Starting phenix.real_space_refine on Wed May 14 23:00:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a5d_15165/05_2025/8a5d_15165_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a5d_15165/05_2025/8a5d_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8a5d_15165/05_2025/8a5d_15165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a5d_15165/05_2025/8a5d_15165.map" model { file = "/net/cci-nas-00/data/ceres_data/8a5d_15165/05_2025/8a5d_15165_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a5d_15165/05_2025/8a5d_15165_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.14, per 1000 atoms: 0.58 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: 3.04 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.84 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: 4.15 Time building geometry restraints manager: 3.51 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 1.949 1.795 0.154 2.00e-02 2.50e+03 5.95e+01 bond pdb=" O2B AGS V 500 " pdb=" PB AGS V 500 " ideal model delta sigma weight residual 1.531 1.413 0.118 1.60e-02 3.91e+03 5.48e+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=" O2B AGS W 500 " pdb=" PB AGS W 500 " ideal model delta sigma weight residual 1.531 1.436 0.095 1.60e-02 3.91e+03 3.55e+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 ... (remaining 12496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.80: 16681 4.80 - 9.60: 256 9.60 - 14.40: 7 14.40 - 19.20: 2 19.20 - 24.00: 1 Bond angle restraints: 16947 Sorted by residual: angle pdb=" O3A AGS W 500 " pdb=" PB AGS W 500 " pdb=" O3B AGS W 500 " ideal model delta sigma weight residual 109.69 85.69 24.00 3.00e+00 1.11e-01 6.40e+01 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=" O3A AGS U 900 " pdb=" PB AGS U 900 " pdb=" O3B AGS U 900 " ideal model delta sigma weight residual 109.69 92.05 17.64 3.00e+00 1.11e-01 3.46e+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 ... (remaining 16942 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6936 17.96 - 35.92: 496 35.92 - 53.88: 95 53.88 - 71.85: 26 71.85 - 89.81: 16 Dihedral angle restraints: 7569 sinusoidal: 3160 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 7566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 938 0.065 - 0.129: 613 0.129 - 0.194: 214 0.194 - 0.258: 55 0.258 - 0.323: 12 Chirality restraints: 1832 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 1829 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: 1.490 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: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.370 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 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 0.154 12501 Z= 1.137 Angle : 1.878 23.997 16947 Z= 1.296 Chirality : 0.093 0.323 1832 Planarity : 0.011 0.065 2185 Dihedral : 14.052 89.808 4723 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.100 0.016 TRP W 433 HIS 0.033 0.005 HIS V 371 PHE 0.070 0.012 PHE V 132 TYR 0.072 0.014 TYR V 133 ARG 0.029 0.003 ARG V 312 Details of bonding type rmsd hydrogen bonds : bond 0.17972 ( 578) hydrogen bonds : angle 6.94526 ( 1563) covalent geometry : bond 0.01574 (12501) covalent geometry : angle 1.87800 (16947) *********************** 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 : 1.331 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: 0.7019 (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: 0.7925 (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: 0.8358 (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: 0.8417 (mt-10) outliers start: 3 outliers final: 1 residues processed: 244 average time/residue: 1.5203 time to fit residues: 396.4262 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 : 1.386 ------------------------------------------------------------------------------- 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 126 optimal weight: 0.7980 chunk 113 optimal weight: 0.0870 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 117 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 776 GLN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.139966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.116954 restraints weight = 14794.152| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.61 r_work: 0.3321 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12501 Z= 0.131 Angle : 0.610 8.899 16947 Z= 0.322 Chirality : 0.044 0.147 1832 Planarity : 0.004 0.037 2185 Dihedral : 7.283 56.376 1729 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.53 % Allowed : 9.51 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.22), residues: 1501 helix: 