Starting phenix.real_space_refine on Wed Jul 30 12:49:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a5d_15165/07_2025/8a5d_15165_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a5d_15165/07_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_15165/07_2025/8a5d_15165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a5d_15165/07_2025/8a5d_15165.map" model { file = "/net/cci-nas-00/data/ceres_data/8a5d_15165/07_2025/8a5d_15165_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a5d_15165/07_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-5711/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: 7.04, 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: 2.72 Conformation dependent library (CDL) restraints added in 1.5 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: 1.71 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: 3.80 Time building geometry restraints manager: 3.25 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: 0.720 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: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.750 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.510 ------------------------------------------------------------------------------- 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 : 1.356 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: 1.5583 time to fit residues: 405.3259 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 : 1.470 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.116879 restraints weight = 14794.152| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.63 r_work: 0.3320 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 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 : 1.468 Fit side-chains revert: symmetry clash REVERT: G 733 GLN cc_start: 0.7453 (tt0) cc_final: 0.7158 (tt0) REVERT: G 748 ARG cc_start: 0.8265 (ttm170) cc_final: 0.8041 (ttp-110) REVERT: G 777 LEU cc_start: 0.8963 (mp) cc_final: 0.8656 (mp) REVERT: U 36 LYS cc_start: 0.8633 (tttt) cc_final: 0.8002 (mmpt) REVERT: U 41 ASP cc_start: 0.8250 (t70) cc_final: 0.7549 (t0) REVERT: U 56 ASN cc_start: 0.7768 (m-40) cc_final: 0.7376 (m-40) REVERT: U 160 GLN cc_start: 0.7721 (mt0) cc_final: 0.7461 (tm-30) REVERT: U 224 LYS cc_start: 0.7818 (tttt) cc_final: 0.7593 (tmtt) REVERT: U 250 LYS cc_start: 0.8428 (tttt) cc_final: 0.8224 (tttm) REVERT: U 275 ASP cc_start: 0.7819 (m-30) cc_final: 0.7439 (m-30) REVERT: U 292 THR cc_start: 0.8935 (m) cc_final: 0.8709 (p) REVERT: U 298 LYS cc_start: 0.8439 (pttt) cc_final: 0.8181 (mttp) REVERT: U 437 LEU cc_start: 0.8520 (tp) cc_final: 0.8198 (tt) REVERT: V 72 GLU cc_start: 0.8301 (tt0) cc_final: 0.8033 (mt-10) REVERT: V 93 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7592 (mm-30) REVERT: V 210 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7924 (ttp-110) REVERT: V 246 GLN cc_start: 0.8177 (pt0) cc_final: 0.7463 (tp40) REVERT: V 325 MET cc_start: 0.8154 (mmt) cc_final: 0.7951 (mmm) REVERT: W 63 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: W 77 MET cc_start: 0.8950 (mmt) cc_final: 0.8655 (mmt) REVERT: W 94 GLU cc_start: 0.8190 (tp30) cc_final: 0.7826 (mt-10) REVERT: W 203 THR cc_start: 0.8864 (m) cc_final: 0.8546 (m) REVERT: W 215 LYS cc_start: 0.8645 (mttt) cc_final: 0.8174 (mtpt) REVERT: W 253 ASN cc_start: 0.7838 (m-40) cc_final: 0.7294 (p0) REVERT: W 264 ASP cc_start: 0.7886 (m-30) cc_final: 0.7683 (t70) outliers start: 20 outliers final: 9 residues processed: 194 average time/residue: 1.4959 time to fit residues: 311.5091 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 : 1.375 ------------------------------------------------------------------------------- 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: 0.8980 chunk 124 optimal weight: 0.0980 chunk 119 optimal weight: 4.9990 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: 1.9990 chunk 145 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3712 r_free = 0.3712 target = 0.137248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113930 restraints weight = 15066.835| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.68 r_work: 0.3284 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12501 Z= 0.170 Angle : 0.584 9.128 16947 Z= 0.305 Chirality : 0.045 0.152 1832 Planarity : 0.005 0.045 2185 Dihedral : 6.808 62.593 1728 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.22 % Allowed : 11.66 % Favored : 85.12 % 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: 1.47 (0.22), residues: 1501 helix: 1.56 (0.22), residues: 616 sheet: 0.48 (0.33), residues: 215 loop : 0.77 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 735 HIS 0.007 0.001 HIS V 235 PHE 0.025 0.002 PHE U 397 TYR 0.016 0.002 TYR V 69 ARG 0.005 0.001 ARG G 774 Details of bonding type rmsd hydrogen bonds : bond 0.04605 ( 578) hydrogen bonds : angle 4.57023 ( 1563) covalent geometry : bond 0.00409 (12501) covalent geometry : angle 0.58404 (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 189 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 1.395 Fit side-chains REVERT: G 733 GLN cc_start: 0.7342 (tt0) cc_final: 0.7108 (tt0) REVERT: U 36 LYS cc_start: 0.8547 (tttt) cc_final: 0.7903 (mmpt) REVERT: U 127 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8118 (mtmt) REVERT: U 159 GLU cc_start: 0.6712 (tm-30) cc_final: 0.6496 (tm-30) REVERT: U 193 LYS cc_start: 0.7043 (mmpt) cc_final: 0.6434 (mmmt) REVERT: U 224 LYS cc_start: 0.7883 (tttt) cc_final: 0.7643 (tttt) REVERT: U 298 LYS cc_start: 0.8520 (pttt) cc_final: 0.8252 (mttp) REVERT: U 437 LEU cc_start: 0.8488 (tp) cc_final: 0.8224 (tt) REVERT: U 695 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8564 (mt) REVERT: V 93 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7539 (mm-30) REVERT: V 210 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8043 (ttp-110) REVERT: V 246 GLN cc_start: 0.8076 (pt0) cc_final: 0.7439 (tp40) REVERT: V 305 MET cc_start: 0.9051 (mmm) cc_final: 0.8688 (mmt) REVERT: W 63 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6572 (mp0) REVERT: W 77 MET cc_start: 0.8975 (mmt) cc_final: 0.8763 (mmt) REVERT: W 203 THR cc_start: 0.8852 (m) cc_final: 0.8548 (m) REVERT: W 215 LYS cc_start: 0.8730 (mttt) cc_final: 0.8278 (mtpt) REVERT: W 284 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7588 (mt-10) REVERT: W 465 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7257 (mmmt) outliers start: 42 outliers final: 18 residues processed: 175 average time/residue: 1.5220 time to fit residues: 285.5279 Evaluate side-chains 154 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 1.515 ------------------------------------------------------------------------------- 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 401 ASP Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 685 ILE Chi-restraints excluded: chain U residue 692 ASP Chi-restraints excluded: chain U residue 695 LEU Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 210 ARG Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain V residue 288 ASP Chi-restraints excluded: chain V residue 358 SER Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 246 VAL Chi-restraints excluded: chain W residue 276 ASP Chi-restraints excluded: chain W residue 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: 2.9990 chunk 109 optimal weight: 0.0870 chunk 8 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 100 optimal weight: 0.0970 chunk 98 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 144 optimal weight: 0.7980 chunk 50 optimal weight: 0.1980 chunk 105 optimal weight: 0.9980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 776 GLN U 114 GLN ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.140445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.117750 restraints weight = 14846.802| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.58 r_work: 0.3329 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12501 Z= 0.100 Angle : 0.508 7.131 16947 Z= 0.265 Chirality : 0.042 0.140 1832 Planarity : 0.004 0.047 2185 Dihedral : 6.297 59.306 1728 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.61 % Allowed : 13.19 % 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: 1.66 (0.22), residues: 1501 helix: 1.73 (0.22), residues: 628 sheet: 0.63 (0.34), residues: 211 loop : 0.83 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 254 HIS 0.004 0.001 HIS V 87 PHE 0.019 0.001 PHE U 397 TYR 0.013 0.001 TYR V 69 ARG 0.004 0.000 ARG U 117 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 578) hydrogen bonds : angle 4.32068 ( 1563) covalent geometry : bond 0.00211 (12501) covalent geometry : angle 0.50841 (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 176 