'W' and resid 224 through 239 Processing helix chain 'W' and resid 247 through 249 No H-bonds generated for 'chain 'W' and resid 247 through 249' Processing helix chain 'W' and resid 275 through 294 removed outlier: 3.748A pdb=" N ARG W 285 " --> pdb=" O PHE W 281 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL W 286 " --> pdb=" O GLU W 282 " (cutoff:3.500A) Processing helix chain 'W' and resid 308 through 314 Processing helix chain 'W' and resid 333 through 341 removed outlier: 4.624A pdb=" N ALA W 339 " --> pdb=" O ARG W 335 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY W 341 " --> pdb=" O ARG W 337 " (cutoff:3.500A) Processing helix chain 'W' and resid 360 through 363 Processing helix chain 'W' and resid 364 through 374 Processing helix chain 'W' and resid 375 through 376 No H-bonds generated for 'chain 'W' and resid 375 through 376' Processing helix chain 'W' and resid 377 through 379 No H-bonds generated for 'chain 'W' and resid 377 through 379' Processing helix chain 'W' and resid 380 through 386 Processing helix chain 'W' and resid 392 through 397 Processing helix chain 'W' and resid 399 through 412 Processing helix chain 'W' and resid 431 through 440 Processing helix chain 'W' and resid 441 through 448 removed outlier: 6.511A pdb=" N THR W 444 " --> pdb=" O SER W 441 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN W 447 " --> pdb=" O THR W 444 " (cutoff:3.500A) Processing helix chain 'W' and resid 452 through 457 Processing helix chain 'W' and resid 461 through 466 Processing sheet with id=AA1, first strand: chain 'U' and resid 127 through 130 Processing sheet with id=AA2, first strand: chain 'U' and resid 235 through 236 Processing sheet with id=AA3, first strand: chain 'U' and resid 206 through 207 removed outlier: 5.992A pdb=" N ALA U 439 " --> pdb=" O PRO U 443 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'U' and resid 257 through 258 Processing sheet with id=AA5, first strand: chain 'U' and resid 368 through 369 Processing sheet with id=AA6, first strand: chain 'U' and resid 368 through 369 Processing sheet with id=AA7, first strand: chain 'V' and resid 29 through 32 removed outlier: 6.383A pdb=" N LEU V 8 " --> pdb=" O LEU V 104 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N THR V 106 " --> pdb=" O LEU V 8 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE V 10 " --> pdb=" O THR V 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'V' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'V' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'V' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'V' and resid 169 through 170 removed outlier: 6.205A pdb=" N ILE V 151 " --> pdb=" O VAL V 298 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N SER V 300 " --> pdb=" O ILE V 151 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU V 153 " --> pdb=" O SER V 300 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE V 297 " --> pdb=" O ILE V 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'V' and resid 238 through 241 removed outlier: 3.639A pdb=" N LYS V 238 " --> pdb=" O ILE V 250 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'W' and resid 45 through 48 removed outlier: 6.489A pdb=" N LEU W 24 " --> pdb=" O LEU W 147 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N THR W 149 " --> pdb=" O LEU W 24 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU W 26 " --> pdb=" O THR W 149 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'W' and resid 58 through 59 Processing sheet with id=AB6, first strand: chain 'W' and resid 212 through 213 Processing sheet with id=AB7, first strand: chain 'W' and resid 212 through 213 removed outlier: 6.112A pdb=" N LEU W 194 " --> pdb=" O VAL W 389 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR W 391 " --> pdb=" O LEU W 194 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE W 196 " --> pdb=" O THR W 391 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'W' and resid 251 through 255 removed outlier: 3.669A pdb=" N ASN W 253 " --> pdb=" O ARG W 266 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP W 264 " --> pdb=" O LYS W 255 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'W' and resid 319 through 322 Processing sheet with id=AC1, first strand: chain 'X' and resid 172 through 179 584 hydrogen bonds defined for protein. 1563 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: 2.16 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2037 1.30 - 1.44: 3314 1.44 - 1.58: 7031 1.58 - 1.72: 8 1.72 - 1.86: 111 Bond restraints: 12501 Sorted by residual: bond pdb=" PG AGS U 900 " pdb=" S1G AGS U 900 " ideal model delta sigma weight residual 1.936 1.795 0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" C SER V 155 " pdb=" O SER V 155 " ideal model delta sigma weight residual 1.235 1.309 -0.075 1.13e-02 7.83e+03 4.36e+01 bond pdb=" O3A AGS W 500 " pdb=" PA AGS W 500 " ideal model delta sigma weight residual 1.664 1.533 0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" C PRO V 164 " pdb=" O PRO V 164 " ideal model delta sigma weight residual 1.233 1.168 0.065 1.10e-02 8.26e+03 3.52e+01 bond pdb=" C PHE U 120 " pdb=" O PHE U 120 " ideal model delta sigma weight residual 1.234 1.162 0.072 1.23e-02 6.61e+03 3.45e+01 ... (remaining 12496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 15089 2.94 - 5.87: 1767 5.87 - 8.81: 80 8.81 - 11.75: 8 11.75 - 14.69: 3 Bond angle restraints: 16947 Sorted by residual: angle pdb=" C PRO W 28 " pdb=" N GLY W 29 " pdb=" CA GLY W 29 " ideal model delta sigma weight residual 121.48 127.73 -6.25 1.06e+00 8.90e-01 3.47e+01 angle pdb=" C GLN W 334 " pdb=" N ARG W 335 " pdb=" CA ARG W 335 " ideal model delta sigma weight residual 120.38 127.85 -7.47 1.37e+00 5.33e-01 