1.23 (0.21), residues: 620 sheet: 0.62 (0.34), residues: 203 loop : 0.79 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 735 HIS 0.005 0.001 HIS V 235 PHE 0.019 0.001 PHE U 397 TYR 0.019 0.002 TYR V 69 ARG 0.005 0.001 ARG U 117 Details of bonding type rmsd hydrogen bonds : bond 0.04662 ( 578) hydrogen bonds : angle 4.80277 ( 1563) covalent geometry : bond 0.00273 (12501) covalent geometry : angle 0.61038 (16947) *********************** 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 203 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 1.414 Fit side-chains revert: symmetry clash REVERT: G 733 GLN cc_start: 0.7467 (tt0) cc_final: 0.7173 (tt0) REVERT: G 748 ARG cc_start: 0.8281 (ttm170) cc_final: 0.8048 (ttp-110) REVERT: G 777 LEU cc_start: 0.8966 (mp) cc_final: 0.8659 (mp) REVERT: U 36 LYS cc_start: 0.8633 (tttt) cc_final: 0.8003 (mmpt) REVERT: U 41 ASP cc_start: 0.8244 (t70) cc_final: 0.7543 (t0) REVERT: U 56 ASN cc_start: 0.7780 (m-40) cc_final: 0.7390 (m-40) REVERT: U 160 GLN cc_start: 0.7712 (mt0) cc_final: 0.7470 (tm-30) REVERT: U 224 LYS cc_start: 0.7825 (tttt) cc_final: 0.7609 (tmtt) REVERT: U 250 LYS cc_start: 0.8432 (tttt) cc_final: 0.8231 (tttm) REVERT: U 275 ASP cc_start: 0.7832 (m-30) cc_final: 0.7453 (m-30) REVERT: U 292 THR cc_start: 0.8930 (m) cc_final: 0.8703 (p) REVERT: U 298 LYS cc_start: 0.8438 (pttt) cc_final: 0.8179 (mttp) REVERT: U 437 LEU cc_start: 0.8534 (tp) cc_final: 0.8214 (tt) REVERT: V 72 GLU cc_start: 0.8282 (tt0) cc_final: 0.8019 (mt-10) REVERT: V 93 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7581 (mm-30) REVERT: V 210 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7934 (ttp-110) REVERT: V 246 GLN cc_start: 0.8185 (pt0) cc_final: 0.7475 (tp40) REVERT: V 325 MET cc_start: 0.8153 (mmt) cc_final: 0.7949 (mmm) REVERT: W 63 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6534 (mp0) REVERT: W 77 MET cc_start: 0.8950 (mmt) cc_final: 0.8655 (mmt) REVERT: W 94 GLU cc_start: 0.8174 (tp30) cc_final: 0.7823 (mt-10) REVERT: W 203 THR cc_start: 0.8860 (m) cc_final: 0.8543 (m) REVERT: W 215 LYS cc_start: 0.8659 (mttt) cc_final: 0.8182 (mtpt) REVERT: W 253 ASN cc_start: 0.7839 (m-40) cc_final: 0.7302 (p0) REVERT: W 264 ASP cc_start: 0.7905 (m-30) cc_final: 0.7700 (t70) outliers start: 20 outliers final: 9 residues processed: 194 average time/residue: 1.4267 time to fit residues: 297.6745 Evaluate side-chains 155 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 665 VAL 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 108 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 124 optimal weight: 0.1980 chunk 119 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3720 r_free = 0.3720 target = 0.137910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114913 restraints weight = 15046.868| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.60 r_work: 0.3306 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2375 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= 0.153 Angle : 0.568 8.717 16947 Z= 0.297 Chirality : 0.044 0.150 1832 Planarity : 0.005 0.045 2185 Dihedral : 6.752 61.093 1728 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.14 % Allowed : 11.66 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.22), residues: 1501 helix: 1.59 (0.22), residues: 616 sheet: 0.51 (0.33), residues: 215 loop : 0.81 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 735 HIS 0.008 0.001 HIS V 235 PHE 0.023 0.002 PHE U 397 TYR 0.016 0.002 TYR V 69 ARG 0.005 0.000 ARG G 774 Details of bonding type rmsd hydrogen bonds : bond 0.04450 ( 578) hydrogen bonds : angle 4.54625 ( 1563) covalent geometry : bond 0.00364 (12501) covalent geometry : angle 0.56816 (16947) *********************** 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 191 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 1.468 Fit side-chains REVERT: G 733 GLN cc_start: 0.7341 (tt0) cc_final: 0.7073 (tt0) REVERT: G 777 LEU cc_start: 0.8984 (mp) cc_final: 0.8752 (mp) REVERT: U 36 LYS cc_start: 0.8561 (tttt) cc_final: 0.7909 (mmpt) REVERT: U 127 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8106 (mtmt) REVERT: U 193 LYS cc_start: 0.7035 (mmpt) cc_final: 0.6422 (mmmt) REVERT: U 224 LYS cc_start: 0.7916 (tttt) cc_final: 0.7683 (tttt) REVERT: U 298 LYS cc_start: 0.8504 (pttt) cc_final: 0.8242 (mttp) REVERT: U 437 LEU cc_start: 0.8475 (tp) cc_final: 0.8222 (tt) REVERT: U 695 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8540 (mt) REVERT: V 93 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7531 (mm-30) REVERT: V 210 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8033 (ttp-110) REVERT: V 246 GLN cc_start: 0.8065 (pt0) cc_final: 0.7452 (tp40) REVERT: V 305 MET cc_start: 0.9051 (mmm) cc_final: 0.8684 (mmt) REVERT: W 63 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6625 (mp0) REVERT: W 77 MET cc_start: 0.8971 (mmt) cc_final: 0.8749 (mmt) REVERT: W 203 THR cc_start: 0.8841 (m) cc_final: 0.8534 (m) REVERT: W 215 LYS cc_start: 0.8716 (mttt) cc_final: 0.8249 (mtpt) REVERT: W 284 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7597 (mt-10) REVERT: W 310 GLU cc_start: 0.8144 (tt0) cc_final: 0.7941 (tt0) REVERT: W 465 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7202 (mmmt) outliers start: 41 outliers final: 18 residues processed: 176 average time/residue: 1.4446 time to fit residues: 273.3481 Evaluate side-chains 156 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 206 GLU 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 267 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 140 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 110 HIS ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.139240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.115691 restraints weight = 14917.880| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.72 r_work: 0.3306 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2655 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= 0.134 Angle : 0.530 8.100 16947 Z= 0.276 Chirality : 0.043 0.148 1832 Planarity : 0.004 0.047 2185 Dihedral : 6.422 61.546 1728 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.22 % Allowed : 12.58 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.22), residues: 1501 helix: 1.70 (0.21), residues: 622 sheet: 0.51 (0.34), residues: 215 loop : 0.79 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 340 HIS 0.005 0.001 HIS V 235 PHE 0.020 0.001 PHE U 397 TYR 0.012 0.001 TYR V 69 ARG 0.004 0.000 ARG V 372 Details of bonding type rmsd hydrogen bonds : bond 0.03994 ( 578) hydrogen bonds : angle 4.36412 ( 1563) covalent geometry : bond 0.00315 (12501) covalent geometry : angle 0.53011 (16947) *********************** 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 185 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 1.549 Fit side-chains revert: symmetry clash REVERT: G 745 LYS cc_start: 0.8117 (mttt) cc_final: 0.7569 (tptp) REVERT: U 36 LYS cc_start: 0.8545 (tttt) cc_final: 0.7886 (mmtt) REVERT: U 224 LYS cc_start: 0.7904 (tttt) cc_final: 0.7623 (tttm) REVERT: U 275 ASP cc_start: 0.7954 (m-30) cc_final: 0.7610 (m-30) REVERT: U 298 LYS cc_start: 0.8514 (pttt) cc_final: 0.8238 (mttp) REVERT: U 392 MET cc_start: 0.7954 (mmm) cc_final: 0.7733 (mmm) REVERT: U 401 ASP cc_start: 0.8026 (t0) cc_final: 0.7812 (t0) REVERT: U 446 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.7879 (ttmm) REVERT: U 695 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8567 (mt) REVERT: V 93 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7535 (mm-30) REVERT: V 210 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8126 (ttp-110) REVERT: V 246 GLN cc_start: 0.8208 (pt0) cc_final: 0.7695 (tp40) REVERT: V 305 MET cc_start: 0.8972 (mmm) cc_final: 0.8565 (mmt) REVERT: W 63 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6592 (mp0) REVERT: W 77 MET cc_start: 0.8939 (mmt) cc_final: 0.8648 (mmt) REVERT: W 203 THR cc_start: 0.8793 (m) cc_final: 0.8523 (m) REVERT: W 215 LYS cc_start: 0.8829 (mttt) cc_final: 0.8343 (mtpt) REVERT: W 266 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7127 (ptp-110) REVERT: W 312 PHE cc_start: 0.8481 (t80) cc_final: 0.8075 (t80) REVERT: X 187 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7676 (mm-30) outliers start: 42 outliers final: 16 residues processed: 167 average time/residue: 1.5419 time to fit residues: 276.0802 Evaluate side-chains 152 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 685 ILE 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 208 ILE Chi-restraints excluded: chain V residue 210 ARG Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain V residue 267 LEU 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 276 ASP Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 325 ASP Chi-restraints excluded: chain X residue 172 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 90 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 chunk 38 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 24 GLN U 160 GLN ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 253 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.139297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.116098 