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 3.124 Fit side-chains revert: symmetry clash REVERT: G 745 LYS cc_start: 0.8099 (mttt) cc_final: 0.7544 (tptp) REVERT: U 36 LYS cc_start: 0.8539 (tttt) cc_final: 0.7876 (mmtt) REVERT: U 159 GLU cc_start: 0.6528 (tm-30) cc_final: 0.6273 (tm-30) REVERT: U 224 LYS cc_start: 0.7877 (tttt) cc_final: 0.7628 (tttm) REVERT: U 275 ASP cc_start: 0.7869 (m-30) cc_final: 0.7549 (m-30) REVERT: U 298 LYS cc_start: 0.8484 (pttt) cc_final: 0.8226 (mttp) REVERT: U 446 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.7545 (tmmm) REVERT: V 93 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7499 (mm-30) REVERT: V 210 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8161 (ttp-110) REVERT: V 246 GLN cc_start: 0.8211 (pt0) cc_final: 0.7666 (tp40) REVERT: V 305 MET cc_start: 0.8948 (mmm) cc_final: 0.8500 (mmt) REVERT: W 63 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6503 (mp0) REVERT: W 77 MET cc_start: 0.8919 (mmt) cc_final: 0.8708 (mmt) REVERT: W 215 LYS cc_start: 0.8743 (mttt) cc_final: 0.8272 (mtpt) REVERT: W 312 PHE cc_start: 0.8459 (t80) cc_final: 0.8050 (t80) REVERT: X 187 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7555 (mm-30) outliers start: 34 outliers final: 10 residues processed: 164 average time/residue: 1.6218 time to fit residues: 285.1916 Evaluate side-chains 143 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 699 SER Chi-restraints excluded: chain V residue 83 GLU 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 358 SER Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 320 VAL 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: 8.9990 chunk 84 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 776 GLN U 110 HIS ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.138610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115167 restraints weight = 14963.649| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.65 r_work: 0.3288 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12501 Z= 0.153 Angle : 0.535 8.063 16947 Z= 0.276 Chirality : 0.044 0.152 1832 Planarity : 0.004 0.044 2185 Dihedral : 6.275 61.168 1728 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.68 % Allowed : 14.11 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.74 (0.21), residues: 628 sheet: 0.48 (0.34), residues: 216 loop : 0.76 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 0.003 0.000 ARG U 701 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 578) hydrogen bonds : angle 4.32560 ( 1563) covalent geometry : bond 0.00369 (12501) covalent geometry : angle 0.53488 (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 164 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 1.580 Fit side-chains revert: symmetry clash REVERT: G 745 LYS cc_start: 0.8181 (mttt) cc_final: 0.7637 (tptp) REVERT: U 36 LYS cc_start: 0.8565 (tttt) cc_final: 0.7867 (mmtt) REVERT: U 159 GLU cc_start: 0.6681 (tm-30) cc_final: 0.6443 (tm-30) REVERT: U 224 LYS cc_start: 0.7891 (tttt) cc_final: 0.7609 (tttm) REVERT: U 275 ASP cc_start: 0.8070 (m-30) cc_final: 0.7728 (m-30) REVERT: U 298 LYS cc_start: 0.8536 (pttt) cc_final: 0.8262 (mttp) REVERT: U 446 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.7661 (tmmm) REVERT: U 695 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8547 (mt) REVERT: V 93 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7537 (mm-30) REVERT: V 210 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8171 (ttp-110) REVERT: V 246 GLN cc_start: 0.8373 (pt0) cc_final: 0.7621 (tp40) REVERT: V 305 MET cc_start: 0.8944 (mmm) cc_final: 0.8542 (mmt) REVERT: W 63 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6648 (mp0) REVERT: W 77 MET cc_start: 0.8942 (mmt) cc_final: 0.8707 (mmt) REVERT: W 215 LYS cc_start: 0.8860 (mttt) cc_final: 0.8349 (mtpt) REVERT: W 253 ASN cc_start: 0.7975 (m-40) cc_final: 0.7768 (m-40) REVERT: W 310 GLU cc_start: 0.8166 (tt0) cc_final: 0.7951 (tt0) REVERT: W 312 PHE cc_start: 0.8490 (t80) cc_final: 0.8107 (t80) REVERT: X 187 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7746 (mm-30) outliers start: 35 outliers final: 20 residues processed: 150 average time/residue: 1.5825 time to fit residues: 255.1460 Evaluate side-chains 148 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 60 ARG Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 695 LEU Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 