2.98e+01 angle pdb=" C ALA W 460 " pdb=" N GLY W 461 " pdb=" CA GLY W 461 " ideal model delta sigma weight residual 120.13 126.99 -6.86 1.26e+00 6.30e-01 2.97e+01 angle pdb=" C GLN V 354 " pdb=" CA GLN V 354 " pdb=" CB GLN V 354 " ideal model delta sigma weight residual 111.45 120.75 -9.30 1.72e+00 3.38e-01 2.93e+01 angle pdb=" CA THR U 721 " pdb=" CB THR U 721 " pdb=" OG1 THR U 721 " ideal model delta sigma weight residual 109.60 101.50 8.10 1.50e+00 4.44e-01 2.92e+01 ... (remaining 16942 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.41: 7386 31.41 - 62.82: 169 62.82 - 94.23: 56 94.23 - 125.65: 8 125.65 - 157.06: 4 Dihedral angle restraints: 7623 sinusoidal: 3214 harmonic: 4409 Sorted by residual: dihedral pdb=" CA ARG U 406 " pdb=" C ARG U 406 " pdb=" N ARG U 407 " pdb=" CA ARG U 407 " ideal model delta harmonic sigma weight residual 180.00 -153.76 -26.24 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ASP W 240 " pdb=" C ASP W 240 " pdb=" N PRO W 241 " pdb=" CA PRO W 241 " ideal model delta harmonic sigma weight residual 180.00 154.15 25.85 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ASN W 169 " pdb=" C ASN W 169 " pdb=" N TRP W 170 " pdb=" CA TRP W 170 " ideal model delta harmonic sigma weight residual -180.00 -154.61 -25.39 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 7620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 930 0.065 - 0.129: 612 0.129 - 0.194: 214 0.194 - 0.258: 57 0.258 - 0.323: 13 Chirality restraints: 1826 Sorted by residual: chirality pdb=" CA VAL U 30 " pdb=" N VAL U 30 " pdb=" C VAL U 30 " pdb=" CB VAL U 30 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA SER V 281 " pdb=" N SER V 281 " pdb=" C SER V 281 " pdb=" CB SER V 281 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA SER W 178 " pdb=" N SER W 178 " pdb=" C SER W 178 " pdb=" CB SER W 178 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 1823 not shown) Planarity restraints: 2185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP W 433 " 0.100 2.00e-02 2.50e+03 5.92e-02 8.76e+01 pdb=" CG TRP W 433 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP W 433 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP W 433 " -0.075 2.00e-02 2.50e+03 pdb=" NE1 TRP W 433 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP W 433 " -0.047 2.00e-02 2.50e+03 pdb=" CE3 TRP W 433 " -0.088 2.00e-02 2.50e+03 pdb=" CZ2 TRP W 433 " 0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP W 433 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP W 433 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AGS W 500 " 0.077 2.00e-02 2.50e+03 3.71e-02 3.79e+01 pdb=" C2 AGS W 500 " 0.016 2.00e-02 2.50e+03 pdb=" C4 AGS W 500 " -0.022 2.00e-02 2.50e+03 pdb=" C5 AGS W 500 " -0.015 2.00e-02 2.50e+03 pdb=" C6 AGS W 500 " -0.037 2.00e-02 2.50e+03 pdb=" C8 AGS W 500 " -0.008 2.00e-02 2.50e+03 pdb=" N1 AGS W 500 " -0.000 2.00e-02 2.50e+03 pdb=" N3 AGS W 500 " -0.020 2.00e-02 2.50e+03 pdb=" N6 AGS W 500 " 0.064 2.00e-02 2.50e+03 pdb=" N7 AGS W 500 " -0.007 2.00e-02 2.50e+03 pdb=" N9 AGS W 500 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP V 340 " 0.062 2.00e-02 2.50e+03 3.77e-02 3.55e+01 pdb=" CG TRP V 340 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP V 340 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP V 340 " -0.043 2.00e-02 2.50e+03 pdb=" NE1 TRP V 340 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP V 340 " -0.031 2.00e-02 2.50e+03 pdb=" CE3 TRP V 340 " -0.060 2.00e-02 2.50e+03 pdb=" CZ2 TRP V 340 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP V 340 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP V 340 " 0.059 2.00e-02 2.50e+03 ... (remaining 2182 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 14 2.58 - 3.16: 9581 3.16 - 3.74: 17820 3.74 - 4.32: 26886 4.32 - 4.90: 44194 Nonbonded interactions: 98495 Sorted by model distance: nonbonded pdb=" O3G AGS U 900 " pdb="MG MG U 901 " model vdw 2.001 2.170 nonbonded pdb=" O2G AGS W 500 " pdb="MG MG W 501 " model vdw 2.007 2.170 nonbonded pdb=" O2G AGS V 500 " pdb="MG MG V 501 " model vdw 2.013 2.170 nonbonded pdb=" O1B AGS V 500 " pdb="MG MG V 501 " model vdw 2.221 2.170 nonbonded pdb=" OD1 ASP U 276 " pdb=" ND1 HIS V 235 " model vdw 2.247 3.120 ... (remaining 98490 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: 1.570 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.530 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.016 0.141 12501 Z= 1.142 Angle : 1.860 14.687 16947 Z= 1.292 Chirality : 0.094 0.323 1826 Planarity : 0.011 0.065 2185 Dihedral : 16.413 157.058 4777 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.60 % Favored : 97.27 % Rotamer: Outliers : 0.23 % Allowed : 3.07 % Favored : 96.70 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.20 % 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 (0.20), residues: 1501 helix: -1.11 (0.18), residues: 617 sheet: 0.08 (0.34), residues: 201 loop : 0.07 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.003 ARG V 312 TYR 0.072 0.014 TYR V 133 PHE 0.070 0.012 PHE V 132 TRP 0.100 0.016 TRP W 433 HIS 0.033 0.005 HIS V 371 Details of bonding type rmsd/Z covalent geometry : bond 0.01593 / 1.14 (12501) covalent geometry : angle 1.85959 / 1.29 (16947) hydrogen bonds : bond 0.17972 / 12.08 ( 578) hydrogen bonds : angle 6.94526 / 5.04 ( 1563) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 241 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: G 733 GLN cc_start: 0.7665 (tt0) cc_final: 0.7360 (tt0) REVERT: G 737 ASP cc_start: 0.8185 (m-30) cc_final: 0.7884 (m-30) REVERT: G 777 LEU cc_start: 0.8581 (mp) cc_final: 0.8367 (mp) REVERT: G 778 ARG cc_start: 0.7860 (mtt180) cc_final: 0.7589 (mtt180) REVERT: G 781 LYS cc_start: 0.7069 (tttt) cc_final: 