restraints weight = 14869.993| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.64 r_work: 0.3313 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12501 Z= 0.112 Angle : 0.500 7.248 16947 Z= 0.258 Chirality : 0.042 0.141 1832 Planarity : 0.004 0.047 2185 Dihedral : 6.149 59.438 1728 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.61 % Allowed : 13.80 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.22), residues: 1501 helix: 1.76 (0.22), residues: 628 sheet: 0.50 (0.34), residues: 220 loop : 0.80 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 186 HIS 0.005 0.001 HIS V 235 PHE 0.016 0.001 PHE U 397 TYR 0.011 0.001 TYR V 69 ARG 0.004 0.000 ARG U 475 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 578) hydrogen bonds : angle 4.25866 ( 1563) covalent geometry : bond 0.00257 (12501) covalent geometry : angle 0.50034 (16947) *********************** 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 165 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 1.416 Fit side-chains revert: symmetry clash REVERT: G 745 LYS cc_start: 0.8147 (mttt) cc_final: 0.7622 (tptp) REVERT: G 771 GLU cc_start: 0.7682 (mp0) cc_final: 0.7392 (mm-30) REVERT: U 36 LYS cc_start: 0.8561 (tttt) cc_final: 0.7876 (mmtt) REVERT: U 191 ASN cc_start: 0.6269 (p0) cc_final: 0.5628 (t0) REVERT: U 195 LEU cc_start: 0.7575 (mt) cc_final: 0.7253 (mt) REVERT: U 224 LYS cc_start: 0.7897 (tttt) cc_final: 0.7622 (tttm) REVERT: U 275 ASP cc_start: 0.8048 (m-30) cc_final: 0.7706 (m-30) REVERT: U 298 LYS cc_start: 0.8527 (pttt) cc_final: 0.8263 (mttp) REVERT: U 401 ASP cc_start: 0.8009 (t0) cc_final: 0.7657 (t0) REVERT: U 446 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7607 (tmmm) REVERT: V 93 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7538 (mm-30) REVERT: V 210 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8216 (ttp-110) REVERT: V 246 GLN cc_start: 0.8361 (pt0) cc_final: 0.7680 (tp40) REVERT: V 305 MET cc_start: 0.8914 (mmm) cc_final: 0.8487 (mmt) REVERT: W 63 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6631 (mp0) REVERT: W 77 MET cc_start: 0.8920 (mmt) cc_final: 0.8679 (mmt) REVERT: W 215 LYS cc_start: 0.8853 (mttt) cc_final: 0.8361 (mtpt) REVERT: W 312 PHE cc_start: 0.8476 (t80) cc_final: 0.8094 (t80) REVERT: X 187 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7718 (mm-30) outliers start: 34 outliers final: 15 residues processed: 151 average time/residue: 1.4939 time to fit residues: 242.6037 Evaluate side-chains 143 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 699 SER Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 179 ASP 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 246 VAL Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 325 ASP Chi-restraints excluded: chain W residue 411 MET Chi-restraints excluded: chain X residue 172 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 45 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 101 optimal weight: 0.0030 chunk 112 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3755 r_free = 0.3755 target = 0.140799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.117120 restraints weight = 15114.453| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.73 r_work: 0.3326 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12501 Z= 0.105 Angle : 0.492 7.281 16947 Z= 0.253 Chirality : 0.042 0.137 1832 Planarity : 0.004 0.044 2185 Dihedral : 5.995 57.191 1728 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.61 % Allowed : 14.26 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.22), residues: 1501 helix: 1.83 (0.22), residues: 629 sheet: 0.58 (0.34), residues: 216 loop : 0.79 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 735 HIS 0.003 0.001 HIS V 87 PHE 0.015 0.001 PHE U 397 TYR 0.010 0.001 TYR W 304 ARG 0.004 0.000 ARG W 266 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 578) hydrogen bonds : angle 4.18594 ( 1563) covalent geometry : bond 0.00239 (12501) covalent geometry : angle 0.49211 (16947) *********************** 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: 34 poor density : 130 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: G 745 LYS cc_start: 0.8168 (mttt) cc_final: 0.7614 (tptp) REVERT: U 36 LYS cc_start: 0.8546 (tttt) cc_final: 0.7902 (mptt) REVERT: U 191 ASN cc_start: 0.6302 (p0) cc_final: 0.5637 (t0) REVERT: U 195 LEU cc_start: 0.7536 (mt) cc_final: 0.7213 (mt) REVERT: U 224 LYS cc_start: 0.7888 (tttt) cc_final: 0.7603 (tttm) REVERT: U 275 ASP cc_start: 0.8114 (m-30) cc_final: 0.7757 (m-30) REVERT: U 298 LYS cc_start: 0.8515 (pttt) cc_final: 0.8243 (mttp) REVERT: U 401 ASP cc_start: 0.7977 (t0) cc_final: 0.7565 (t0) REVERT: U 446 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.7628 (tmmm) REVERT: U 695 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8539 (mt) REVERT: V 93 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7546 (mm-30) REVERT: V 210 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8229 (ttp-110) REVERT: V 246 GLN cc_start: 0.8247 (pt0) cc_final: 0.7674 (tp40) REVERT: V 305 MET cc_start: 0.8896 (mmm) cc_final: 0.8465 (mmt) REVERT: W 63 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6613 (mp0) REVERT: W 215 LYS cc_start: 0.8832 (mttt) cc_final: 0.8342 (mtpt) REVERT: W 312 PHE cc_start: 0.8444 (t80) cc_final: 0.8111 (t80) REVERT: X 187 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7710 (mm-30) outliers start: 34 outliers final: 19 residues processed: 152 average time/residue: 1.4737 time to fit residues: 241.3111 Evaluate side-chains 147 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 111 ASN Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 179 ASP 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 246 VAL Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 325 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 47 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3717 r_free = 0.3717 target = 0.137622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113689 restraints weight = 15084.011| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.72 r_work: 0.3273 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12501 Z= 0.193 Angle : 0.557 8.308 16947 Z= 0.285 Chirality : 0.045 0.146 1832 Planarity : 0.005 0.045 2185 Dihedral : 6.247 59.518 1728 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.84 % Allowed : 14.65 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.22), residues: 1501 helix: 1.71 (0.21), residues: 622 sheet: 0.46 (0.34), residues: 216 loop : 0.63 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 433 HIS 0.005 0.001 HIS V 235 PHE 0.019 0.002 PHE V 132 TYR 0.011 0.002 TYR U 379 ARG 0.004 0.000 ARG U 701 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 578) hydrogen bonds : angle 4.31531 ( 1563) covalent geometry : bond 0.00470 (12501) covalent geometry : angle 0.55704 (16947) *********************** 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 162 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 1.469 Fit side-chains revert: symmetry clash REVERT: G 745 LYS cc_start: 0.8205 (mttt) cc_final: 0.7629 (tptp) REVERT: U 22 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8490 (mtt) REVERT: U 36 LYS cc_start: 0.8560 (tttt) cc_final: 0.7864 (mmtt) REVERT: U 224 LYS cc_start: 0.7785 (tttt) cc_final: 0.7576 (tttm) REVERT: U 232 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7390 (mm-40) REVERT: U 275 ASP cc_start: 0.8143 (m-30) cc_final: 0.7826 (m-30) REVERT: U 298 LYS cc_start: 0.8562 (pttt) cc_final: 0.8275 (mttp) REVERT: U 401 ASP cc_start: 0.8050 (t0) cc_final: 0.7672 (t0) REVERT: U 446 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.7690 (tmmm) REVERT: U 695 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8575 (mt) REVERT: V 93 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7579 (mm-30) REVERT: V 210 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8200 (ttp-110) REVERT: V 246 GLN cc_start: 0.8233 (pt0) cc_final: 0.7607 (tp40) REVERT: V 305 MET cc_start: 0.8909 (mmm) cc_final: 0.8526 (mmt) REVERT: W 63 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: W 312 PHE cc_start: 0.8473 (t80) cc_final: 0.8072 (t80) REVERT: X 187 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7808 (mm-30) outliers start: 37 outliers final: 24 residues processed: 151 average time/residue: 1.4668 time to fit residues: 238.3546 Evaluate side-chains 150 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain U residue 22 MET Chi-restraints excluded: chain U residue 60 ARG Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 232 GLN 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 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 358 SER Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 203 THR 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 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 Chi-restraints excluded: chain X residue 178 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 66 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.0570 chunk 76 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 235 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.139370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.115949 