111 ASN Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 45 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.138331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114472 restraints weight = 15198.927| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.72 r_work: 0.3285 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12501 Z= 0.151 Angle : 0.531 7.944 16947 Z= 0.274 Chirality : 0.043 0.143 1832 Planarity : 0.004 0.045 2185 Dihedral : 6.258 59.767 1728 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.14 % Allowed : 13.80 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.51 (0.22), residues: 1501 helix: 1.73 (0.21), residues: 622 sheet: 0.45 (0.34), residues: 216 loop : 0.65 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 340 HIS 0.004 0.001 HIS V 235 PHE 0.018 0.001 PHE U 397 TYR 0.011 0.001 TYR V 69 ARG 0.004 0.000 ARG U 117 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 578) hydrogen bonds : angle 4.30121 ( 1563) covalent geometry : bond 0.00361 (12501) covalent geometry : angle 0.53075 (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 172 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 1.398 Fit side-chains revert: symmetry clash REVERT: G 745 LYS cc_start: 0.8180 (mttt) cc_final: 0.7629 (tptp) REVERT: G 771 GLU cc_start: 0.7734 (mp0) cc_final: 0.7438 (mm-30) REVERT: U 36 LYS cc_start: 0.8557 (tttt) cc_final: 0.7860 (mmtt) REVERT: U 101 MET cc_start: 0.6422 (OUTLIER) cc_final: 0.6059 (mtt) REVERT: U 127 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8015 (mtmt) REVERT: U 191 ASN cc_start: 0.6278 (p0) cc_final: 0.5496 (t0) REVERT: U 232 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7473 (mt0) REVERT: U 275 ASP cc_start: 0.8121 (m-30) cc_final: 0.7777 (m-30) REVERT: U 298 LYS cc_start: 0.8529 (pttt) cc_final: 0.8251 (mttp) REVERT: U 446 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7683 (tmmm) REVERT: U 695 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8561 (mt) REVERT: V 93 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7569 (mm-30) REVERT: V 210 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8175 (ttp-110) REVERT: V 246 GLN cc_start: 0.8234 (pt0) cc_final: 0.7641 (tp40) REVERT: V 305 MET cc_start: 0.8940 (mmm) cc_final: 0.8563 (mmt) REVERT: W 63 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: W 77 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8682 (mmt) REVERT: W 215 LYS cc_start: 0.8899 (mttt) cc_final: 0.8391 (mtpt) REVERT: W 253 ASN cc_start: 0.8080 (m-40) cc_final: 0.7879 (m-40) REVERT: W 312 PHE cc_start: 0.8489 (t80) cc_final: 0.8105 (t80) REVERT: X 187 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7788 (mm-30) outliers start: 41 outliers final: 22 residues processed: 156 average time/residue: 1.5307 time to fit residues: 256.2591 Evaluate side-chains 152 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain U residue 101 MET Chi-restraints excluded: chain U residue 127 LYS Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 232 GLN Chi-restraints excluded: chain U residue 233 LYS Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 494 ASP Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 695 LEU Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 111 ASN Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 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 77 MET Chi-restraints excluded: chain W residue 163 ILE Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 246 VAL Chi-restraints excluded: chain W residue 276 ASP Chi-restraints excluded: chain W residue 284 GLU Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 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: 0.8980 chunk 21 optimal weight: 0.9990 chunk 130 optimal weight: 0.0980 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 24 GLN ** 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 = 0.139304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.116053 restraints weight = 14961.454| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.64 r_work: 0.3312 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12501 Z= 0.106 Angle : 0.499 7.372 16947 Z= 0.256 Chirality : 0.042 0.135 1832 Planarity : 0.004 0.044 2185 Dihedral : 6.043 56.621 1728 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.53 % Allowed : 15.26 