0.6437 (tppt) REVERT: G 784 LYS cc_start: 0.7146 (mttt) cc_final: 0.6784 (mptt) REVERT: U 19 ASP cc_start: 0.7043 (m-30) cc_final: 0.6788 (p0) REVERT: U 36 LYS cc_start: 0.8076 (tttt) cc_final: 0.7456 (mmpt) REVERT: U 47 ASP cc_start: 0.8449 (t0) cc_final: 0.7939 (p0) REVERT: U 56 ASN cc_start: 0.7016 (m-40) cc_final: 0.6583 (m-40) REVERT: U 60 ARG cc_start: 0.7885 (ttt180) cc_final: 0.7549 (mmt180) REVERT: U 146 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7873 (pt0) REVERT: U 159 GLU cc_start: 0.7509 (tt0) cc_final: 0.7052 (pp20) REVERT: U 160 GLN cc_start: 0.7514 (mt0) cc_final: 0.7122 (tm-30) REVERT: U 218 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7888 (pm20) REVERT: U 224 LYS cc_start: 0.7091 (tttt) cc_final: 0.6837 (tmtt) REVERT: U 250 LYS cc_start: 0.8063 (tttt) cc_final: 0.7785 (tttt) REVERT: U 266 ASP cc_start: 0.7969 (m-30) cc_final: 0.7712 (t70) REVERT: U 292 THR cc_start: 0.9020 (m) cc_final: 0.8809 (p) REVERT: U 298 LYS cc_start: 0.7796 (pttt) cc_final: 0.7457 (mttp) REVERT: U 371 GLU cc_start: 0.7954 (tt0) cc_final: 0.7688 (mt-10) REVERT: U 392 MET cc_start: 0.8125 (mtm) cc_final: 0.7585 (mmm) REVERT: U 401 ASP cc_start: 0.8544 (m-30) cc_final: 0.8127 (t0) REVERT: U 415 GLU cc_start: 0.7509 (tt0) cc_final: 0.7126 (tp30) REVERT: U 418 MET cc_start: 0.8379 (mtt) cc_final: 0.8173 (mtm) REVERT: U 437 LEU cc_start: 0.8034 (tp) cc_final: 0.7771 (tt) REVERT: U 653 GLU cc_start: 0.7485 (pt0) cc_final: 0.7020 (pp20) REVERT: U 702 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8782 (mp0) REVERT: V 16 MET cc_start: 0.8745 (mmt) cc_final: 0.8423 (mmt) REVERT: V 57 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7016 (mt-10) REVERT: V 72 GLU cc_start: 0.8370 (tt0) cc_final: 0.7677 (mt-10) REVERT: V 82 MET cc_start: 0.9139 (tpt) cc_final: 0.8910 (tpp) REVERT: V 93 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7856 (mm-30) REVERT: V 118 LYS cc_start: 0.7608 (tptt) cc_final: 0.7079 (ttmt) REVERT: V 191 LYS cc_start: 0.7827 (tttt) cc_final: 0.7574 (ttpt) REVERT: V 195 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7446 (mp0) REVERT: V 241 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8007 (tm-30) REVERT: V 246 GLN cc_start: 0.7926 (pt0) cc_final: 0.6756 (tp40) REVERT: V 288 ASP cc_start: 0.8492 (m-30) cc_final: 0.8156 (p0) REVERT: V 325 MET cc_start: 0.7938 (mmt) cc_final: 0.7736 (mmm) REVERT: V 358 SER cc_start: 0.8483 (t) cc_final: 0.8142 (p) REVERT: V 360 GLN cc_start: 0.7867 (mt0) cc_final: 0.7427 (mp10) REVERT: V 372 ARG cc_start: 0.7958 (ttm170) cc_final: 0.7598 (mtm110) REVERT: W 105 ARG cc_start: 0.7807 (mtt180) cc_final: 0.7344 (mmp80) REVERT: W 143 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8082 (mp0) REVERT: W 167 MET cc_start: 0.8653 (mmt) cc_final: 0.8357 (mmt) REVERT: W 203 THR cc_start: 0.8836 (m) cc_final: 0.8497 (m) REVERT: W 215 LYS cc_start: 0.8366 (mttt) cc_final: 0.7908 (mtpt) REVERT: W 253 ASN cc_start: 0.8066 (m-40) cc_final: 0.7351 (p0) REVERT: W 255 LYS cc_start: 0.8148 (mttt) cc_final: 0.7862 (mmtt) REVERT: W 385 LEU cc_start: 0.8526 (mt) cc_final: 0.8235 (mm) REVERT: X 187 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8418 (mt-10) outliers start: 3 outliers final: 1 residues processed: 244 average time/residue: 0.7552 time to fit residues: 196.8668 Evaluate side-chains 170 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 451 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.4980 chunk 149 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 259 HIS U 436 HIS U 442 GLN V 73 HIS V 78 ASN V 92 ASN V 128 ASN V 235 HIS V 246 GLN V 275 HIS W 154 ASN W 316 GLN W 458 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.139514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117605 restraints weight = 14936.891| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.53 r_work: 0.3334 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12501 Z= 0.133 Angle : 0.612 8.981 16947 Z= 0.322 Chirality : 0.045 0.142 1826 Planarity : 0.004 0.038 2185 Dihedral : 14.461 171.168 1783 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.30 % Allowed : 9.97 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.22), residues: 1501 helix: 1.24 (0.21), residues: 619 sheet: 0.61 (0.34), residues: 205 loop : 0.80 (0.25), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 774 TYR 0.018 0.002 TYR V 69 PHE 0.020 0.002 PHE U 397 TRP 0.019 0.002 TRP G 735 HIS 0.005 0.001 HIS V 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (12501) covalent geometry : angle 0.61235 / 0.32 (16947) hydrogen bonds : bond 0.04769 / 3.20 ( 578) hydrogen bonds : angle 4.80879 / 3.48 ( 1563) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: G 733 GLN cc_start: 0.7425 (tt0) cc_final: 0.7124 (tt0) REVERT: G 748 ARG cc_start: 0.8260 (ttm170) cc_final: 0.8036 (ttp-110) REVERT: G 777 LEU cc_start: 0.8966 (mp) cc_final: 0.8668 (mp) REVERT: U 36 LYS cc_start: 0.8626 (tttt) cc_final: 0.8009 (mmpt) REVERT: U 41 ASP cc_start: 0.8286 (t70) cc_final: 0.7510 (OUTLIER) REVERT: U 56 ASN cc_start: 0.7735 (m-40) cc_final: 0.7337 (m-40) REVERT: U 160 GLN cc_start: 0.7725 (mt0) cc_final: 0.7449 (tm-30) REVERT: U 193 LYS cc_start: 0.7025 (tppt) cc_final: 0.6823 (mmpt) REVERT: U 224 LYS cc_start: 0.7833 (tttt) cc_final: 0.7598 (tmtt) REVERT: U 250 LYS cc_start: 0.8423 (tttt) cc_final: 0.8222 (tttm) REVERT: U 275 ASP cc_start: 0.7811 (m-30) cc_final: 0.7438 (m-30) REVERT: U 292 THR cc_start: 0.8921 (m) cc_final: 0.8711 (p) REVERT: U 298 LYS cc_start: 0.8444 (pttt) cc_final: 0.8213 (mttp) REVERT: U 437 LEU cc_start: 0.8449 (tp) cc_final: 0.8189 (tt) REVERT: U 490 VAL cc_start: 0.8484 (p) cc_final: 0.8283 (m) REVERT: V 72 GLU cc_start: 0.8239 (tt0) cc_final: 0.7967 (mt-10) REVERT: V 93 