restraints weight = 15085.264| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.70 r_work: 0.3315 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12501 Z= 0.102 Angle : 0.493 7.369 16947 Z= 0.254 Chirality : 0.042 0.134 1832 Planarity : 0.004 0.043 2185 Dihedral : 6.003 54.950 1728 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.68 % Allowed : 14.88 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.22), residues: 1501 helix: 1.79 (0.21), residues: 628 sheet: 0.46 (0.34), residues: 218 loop : 0.74 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 735 HIS 0.004 0.001 HIS V 235 PHE 0.012 0.001 PHE U 397 TYR 0.009 0.001 TYR V 69 ARG 0.004 0.000 ARG W 466 Details of bonding type rmsd hydrogen bonds : bond 0.03467 ( 578) hydrogen bonds : angle 4.18307 ( 1563) covalent geometry : bond 0.00228 (12501) covalent geometry : angle 0.49332 (16947) *********************** 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 158 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 1.642 Fit side-chains revert: symmetry clash REVERT: G 745 LYS cc_start: 0.8165 (mttt) cc_final: 0.7608 (tptp) REVERT: U 22 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8416 (mtm) REVERT: U 36 LYS cc_start: 0.8547 (tttt) cc_final: 0.7861 (mmpt) REVERT: U 191 ASN cc_start: 0.6407 (p0) cc_final: 0.5692 (t0) REVERT: U 275 ASP cc_start: 0.8020 (m-30) cc_final: 0.7658 (m-30) REVERT: U 298 LYS cc_start: 0.8539 (pttt) cc_final: 0.8271 (mttp) REVERT: U 401 ASP cc_start: 0.8032 (t0) cc_final: 0.7632 (t0) REVERT: U 446 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.7599 (tmmm) REVERT: U 695 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8528 (mt) REVERT: V 93 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7551 (mm-30) REVERT: V 246 GLN cc_start: 0.8253 (pt0) cc_final: 0.7647 (tp40) REVERT: V 305 MET cc_start: 0.8885 (mmm) cc_final: 0.8455 (mmt) REVERT: W 63 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: W 312 PHE cc_start: 0.8456 (t80) cc_final: 0.8126 (t80) REVERT: X 187 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7696 (mm-30) outliers start: 35 outliers final: 18 residues processed: 149 average time/residue: 1.4205 time to fit residues: 228.3783 Evaluate side-chains 139 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain U residue 22 MET 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 208 ILE 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 246 VAL Chi-restraints excluded: chain W residue 276 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 93 optimal weight: 0.3980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.138101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.114998 restraints weight = 14958.815| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.59 r_work: 0.3299 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12501 Z= 0.135 Angle : 0.520 7.871 16947 Z= 0.266 Chirality : 0.043 0.138 1832 Planarity : 0.004 0.043 2185 Dihedral : 6.038 55.181 1728 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.22), residues: 1501 helix: 1.75 (0.21), residues: 628 sheet: 0.46 (0.34), residues: 216 loop : 0.71 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 340 HIS 0.015 0.001 HIS V 235 PHE 0.015 0.001 PHE U 397 TYR 0.010 0.001 TYR W 304 ARG 0.003 0.000 ARG U 475 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 578) hydrogen bonds : angle 4.19312 ( 1563) covalent geometry : bond 0.00321 (12501) covalent geometry : angle 0.52038 (16947) *********************** 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 154 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 1.558 Fit side-chains revert: symmetry clash REVERT: G 745 LYS cc_start: 0.8172 (mttt) cc_final: 0.7637 (tptp) REVERT: U 22 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8430 (mtm) REVERT: U 36 LYS cc_start: 0.8556 (tttt) cc_final: 0.7878 (mmtt) REVERT: U 181 MET cc_start: 0.7891 (ttm) cc_final: 0.7600 (mtm) REVERT: U 191 ASN cc_start: 0.6374 (p0) cc_final: 0.5666 (t0) REVERT: U 195 LEU cc_start: 0.7332 (mt) cc_final: 0.7114 (mt) REVERT: U 298 LYS cc_start: 0.8579 (pttt) cc_final: 0.8324 (mttp) REVERT: U 401 ASP cc_start: 0.8070 (t0) cc_final: 0.7661 (t0) REVERT: U 446 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.7708 (tmmm) REVERT: U 695 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8548 (mt) REVERT: V 93 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7572 (mm-30) REVERT: V 246 GLN cc_start: 0.8265 (pt0) cc_final: 0.7676 (tp40) REVERT: V 305 MET cc_start: 0.8903 (mmm) cc_final: 0.8494 (mmt) REVERT: W 63 