Starting phenix.real_space_refine on Mon Dec 30 05:58:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a5d_15165/12_2024/8a5d_15165_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a5d_15165/12_2024/8a5d_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_15165/12_2024/8a5d_15165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a5d_15165/12_2024/8a5d_15165.map" model { file = "/net/cci-nas-00/data/ceres_data/8a5d_15165/12_2024/8a5d_15165_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a5d_15165/12_2024/8a5d_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 7.26, per 1000 atoms: 0.59 Number of scatterers: 12222 At special positions: 0 Unit cell: (85.779, 105.9, 160.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 64 16.00 P 9 15.00 Mg 3 11.99 O 2288 8.00 N 2139 7.00 C 7719 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.8 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: 2.06 Creating SS restraints... Processing helix chain 'G' and resid 724 through 741 Processing helix chain 'G' and resid 741 through 775 removed outlier: 3.564A pdb=" N LYS G 773 " --> pdb=" O SER G 769 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TRP G 775 " --> pdb=" O GLU G 771 " (cutoff:3.500A) Processing helix chain 'G' and resid 779 through 808 removed outlier: 3.955A pdb=" N ARG G 806 " --> pdb=" O LYS G 802 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 14 Processing helix chain 'U' and resid 45 through 48 Processing helix chain 'U' and resid 49 through 64 Processing helix chain 'U' and resid 102 through 104 No H-bonds generated for 'chain 'U' and resid 102 through 104' Processing helix chain 'U' and resid 157 through 163 Processing helix chain 'U' and resid 163 through 184 Processing helix chain 'U' and resid 191 through 202 Processing helix chain 'U' and resid 237 through 242 Processing helix chain 'U' and resid 264 through 267 Processing helix chain 'U' and resid 269 through 288 Processing helix chain 'U' and resid 293 through 300 removed outlier: 4.292A pdb=" N LYS U 298 " --> pdb=" O ALA U 295 " (cutoff:3.500A) Processing helix chain 'U' and resid 311 through 325 Processing helix chain 'U' and resid 336 through 345 Processing helix chain 'U' and resid 371 through 374 removed outlier: 3.845A pdb=" N ARG U 374 " --> pdb=" O GLU U 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 371 through 374' Processing helix chain 'U' and resid 380 through 395 removed outlier: 3.542A pdb=" N VAL U 384 " --> pdb=" O GLY U 380 " (cutoff:3.500A) Processing helix chain 'U' and resid 406 through 421 Processing helix chain 'U' and resid 424 through 428 Processing helix chain 'U' and resid 453 through 461 Proline residue: U 459 - end of helix Processing helix chain 'U' and resid 462 through 468 Proline residue: U 465 - end of helix Processing helix chain 'U' and resid 498 through 509 removed outlier: 3.509A pdb=" N VAL U 508 " --> pdb=" O ILE U 504 " (cutoff:3.500A) Processing helix chain 'U' and resid 620 through 629 Processing helix chain 'U' and resid 636 through 650 Processing helix chain 'U' and resid 652 through 661 Processing helix chain 'U' and resid 667 through 672 removed outlier: 4.035A pdb=" N ILE U 672 " --> pdb=" O GLY U 669 " (cutoff:3.500A) Processing helix chain 'U' and resid 674 through 687 Processing helix chain 'U' and resid 707 through 719 Processing helix chain 'U' and resid 728 through 735 Processing helix chain 'U' and resid 736 through 743 removed outlier: 4.057A pdb=" N TYR U 740 " --> pdb=" O SER U 736 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET U 741 " --> pdb=" O ARG U 737 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 61 Processing helix chain 'V' and resid 78 through 92 Processing helix chain 'V' and resid 97 through 101 Processing helix chain 'V' and resid 112 through 126 removed outlier: 3.604A pdb=" N ARG V 116 " --> pdb=" O PRO V 112 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE V 124 " --> pdb=" O THR V 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 137 through 145 Processing helix chain 'V' and resid 172 through 175 Processing helix chain 'V' and resid 181 through 196 Processing helix chain 'V' and resid 202 through 217 removed outlier: 3.546A pdb=" N CYS V 217 " --> pdb=" O LYS V 213 " (cutoff:3.500A) Processing helix chain 'V' and resid 222 through 