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7561 (mm-30) REVERT: V 210 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7900 (ttp-110) REVERT: V 246 GLN cc_start: 0.8165 (pt0) cc_final: 0.7467 (tp40) REVERT: V 325 MET cc_start: 0.8131 (mmt) cc_final: 0.7927 (mmm) REVERT: W 63 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6542 (mp0) REVERT: W 77 MET cc_start: 0.8921 (mmt) cc_final: 0.8617 (mmt) REVERT: W 94 GLU cc_start: 0.8141 (tp30) cc_final: 0.7798 (mt-10) REVERT: W 203 THR cc_start: 0.8860 (m) cc_final: 0.8529 (m) REVERT: W 215 LYS cc_start: 0.8649 (mttt) cc_final: 0.8171 (mtpt) REVERT: W 253 ASN cc_start: 0.7875 (m-40) cc_final: 0.7296 (p0) outliers start: 17 outliers final: 9 residues processed: 191 average time/residue: 0.7206 time to fit residues: 147.4801 Evaluate side-chains 154 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 692 ASP Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 210 ARG Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 276 ASP Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 426 SER Chi-restraints excluded: chain X residue 172 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 15 optimal weight: 0.0980 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 138 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 253 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.137248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113722 restraints weight = 15037.867| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.64 r_work: 0.3276 rms_B_bonded: 2.37 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: 0.8567 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12501 Z= 0.171 Angle : 0.585 9.225 16947 Z= 0.304 Chirality : 0.045 0.153 1826 Planarity : 0.005 0.045 2185 Dihedral : 13.620 179.674 1782 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.22 % Allowed : 11.73 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.22), residues: 1501 helix: 1.56 (0.22), residues: 616 sheet: 0.44 (0.33), residues: 215 loop : 0.77 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 774 TYR 0.016 0.002 TYR V 69 PHE 0.024 0.002 PHE U 397 TRP 0.015 0.002 TRP G 735 HIS 0.007 0.001 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (12501) covalent geometry : angle 0.58527 / 0.30 (16947) hydrogen bonds : bond 0.04510 / 3.05 ( 578) hydrogen bonds : angle 4.53456 / 3.28 ( 1563) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: G 733 GLN cc_start: 0.7351 (tt0) cc_final: 0.7085 (tt0) REVERT: G 745 LYS cc_start: 0.8149 (mttt) cc_final: 0.7647 (tptp) REVERT: U 36 LYS cc_start: 0.8548 (tttt) cc_final: 0.7902 (mmpt) REVERT: U 127 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8117 (mtmt) REVERT: U 224 LYS cc_start: 0.7906 (tttt) cc_final: 0.7639 (tttt) REVERT: U 298 LYS cc_start: 0.8527 (pttt) cc_final: 0.8266 (mttp) REVERT: U 437 LEU cc_start: 0.8449 (tp) cc_final: 0.8172 (tt) REVERT: U 695 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8592 (mt) REVERT: V 93 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7587 (mm-30) REVERT: V 210 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8048 (ttp-110) REVERT: V 246 GLN cc_start: 0.8052 (pt0) cc_final: 0.7470 (tp40) REVERT: V 305 MET cc_start: 0.9027 (mmm) cc_final: 0.8647 (mmt) REVERT: W 63 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: W 77 MET cc_start: 0.8981 (mmt) cc_final: 0.8768 (mmt) REVERT: W 203 THR cc_start: 0.8871 (m) cc_final: 0.8562 (m) REVERT: W 215 LYS cc_start: 0.8796 (mttt) cc_final: 0.8322 (mtpt) REVERT: W 266 ARG cc_start: 0.7563 (ptt90) cc_final: 0.7345 (pmm-80) outliers start: 42 outliers final: 16 residues processed: 177 average time/residue: 0.7378 time to fit residues: 140.0478 Evaluate side-chains 154 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain U residue 60 ARG Chi-restraints excluded: chain U residue 127 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 685 ILE Chi-restraints excluded: chain U residue 692 ASP Chi-restraints excluded: chain U residue 695 LEU Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 210 ARG Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain V residue 288 ASP Chi-restraints excluded: chain V residue 358 SER Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 246 VAL Chi-restraints excluded: chain W residue 276 ASP Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 426 SER Chi-restraints excluded: chain X residue 172 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 81 optimal weight: 0.9990 chunk 140 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 131 optimal weight: 0.0040 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 733 GLN G 776 GLN U 110 HIS U 114 GLN ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.140385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.118092 restraints weight = 14969.202| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.54 r_work: 0.3341 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12501 Z= 0.104 Angle : 0.506 7.028 16947 Z= 0.262 Chirality : 0.042 0.140 1826 Planarity : 0.004 0.045 2185 Dihedral : 12.239 179.908 1782 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.07 % Allowed : 12.88 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.22), residues: 1501 helix: 1.72 (0.22), residues: 628 sheet: 0.57 (0.34), residues: 211 loop : 0.82 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 372 TYR 0.012 0.001 TYR V 69 PHE 0.017 0.001 PHE U 397 TRP 0.011 0.001 TRP X 186 HIS 0.007 0.001 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (12501) covalent geometry : angle 0.50617 / 0.26 (16947) hydrogen bonds : bond 0.03599 / 2.43 ( 578) hydrogen bonds : angle 4.27457 / 3.08 ( 1563) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: G 745 LYS cc_start: 0.8114 (mttt) cc_final: 0.7562 (tptp) REVERT: U 36 LYS cc_start: 0.8558 (tttt) cc_final: 0.7880 (mmtt) REVERT: U 224 LYS cc_start: 0.7909 (tttt) cc_final: 0.7644 (tttm) REVERT: U 275 ASP cc_start: 0.7951 (m-30) cc_final: 0.7607 (m-30) REVERT: U 298 LYS cc_start: 0.8504 (pttt) cc_final: 0.8255 (mttp) REVERT: U 446 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.7769 (ttmm) REVERT: V 93 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7504 (mm-30) REVERT: V 210 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8157 (ttp-110) REVERT: V 246 GLN cc_start: 0.8101 (pt0) cc_final: 0.7450 (tp40) REVERT: V 305 MET cc_start: 0.8927 (mmm) cc_final: 0.8510 (mmt) REVERT: W 63 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6573 (mp0) REVERT: W 215 LYS cc_start: 0.8772 (mttt) cc_final: 0.8300 (mtpt) REVERT: W 266 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7116 (ptp-110) REVERT: W 312 PHE cc_start: 0.8468 (t80) cc_final: 0.8084 (t80) REVERT: W 465 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6959 (mmmt) REVERT: X 187 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7643 (mm-30) outliers start: 40 outliers final: 15 residues processed: 166 average time/residue: 0.7609 time to fit residues: 135.5436 Evaluate side-chains 148 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 665 VAL Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 208 ILE Chi-restraints excluded: chain V residue 210 ARG Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain V residue 358 SER Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 266 ARG Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 325 ASP Chi-restraints excluded: chain W residue 465 LYS Chi-restraints excluded: chain X residue 172 THR Chi-restraints excluded: chain X residue 178 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 33 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 125 optimal weight: 0.0980 chunk 22 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 253 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.138660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.114780 restraints weight = 15101.700| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.72 r_work: 0.3284 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12501 Z= 0.152 Angle : 0.536 7.911 16947 Z= 0.275 Chirality : 0.044 0.149 1826 Planarity : 0.004 0.043 2185 Dihedral : 12.095 177.699 1782 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.30 % Allowed : 13.19 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.22), residues: 1501 helix: 1.78 (0.22), residues: 616 sheet: 0.42 (0.34), residues: 216 loop : 0.73 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 475 TYR 0.011 0.001 TYR V 69 PHE 0.019 0.001 PHE U 397 TRP 0.012 0.001 TRP V 340 HIS 0.006 0.001 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (12501) covalent geometry : angle 0.53576 / 0.28 (16947) hydrogen bonds : bond 0.03994 / 2.70 ( 578) hydrogen bonds : angle 4.28790 / 3.10 ( 1563) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: G 745 LYS cc_start: 0.8197 (mttt) cc_final: 0.7638 (tptp) REVERT: U 36 LYS cc_start: 0.8556 (tttt) cc_final: 0.7879 (mmtt) REVERT: U 101 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.6056 (mtt) REVERT: U 191 ASN cc_start: 0.6190 (p0) cc_final: 0.5411 (t0) REVERT: U 224 LYS cc_start: 0.7908 (tttt) cc_final: 0.7607 (tttm) REVERT: U 232 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7371 (mt0) REVERT: U 275 ASP cc_start: 0.8090 (m-30) cc_final: 0.7788 (m-30) REVERT: U 298 LYS cc_start: 0.8537 (pttt) cc_final: 0.8259 (mttp) REVERT: U 446 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.7710 (tmmm) REVERT: U 695 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8634 (mt) REVERT: V 83 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: V 93 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7572 (mm-30) REVERT: V 210 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8193 (ttp-110) REVERT: V 246 GLN cc_start: 0.8252 (pt0) cc_final: 0.7567 (tp40) REVERT: V 305 MET cc_start: 0.8934 (mmm) cc_final: 0.8535 (mmt) REVERT: W 63 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6676 (mp0) REVERT: W 215 LYS cc_start: 0.8885 (mttt) cc_final: 0.8377 (mtpt) REVERT: W 266 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7319 (pmm-80) REVERT: W 310 GLU cc_start: 0.8185 (tt0) cc_final: 0.7976 (tt0) REVERT: W 312 PHE cc_start: 0.8485 (t80) cc_final: 0.8128 (t80) REVERT: W 465 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7231 (mmmt) REVERT: X 187 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7820 (mm-30) outliers start: 43 outliers final: 23 residues processed: 155 average time/residue: 0.7476 time to fit residues: 124.3480 Evaluate side-chains 158 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain U residue 60 ARG Chi-restraints excluded: chain U residue 101 MET Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 232 GLN Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 695 LEU Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain U residue 733 MET Chi-restraints excluded: chain V residue 83 GLU Chi-restraints excluded: chain V residue 111 ASN Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 135 SER Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 208 ILE Chi-restraints excluded: chain V residue 210 ARG Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain V residue 355 MET Chi-restraints excluded: chain V residue 358 SER Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 246 VAL Chi-restraints excluded: chain W residue 266 ARG Chi-restraints excluded: chain W residue 276 ASP Chi-restraints excluded: chain W residue 284 GLU Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 426 SER Chi-restraints excluded: chain W residue 465 LYS Chi-restraints excluded: chain X residue 172 THR Chi-restraints excluded: chain X residue 175 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.2980 chunk 76 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** V 235 HIS ** 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 = 0.3733 r_free = 0.3733 target = 0.139255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.115766 restraints weight = 15062.428| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.72 r_work: 0.3328 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12501 Z= 0.117 Angle : 0.499 7.108 16947 Z= 0.255 Chirality : 0.042 0.138 1826 Planarity : 0.004 0.044 2185 Dihedral : 11.565 177.370 1782 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.76 % Allowed : 14.34 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.22), residues: 1501 helix: 1.78 (0.21), residues: 628 sheet: 0.48 (0.34), residues: 216 loop : 0.75 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 475 TYR 0.009 0.001 TYR V 69 PHE 0.015 0.001 PHE U 397 TRP 0.011 0.001 TRP G 735 HIS 0.004 0.001 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (12501) covalent geometry : angle 0.49851 / 0.26 (16947) hydrogen bonds : bond 0.03533 / 2.39 ( 578) hydrogen bonds : angle 4.19093 / 3.02 ( 1563) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 745 LYS cc_start: 0.8118 (mttt) cc_final: 0.7601 (tptp) REVERT: U 36 LYS cc_start: 0.8529 (tttt) cc_final: 0.7863 (mmpt) REVERT: U 101 MET cc_start: 0.6402 (OUTLIER) cc_final: 0.6162 (mtt) REVERT: U 191 ASN cc_start: 0.6185 (p0) cc_final: 0.5629 (t0) REVERT: U 275 ASP cc_start: 0.8104 (m-30) cc_final: 0.7780 (m-30) REVERT: U 298 LYS cc_start: 0.8499 (pttt) cc_final: 0.8261 (mttp) REVERT: U 401 ASP cc_start: 0.8004 (t0) cc_final: 0.7530 (t0) REVERT: U 446 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.7582 (tmmm) REVERT: U 695 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8560 (mt) REVERT: V 83 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7790 (tt0) REVERT: V 93 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7520 (mm-30) REVERT: V 210 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8208 (ttp-110) REVERT: V 246 GLN cc_start: 0.8223 (pt0) cc_final: 0.7581 (tp40) REVERT: V 305 MET cc_start: 0.8883 (mmm) cc_final: 0.8474 (mmt) REVERT: W 63 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: W 312 PHE cc_start: 0.8462 (t80) cc_final: 0.8153 (t80) REVERT: W 465 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.7142 (mmmt) REVERT: X 187 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7706 (mm-30) outliers start: 36 outliers final: 19 residues processed: 154 average time/residue: 0.7115 time to fit residues: 117.4291 Evaluate side-chains 145 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain U residue 101 MET Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 695 LEU Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 83 GLU Chi-restraints excluded: chain V residue 111 ASN Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 208 ILE Chi-restraints excluded: chain V residue 210 ARG Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain V residue 358 SER Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 163 ILE Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 246 VAL Chi-restraints excluded: chain W residue 276 ASP Chi-restraints excluded: chain W residue 284 GLU Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 426 SER Chi-restraints excluded: chain W residue 465 LYS Chi-restraints excluded: chain X residue 172 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 55 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** V 235 HIS ** 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 = 0.3704 r_free = 0.3704 target = 0.136772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113147 restraints weight = 15110.349| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.73 r_work: 0.3278 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12501 Z= 0.181 Angle : 0.562 8.458 16947 Z= 0.286 Chirality : 0.044 0.147 1826 Planarity : 0.005 0.045 2185 Dihedral : 11.919 178.617 1782 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.22 % Allowed : 14.80 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.22), residues: 1501 helix: 1.71 (0.21), residues: 622 sheet: 0.40 (0.34), residues: 218 loop : 0.62 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 475 TYR 0.012 0.002 TYR W 304 PHE 0.018 0.002 PHE V 132 TRP 0.012 0.001 TRP V 79 HIS 0.006 0.001 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 (12501) covalent geometry : angle 0.56157 / 0.29 (16947) hydrogen bonds : bond 0.04179 / 2.83 ( 578) hydrogen bonds : angle 4.28320 / 3.10 ( 1563) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: G 745 LYS cc_start: 0.8218 (mttt) cc_final: 0.7663 (tptp) REVERT: U 22 MET cc_start: 0.8682 (mtt) cc_final: 0.8399 (mtm) REVERT: U 36 LYS cc_start: 0.8555 (tttt) cc_final: 0.7870 (mmpt) REVERT: U 191 ASN cc_start: 0.6361 (p0) cc_final: 0.5792 (t0) REVERT: U 298 LYS cc_start: 0.8554 (pttt) cc_final: 0.8287 (mttp) REVERT: U 401 ASP cc_start: 0.8143 (t0) cc_final: 0.7659 (t0) REVERT: U 446 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.7662 (tmmm) REVERT: U 695 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8594 (mt) REVERT: V 93 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7583 (mm-30) REVERT: V 210 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8245 (ttp-110) REVERT: V 246 GLN cc_start: 0.8241 (pt0) cc_final: 0.7595 (tp40) REVERT: V 305 MET cc_start: 0.8919 (mmm) cc_final: 0.8540 (mmt) REVERT: W 157 LYS cc_start: 0.8511 (mttt) cc_final: 0.8239 (mppt) REVERT: W 312 PHE cc_start: 0.8497 (t80) cc_final: 0.8055 (t80) REVERT: X 187 