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6719 (mp0) REVERT: W 312 PHE cc_start: 0.8481 (t80) cc_final: 0.8156 (t80) REVERT: X 187 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7776 (mm-30) outliers start: 32 outliers final: 20 residues processed: 144 average time/residue: 1.4974 time to fit residues: 234.5556 Evaluate side-chains 142 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain U residue 22 MET Chi-restraints excluded: chain U residue 60 ARG 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 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 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 246 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 46 optimal weight: 0.0470 chunk 89 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 63 optimal weight: 0.0970 chunk 126 optimal weight: 0.0470 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 103 optimal weight: 0.2980 chunk 90 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.141336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.118017 restraints weight = 14888.873| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.69 r_work: 0.3342 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12501 Z= 0.090 Angle : 0.481 7.427 16947 Z= 0.246 Chirality : 0.041 0.131 1832 Planarity : 0.004 0.044 2185 Dihedral : 5.781 50.271 1728 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.46 % Allowed : 16.41 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.22), residues: 1501 helix: 1.93 (0.21), residues: 628 sheet: 0.63 (0.35), residues: 214 loop : 0.84 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 170 HIS 0.010 0.001 HIS V 235 PHE 0.010 0.001 PHE W 249 TYR 0.008 0.001 TYR V 69 ARG 0.002 0.000 ARG U 475 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 578) hydrogen bonds : angle 4.07307 ( 1563) covalent geometry : bond 0.00194 (12501) covalent geometry : angle 0.48116 (16947) ********************** 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 147 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 745 LYS cc_start: 0.8162 (mttt) cc_final: 0.7610 (tptp) REVERT: U 36 LYS cc_start: 0.8537 (tttt) cc_final: 0.7873 (mmpt) REVERT: U 181 MET cc_start: 0.7829 (ttm) cc_final: 0.7554 (mtm) REVERT: U 191 ASN cc_start: 0.6209 (p0) cc_final: 0.5805 (t0) REVERT: U 298 LYS cc_start: 0.8547 (pttt) cc_final: 0.8295 (mttp) REVERT: U 401 ASP cc_start: 0.8048 (t0) cc_final: 0.7637 (t0) REVERT: U 446 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.7553 (tmmm) REVERT: U 695 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8516 (mt) REVERT: V 93 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7579 (mm-30) REVERT: V 246 GLN cc_start: 0.8197 (pt0) cc_final: 0.7632 (tp40) REVERT: V 305 MET cc_start: 0.8860 (mmm) cc_final: 0.8412 (mmt) REVERT: W 63 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6377 (mp0) REVERT: W 312 PHE cc_start: 0.8398 (t80) cc_final: 0.8118 (t80) REVERT: X 187 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7761 (mm-30) outliers start: 19 outliers final: 7 residues processed: 140 average time/residue: 1.4316 time to fit residues: 216.1475 Evaluate side-chains 130 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 V residue 179 ASP Chi-restraints excluded: chain V residue 195 GLU Chi-restraints excluded: chain V residue 358 SER Chi-restraints excluded: chain W residue 63 GLU 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 90 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.138598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115199 restraints weight = 15141.022| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.70 r_work: 0.3309 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3216 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= 0.138 Angle : 0.521 7.809 16947 Z= 0.265 Chirality : 0.043 0.138 1832 Planarity : 0.005 0.086 2185 Dihedral : 5.935 54.530 1728 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.46 % Allowed : 16.87 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.22), residues: 1501 helix: 1.87 (0.21), residues: 628 sheet: 0.54 (0.35), residues: 214 loop : 0.79 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 340 HIS 0.016 0.001 HIS V 235 PHE 0.015 0.001 PHE U 397 TYR 0.009 0.001 TYR U 379 ARG 0.003 0.000 ARG U 475 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 578) hydrogen bonds : angle 4.12322 ( 1563) covalent geometry : bond 0.00330 (12501) covalent geometry : angle 0.52087 (16947) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8700.58 seconds wall clock time: 150 minutes 16.20 seconds (9016.20 seconds total)