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.79 (0.21), residues: 628 sheet: 0.50 (0.34), residues: 218 loop : 0.74 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 186 HIS 0.003 0.001 HIS V 87 PHE 0.013 0.001 PHE U 397 TYR 0.011 0.001 TYR W 304 ARG 0.004 0.000 ARG W 466 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 578) hydrogen bonds : angle 4.17976 ( 1563) covalent geometry : bond 0.00237 (12501) covalent geometry : angle 0.49889 (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 158 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 745 LYS cc_start: 0.8129 (mttt) cc_final: 0.7617 (tptp) REVERT: G 771 GLU cc_start: 0.7660 (mp0) cc_final: 0.7375 (mm-30) REVERT: U 22 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8454 (mtt) REVERT: U 36 LYS cc_start: 0.8559 (tttt) cc_final: 0.7874 (mmpt) REVERT: U 181 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7196 (mtp) REVERT: U 191 ASN cc_start: 0.6258 (p0) cc_final: 0.5647 (t0) REVERT: U 275 ASP cc_start: 0.8022 (m-30) cc_final: 0.7664 (m-30) REVERT: U 298 LYS cc_start: 0.8522 (pttt) cc_final: 0.8260 (mttp) REVERT: U 446 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7656 (tmmm) REVERT: U 695 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8542 (mt) REVERT: V 93 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7550 (mm-30) REVERT: V 210 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8250 (ttp-170) REVERT: V 246 GLN cc_start: 0.8255 (pt0) cc_final: 0.7659 (tp40) REVERT: V 305 MET cc_start: 0.8891 (mmm) cc_final: 0.8461 (mmt) REVERT: W 63 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6709 (mp0) REVERT: W 77 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8648 (mmt) REVERT: W 253 ASN cc_start: 0.8003 (m-40) cc_final: 0.7765 (m-40) REVERT: W 266 ARG cc_start: 0.7418 (ptp-110) cc_final: 0.7124 (pmm150) REVERT: W 312 PHE cc_start: 0.8462 (t80) cc_final: 0.8102 (t80) REVERT: X 187 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7759 (mm-30) outliers start: 33 outliers final: 17 residues processed: 149 average time/residue: 1.5001 time to fit residues: 239.7999 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 : 1.381 ------------------------------------------------------------------------------- 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 181 MET Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 695 LEU Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 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 235 HIS Chi-restraints excluded: chain V residue 358 SER Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 77 MET Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 246 VAL Chi-restraints excluded: chain W residue 276 ASP Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 426 SER Chi-restraints excluded: chain X residue 172 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.139045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.115779 restraints weight = 15106.675| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.66 r_work: 0.3320 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3089 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= 0.115 Angle : 0.507 7.776 16947 Z= 0.258 Chirality : 0.042 0.136 1832 Planarity : 0.004 0.044 2185 Dihedral : 5.988 55.185 1728 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.68 % Allowed : 15.18 % 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: 1.64 (0.22), residues: 1501 helix: 1.81 (0.21), residues: 628 sheet: 0.50 (0.34), residues: 218 loop : 0.75 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 340 HIS 0.004 0.001 HIS V 87 PHE 0.014 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 0.03532 ( 578) hydrogen bonds : angle 4.16147 ( 1563) covalent geometry : bond 0.00267 (12501) covalent geometry : angle 0.50663 (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 155 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 1.663 Fit side-chains revert: symmetry clash REVERT: G 745 LYS cc_start: 0.8147 (mttt) cc_final: 0.7630 (tptp) REVERT: G 771 GLU cc_start: 0.7650 (mp0) cc_final: 0.7343 (mm-30) REVERT: U 22 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8431 (mtm) REVERT: U 36 LYS cc_start: 0.8548 (tttt) cc_final: 0.7873 (mmpt) REVERT: U 101 MET cc_start: 0.6392 (OUTLIER) cc_final: 0.6050 (mtt) REVERT: U 159 GLU cc_start: 0.6670 (tp30) cc_final: 0.6348 (tp30) REVERT: U 181 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7262 (mtp) REVERT: U 191 ASN cc_start: 0.6200 (p0) cc_final: 0.5666 (t0) REVERT: U 275 ASP cc_start: 0.7930 (m-30) cc_final: 0.7551 (m-30) REVERT: U 298 LYS cc_start: 0.8511 (pttt) cc_final: 0.8262 (mttp) REVERT: U 446 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.7620 (tmmm) REVERT: U 695 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8536 (mt) REVERT: V 93 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7534 (mm-30) REVERT: V 246 GLN cc_start: 0.8243 (pt0) cc_final: 0.7669 (tp40) REVERT: V 305 MET cc_start: 0.8882 (mmm) cc_final: 0.8482 (mmt) REVERT: W 63 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6766 (mp0) REVERT: W 253 ASN cc_start: 0.8000 (m-40) cc_final: 0.7769 (m-40) REVERT: W 266 ARG cc_start: 0.7356 (ptp-110) cc_final: 0.7111 (pmm150) REVERT: W 312 PHE cc_start: 0.8467 (t80) cc_final: 0.8126 (t80) REVERT: X 187 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7710 (mm-30) outliers start: 35 outliers final: 15 residues processed: 146 average time/residue: 1.9699 time to fit residues: 309.2703 Evaluate side-chains 138 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 2.357 ------------------------------------------------------------------------------- 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 101 MET Chi-restraints excluded: chain U residue 181 MET Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 695 LEU Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 111 ASN Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 135 SER Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.139043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.115690 restraints weight = 14910.222| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.67 r_work: 0.3306 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12501 Z= 0.120 Angle : 0.517 8.183 16947 Z= 0.262 Chirality : 0.042 0.137 1832 Planarity : 0.004 0.045 2185 Dihedral : 5.974 54.074 1728 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.15 % Allowed : 15.80 % Favored : 82.06 % 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: 1.67 (0.22), residues: 1501 helix: 1.80 (0.21), residues: 628 sheet: 0.56 (0.35), residues: 214 loop : 0.79 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 340 HIS 0.004 0.001 HIS V 87 PHE 0.014 0.001 PHE U 397 TYR 0.009 0.001 TYR U 267 ARG 0.004 0.000 ARG W 466 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 578) hydrogen bonds : angle 4.16103 ( 1563) covalent geometry : bond 0.00281 (12501) covalent geometry : angle 0.51738 (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 156 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 1.473 Fit side-chains revert: symmetry clash REVERT: G 745 LYS cc_start: 0.8175 (mttt) cc_final: 0.7641 (tptp) REVERT: U 22 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8425 (mtm) REVERT: U 36 LYS cc_start: 0.8556 (tttt) cc_final: 0.7868 (mmtt) REVERT: U 181 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7466 (mtp) REVERT: U 191 ASN cc_start: 0.6342 (p0) cc_final: 0.5891 (t0) REVERT: U 298 LYS cc_start: 0.8528 (pttt) cc_final: 0.8268 (mttp) REVERT: U 401 ASP cc_start: 0.8089 (t0) cc_final: 0.7819 (t0) REVERT: U 446 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.7637 (tmmm) REVERT: U 695 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8548 (mt) REVERT: V 56 ASP cc_start: 0.7667 (p0) cc_final: 0.7337 (m-30) REVERT: V 83 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: V 93 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7583 (mm-30) REVERT: V 246 GLN cc_start: 0.8265 (pt0) cc_final: 0.7662 (tp40) REVERT: V 305 MET cc_start: 0.8885 (mmm) cc_final: 0.8488 (mmt) REVERT: W 63 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: W 253 ASN cc_start: 0.8035 (m-40) cc_final: 0.7787 (m-40) REVERT: W 266 ARG cc_start: 0.7334 (ptp-110) cc_final: 0.7126 (pmm150) REVERT: W 312 PHE cc_start: 0.8467 (t80) cc_final: 0.8150 (t80) REVERT: X 187 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7772 (mm-30) outliers start: 28 outliers final: 15 residues processed: 148 average time/residue: 1.5331 time to fit residues: 246.2074 Evaluate side-chains 143 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 1.561 ------------------------------------------------------------------------------- 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 