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7848 (mm-30) outliers start: 42 outliers final: 24 residues processed: 153 average time/residue: 0.7141 time to fit residues: 117.3623 Evaluate side-chains 148 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 494 ASP Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 695 LEU Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 111 ASN Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 135 SER Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 208 ILE Chi-restraints excluded: chain V residue 210 ARG Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain V residue 269 LEU Chi-restraints excluded: chain V residue 355 MET Chi-restraints excluded: chain V residue 358 SER Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 246 VAL Chi-restraints excluded: chain W residue 276 ASP Chi-restraints excluded: chain W residue 284 GLU Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 411 MET Chi-restraints excluded: chain W residue 426 SER Chi-restraints excluded: chain X residue 172 THR Chi-restraints excluded: chain X residue 175 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 98 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** V 235 HIS ** 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 = 0.3740 r_free = 0.3740 target = 0.139603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.115823 restraints weight = 14947.857| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.79 r_work: 0.3317 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12501 Z= 0.112 Angle : 0.506 7.471 16947 Z= 0.258 Chirality : 0.042 0.137 1826 Planarity : 0.004 0.043 2185 Dihedral : 11.459 179.388 1782 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.45 % Allowed : 15.18 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.22), residues: 1501 helix: 1.81 (0.21), residues: 628 sheet: 0.46 (0.34), residues: 218 loop : 0.70 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 475 TYR 0.009 0.001 TYR V 69 PHE 0.013 0.001 PHE U 397 TRP 0.010 0.001 TRP G 735 HIS 0.005 0.001 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (12501) covalent geometry : angle 0.50634 / 0.26 (16947) hydrogen bonds : bond 0.03547 / 2.39 ( 578) hydrogen bonds : angle 4.16720 / 3.01 ( 1563) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 745 LYS cc_start: 0.8145 (mttt) cc_final: 0.7578 (tptp) REVERT: U 22 MET cc_start: 0.8620 (mtt) cc_final: 0.8379 (mtm) REVERT: U 36 LYS cc_start: 0.8535 (tttt) cc_final: 0.7846 (mmpt) REVERT: U 181 MET cc_start: 0.7838 (ttm) cc_final: 0.7529 (mtm) REVERT: U 191 ASN cc_start: 0.6332 (p0) cc_final: 0.5904 (t0) REVERT: U 275 ASP cc_start: 0.7977 (m-30) cc_final: 0.7618 (m-30) REVERT: U 298 LYS cc_start: 0.8508 (pttt) cc_final: 0.8246 (mttp) REVERT: U 401 ASP cc_start: 0.8026 (t0) cc_final: 0.7531 (t0) REVERT: U 446 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.7634 (tmmm) REVERT: U 695 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8566 (mt) REVERT: V 93 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7560 (mm-30) REVERT: V 246 GLN cc_start: 0.8223 (pt0) cc_final: 0.7595 (tp40) REVERT: V 305 MET cc_start: 0.8892 (mmm) cc_final: 0.8480 (mmt) REVERT: W 312 PHE cc_start: 0.8456 (t80) cc_final: 0.8098 (t80) REVERT: X 187 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7766 (mm-30) outliers start: 32 outliers final: 22 residues processed: 144 average time/residue: 0.6934 time to fit residues: 107.5335 Evaluate side-chains 138 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 695 LEU Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 111 ASN Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 135 SER Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 195 GLU Chi-restraints excluded: chain V residue 208 ILE Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain V residue 269 LEU Chi-restraints excluded: chain V residue 358 SER Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 246 VAL Chi-restraints excluded: chain W residue 276 ASP Chi-restraints excluded: chain W residue 284 GLU Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 426 SER Chi-restraints excluded: chain X residue 172 THR Chi-restraints excluded: chain X residue 175 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 13 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** V 235 HIS ** 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 = 0.3737 r_free = 0.3737 target = 0.139457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.117492 restraints weight = 14977.486| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.53 r_work: 0.3345 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12501 Z= 0.110 Angle : 0.504 8.020 16947 Z= 0.256 Chirality : 0.042 0.136 1826 Planarity : 0.004 0.044 2185 Dihedral : 11.234 179.922 1782 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.92 % Allowed : 15.49 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.22), residues: 1501 helix: 1.86 (0.21), residues: 628 sheet: 0.51 (0.34), residues: 216 loop : 0.75 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 475 TYR 0.008 0.001 TYR U 314 PHE 0.012 0.001 PHE U 397 TRP 0.010 0.001 TRP V 340 HIS 0.005 0.001 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (12501) covalent geometry : angle 0.50437 / 0.26 (16947) hydrogen bonds : bond 0.03454 / 2.33 ( 578) hydrogen bonds : angle 4.10375 / 2.96 ( 1563) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: G 745 LYS cc_start: 0.8116 (mttt) cc_final: 0.7597 (tptp) REVERT: U 36 LYS cc_start: 0.8532 (tttt) cc_final: 0.7868 (mmpt) REVERT: U 159 GLU cc_start: 0.6823 (tp30) cc_final: 0.6584 (tm-30) REVERT: U 181 MET cc_start: 0.7877 (ttm) cc_final: 0.7595 (mtm) REVERT: U 191 ASN cc_start: 0.6283 (p0) cc_final: 0.5882 (t0) REVERT: U 298 LYS