230 Processing helix chain 'V' and resid 252 through 260 Proline residue: V 258 - end of helix Processing helix chain 'V' and resid 261 through 262 No H-bonds generated for 'chain 'V' and resid 261 through 262' Processing helix chain 'V' and resid 263 through 268 Processing helix chain 'V' and resid 273 through 283 Processing helix chain 'V' and resid 289 through 295 Processing helix chain 'V' and resid 301 through 305 Processing helix chain 'V' and resid 308 through 321 removed outlier: 3.503A pdb=" N LEU V 320 " --> pdb=" O GLU V 316 " (cutoff:3.500A) Processing helix chain 'V' and resid 334 through 336 No H-bonds generated for 'chain 'V' and resid 334 through 336' Processing helix chain 'V' and resid 337 through 347 Processing helix chain 'V' and resid 348 through 355 removed outlier: 6.363A pdb=" N THR V 351 " --> pdb=" O SER V 348 " (cutoff:3.500A) Processing helix chain 'V' and resid 359 through 366 Processing helix chain 'V' and resid 368 through 374 removed outlier: 4.032A pdb=" N ARG V 372 " --> pdb=" O SER V 368 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 98 Processing helix chain 'W' and resid 155 through 171 removed outlier: 3.620A pdb=" N TRP W 170 " --> pdb=" O VAL W 166 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY W 171 " --> pdb=" O MET W 167 " (cutoff:3.500A) Processing helix chain 'W' and resid 180 through 188 Processing helix chain 'W' and resid 215 through 218 removed outlier: 3.649A pdb=" N ILE W 218 " --> pdb=" O LYS W 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 215 through 218' Processing helix chain 'W' and resid 224 through 239 Processing helix chain 'W' and resid 247 through 249 No H-bonds generated for 'chain 'W' and resid 247 through 249' Processing helix chain 'W' and resid 275 through 294 removed outlier: 3.748A pdb=" N ARG W 285 " --> pdb=" O PHE W 281 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL W 286 " --> pdb=" O GLU W 282 " (cutoff:3.500A) Processing helix chain 'W' and resid 308 through 314 Processing helix chain 'W' and resid 333 through 341 removed outlier: 4.624A pdb=" N ALA W 339 " --> pdb=" O ARG W 335 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY W 341 " --> pdb=" O ARG W 337 " (cutoff:3.500A) Processing helix chain 'W' and resid 360 through 363 Processing helix chain 'W' and resid 364 through 374 Processing helix chain 'W' and resid 375 through 376 No H-bonds generated for 'chain 'W' and resid 375 through 376' Processing helix chain 'W' and resid 377 through 379 No H-bonds generated for 'chain 'W' and resid 377 through 379' Processing helix chain 'W' and resid 380 through 386 Processing helix chain 'W' and resid 392 through 397 Processing helix chain 'W' and resid 399 through 412 Processing helix chain 'W' and resid 431 through 440 Processing helix chain 'W' and resid 441 through 448 removed outlier: 6.511A pdb=" N THR W 444 " --> pdb=" O SER W 441 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN W 447 " --> pdb=" O THR W 444 " (cutoff:3.500A) Processing helix chain 'W' and resid 452 through 457 Processing helix chain 'W' and resid 461 through 466 Processing sheet with id=AA1, first strand: chain 'U' and resid 127 through 130 Processing sheet with id=AA2, first strand: chain 'U' and resid 235 through 236 Processing sheet with id=AA3, first strand: chain 'U' and resid 206 through 207 removed outlier: 5.992A pdb=" N ALA U 439 " --> pdb=" O PRO U 443 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'U' and resid 257 through 258 Processing sheet with id=AA5, first strand: chain 'U' and resid 368 through 369 Processing sheet with id=AA6, first strand: chain 'U' and resid 368 through 369 Processing sheet with id=AA7, first strand: chain 'V' and resid 29 through 32 removed outlier: 6.383A pdb=" N LEU V 8 " --> pdb=" O LEU V 104 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N THR V 106 " --> pdb=" O LEU V 8 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE V 10 " --> pdb=" O THR V 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'V' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'V' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'V' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'V' and resid 169 through 170 removed outlier: 6.205A pdb=" N ILE V 151 " --> pdb=" O VAL V 298 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N