181 MET 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 135 SER Chi-restraints excluded: chain V residue 179 ASP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 46 optimal weight: 0.1980 chunk 89 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.139489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.116271 restraints weight = 14894.521| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.65 r_work: 0.3318 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12501 Z= 0.112 Angle : 0.516 7.759 16947 Z= 0.261 Chirality : 0.042 0.136 1832 Planarity : 0.004 0.047 2185 Dihedral : 5.927 53.361 1728 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.84 % Allowed : 16.26 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.73 (0.22), residues: 1501 helix: 1.85 (0.21), residues: 628 sheet: 0.56 (0.35), residues: 214 loop : 0.83 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 79 HIS 0.004 0.001 HIS V 87 PHE 0.013 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 0.03417 ( 578) hydrogen bonds : angle 4.12393 ( 1563) covalent geometry : bond 0.00261 (12501) covalent geometry : angle 0.51614 (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 148 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.525 Fit side-chains revert: symmetry clash REVERT: G 745 LYS cc_start: 0.8161 (mttt) cc_final: 0.7625 (tptp) REVERT: U 36 LYS cc_start: 0.8529 (tttt) cc_final: 0.7866 (mmtt) REVERT: U 101 MET cc_start: 0.6171 (OUTLIER) cc_final: 0.5728 (mtm) REVERT: U 181 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7555 (mtp) REVERT: U 191 ASN cc_start: 0.6312 (p0) cc_final: 0.5882 (t0) REVERT: U 298 LYS cc_start: 0.8522 (pttt) cc_final: 0.8265 (mttp) REVERT: U 401 ASP cc_start: 0.8049 (t0) cc_final: 0.7753 (t0) REVERT: U 446 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.7625 (tmmm) REVERT: U 695 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8538 (mt) REVERT: V 56 ASP cc_start: 0.7718 (p0) cc_final: 0.7390 (m-30) REVERT: V 93 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7582 (mm-30) REVERT: V 246 GLN cc_start: 0.8257 (pt0) cc_final: 0.7670 (tp40) REVERT: V 305 MET cc_start: 0.8878 (mmm) cc_final: 0.8474 (mmt) REVERT: W 63 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6464 (mp0) REVERT: W 253 ASN cc_start: 0.8016 (m-40) cc_final: 0.7774 (m-40) REVERT: W 266 ARG cc_start: 0.7323 (ptp-110) cc_final: 0.7120 (pmm150) REVERT: W 312 PHE cc_start: 0.8461 (t80) cc_final: 0.8138 (t80) REVERT: X 187 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7745 (mm-30) outliers start: 24 outliers final: 14 residues processed: 141 average time/residue: 1.5598 time to fit residues: 236.1938 Evaluate side-chains 139 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain U residue 101 MET Chi-restraints excluded: chain U residue 181 MET Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 695 LEU Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 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 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=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: 4.9990 chunk 63 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 133 optimal weight: 3.9990 chunk 134 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.136963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113433 restraints weight = 15172.275| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.68 r_work: 0.3275 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12501 Z= 0.179 Angle : 0.569 8.768 16947 Z= 0.288 Chirality : 0.044 0.142 1832 Planarity : 0.005 0.085 2185 Dihedral : 6.199 56.863 1728 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.15 % Allowed : 16.18 % 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: 1.54 (0.22), residues: 1501 helix: 1.77 (0.21), residues: 622 sheet: 0.41 (0.34), residues: 214 loop : 0.68 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 433 HIS 0.003 0.001 HIS U 674 PHE 0.018 0.002 PHE V 132 TYR 0.010 0.002 TYR U 379 ARG 0.003 0.000 ARG W 466 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 578) hydrogen bonds : angle 4.23956 ( 1563) covalent geometry : bond 0.00437 (12501) covalent geometry : angle 0.56857 (16947) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9273.98 seconds wall clock time: 160 minutes 58.27 seconds (9658.27 seconds total)