cc_start: 0.8495 (pttt) cc_final: 0.8265 (mttp) REVERT: U 401 ASP cc_start: 0.7973 (t0) cc_final: 0.7491 (t0) REVERT: U 446 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.7620 (tmmm) REVERT: U 695 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8556 (mt) REVERT: V 93 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7559 (mm-30) REVERT: V 246 GLN cc_start: 0.8176 (pt0) cc_final: 0.7640 (tp40) REVERT: V 305 MET cc_start: 0.8874 (mmm) cc_final: 0.8457 (mmt) REVERT: W 312 PHE cc_start: 0.8457 (t80) cc_final: 0.8155 (t80) REVERT: X 187 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7740 (mm-30) outliers start: 25 outliers final: 19 residues processed: 141 average time/residue: 0.6614 time to fit residues: 100.7015 Evaluate side-chains 138 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 695 LEU Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 135 SER Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 208 ILE Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain V residue 269 LEU Chi-restraints excluded: chain V residue 358 SER Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 276 ASP Chi-restraints excluded: chain W residue 284 GLU Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 426 SER Chi-restraints excluded: chain X residue 172 THR Chi-restraints excluded: chain X residue 175 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 144 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** V 235 HIS ** 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 = 0.3746 r_free = 0.3746 target = 0.140177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.116430 restraints weight = 14992.501| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.77 r_work: 0.3319 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12501 Z= 0.113 Angle : 0.508 8.554 16947 Z= 0.256 Chirality : 0.042 0.136 1826 Planarity : 0.004 0.044 2185 Dihedral : 11.206 179.352 1782 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.84 % Allowed : 15.80 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.22), residues: 1501 helix: 1.89 (0.21), residues: 628 sheet: 0.51 (0.34), residues: 216 loop : 0.75 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 475 TYR 0.008 0.001 TYR U 314 PHE 0.013 0.001 PHE U 397 TRP 0.010 0.001 TRP V 340 HIS 0.006 0.001 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (12501) covalent geometry : angle 0.50756 / 0.26 (16947) hydrogen bonds : bond 0.03454 / 2.32 ( 578) hydrogen bonds : angle 4.08756 / 2.95 ( 1563) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 745 LYS cc_start: 0.8145 (mttt) cc_final: 0.7596 (tptp) REVERT: U 36 LYS cc_start: 0.8531 (tttt) cc_final: 0.7848 (mmpt) REVERT: U 181 MET cc_start: 0.7806 (ttm) cc_final: 0.7563 (mtm) REVERT: U 191 ASN cc_start: 0.6262 (p0) cc_final: 0.5856 (t0) REVERT: U 298 LYS cc_start: 0.8506 (pttt) cc_final: 0.8254 (mttp) REVERT: U 401 ASP cc_start: 0.8032 (t0) cc_final: 0.7546 (t0) REVERT: U 446 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7635 (tmmm) REVERT: U 695 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8569 (mt) REVERT: V 83 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7666 (tt0) REVERT: V 93 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7621 (mm-30) REVERT: V 246 GLN cc_start: 0.8233 (pt0) cc_final: 0.7573 (tp40) REVERT: V 305 MET cc_start: 0.8892 (mmm) cc_final: 0.8479 (mmt) REVERT: W 312 PHE cc_start: 0.8450 (t80) cc_final: 0.8137 (t80) REVERT: X 187 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7790 (mm-30) outliers start: 24 outliers final: 20 residues processed: 138 average time/residue: 0.6584 time to fit residues: 98.0252 Evaluate side-chains 140 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 695 LEU Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 83 GLU Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 135 SER Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 195 GLU Chi-restraints excluded: chain V residue 208 ILE Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain V residue 269 LEU Chi-restraints excluded: chain V residue 358 SER Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 276 ASP Chi-restraints excluded: chain W residue 284 GLU Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 426 SER Chi-restraints excluded: chain X residue 172 THR Chi-restraints excluded: chain X residue 175 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 58 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 136 optimal weight: 0.0170 chunk 84 optimal weight: 3.9990 chunk 90 optimal weight: 0.0770 chunk 130 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 235 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.140259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.118187 restraints weight = 14928.512| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.58 r_work: 0.3350 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12501 Z= 0.102 Angle : 0.492 8.474 16947 Z= 0.249 Chirality : 0.041 0.135 1826 Planarity : 0.004 0.084 2185 Dihedral : 11.021 178.315 1782 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.92 % Allowed : 15.87 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.22), residues: 1501 helix: 1.96 (0.21), residues: 628 sheet: 0.54 (0.34), residues: 216 loop : 0.78 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 774 TYR 0.008 0.001 TYR U 314 PHE 0.012 0.001 PHE W 249 TRP 0.010 0.001 TRP V 79 HIS 0.005 0.001 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (12501) covalent geometry : angle 0.49250 / 0.25 (16947) hydrogen bonds : bond 0.03278 / 2.21 ( 578) hydrogen bonds : angle 4.02451 / 2.91 ( 1563) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4489.09 seconds wall clock time: 77 minutes 16.82 seconds (4636.82 seconds total)