SER V 300 " --> pdb=" O ILE V 151 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU V 153 " --> pdb=" O SER V 300 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE V 297 " --> pdb=" O ILE V 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'V' and resid 238 through 241 removed outlier: 3.639A pdb=" N LYS V 238 " --> pdb=" O ILE V 250 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'W' and resid 45 through 48 removed outlier: 6.489A pdb=" N LEU W 24 " --> pdb=" O LEU W 147 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N THR W 149 " --> pdb=" O LEU W 24 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU W 26 " --> pdb=" O THR W 149 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'W' and resid 58 through 59 Processing sheet with id=AB6, first strand: chain 'W' and resid 212 through 213 Processing sheet with id=AB7, first strand: chain 'W' and resid 212 through 213 removed outlier: 6.112A pdb=" N LEU W 194 " --> pdb=" O VAL W 389 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR W 391 " --> pdb=" O LEU W 194 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE W 196 " --> pdb=" O THR W 391 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'W' and resid 251 through 255 removed outlier: 3.669A pdb=" N ASN W 253 " --> pdb=" O ARG W 266 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP W 264 " --> pdb=" O LYS W 255 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'W' and resid 319 through 322 Processing sheet with id=AC1, first strand: chain 'X' and resid 172 through 179 584 hydrogen bonds defined for protein. 1563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.44 Time building geometry restraints manager: 3.80 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 31.400 Find NCS groups from input model: 0.110 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:14.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.180 ------------------------------------------------------------------------------- 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= 1.031 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 *********************** 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 : 1.595 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: 1.6378 time to fit residues: 426.1865 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 : 1.715 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 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= 0.180 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 *********************** 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 : 1.612 Fit side-chains revert: symmetry clash REVERT: G 733 GLN cc_start: 0.7104 (tt0) cc_final: 0.6809 (tt0) REVERT: G 737 ASP cc_start: 0.7950 (m-30) cc_final: 0.7588 (m-30) REVERT: G 748 ARG cc_start: 0.7505 (ttm170) cc_final: 0.6980 (ttp-110) REVERT: G 777 LEU cc_start: 0.8478 (mp) cc_final: 0.8246 (mp) REVERT: G 778 ARG cc_start: 0.7883 (mtt180) cc_final: 0.7677 (mtt180) REVERT: U 19 ASP cc_start: 0.7331 (m-30) cc_final: 0.7103 (p0) REVERT: U 36 LYS cc_start: 0.8204 (tttt) cc_final: 0.7580 (mmpt) REVERT: U 41 ASP cc_start: 0.8211 (t70) cc_final: 0.7698 (t0) REVERT: U 56 ASN cc_start: 0.7004 (m-40) cc_final: 0.6662 (m-40) REVERT: U 60 ARG cc_start: 0.7875 (ttt180) cc_final: 0.7513 (mmt180) REVERT: U 146 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7701 (pt0) REVERT: U 160 GLN cc_start: 0.7668 (mt0) cc_final: 0.7302 (tm-30) REVERT: U 218 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7898 (pm20) REVERT: U 224 LYS cc_start: 0.7057 (tttt) cc_final: 0.6815 (tmtt) REVERT: U 250 LYS cc_start: 0.7819 (tttt) cc_final: 0.7526 (tttm) REVERT: U 266 ASP cc_start: 0.7850 (m-30) cc_final: 0.7595 (t0) REVERT: U 275 ASP cc_start: 0.7238 (m-30) cc_final: 0.7027 (m-30) REVERT: U 292 THR cc_start: 0.8799 (m) cc_final: 0.8553 (p) REVERT: U 298 LYS cc_start: 0.7880 (pttt) cc_final: 0.7553 (mttp) REVERT: U 392 MET cc_start: 0.7922 (mtm) cc_final: 0.7336 (mmm) REVERT: U 401 ASP cc_start: 0.8461 (m-30) cc_final: 0.8066 (t0) REVERT: U 415 GLU cc_start: 0.7244 (tt0) cc_final: 0.6911 (tp30) REVERT: U 437 LEU cc_start: 0.7986 (tp) cc_final: 0.7710 (tt) REVERT: U 657 ARG cc_start: 0.7278 (mmm-85) cc_final: 0.7076 (mmm-85) REVERT: U 702 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8605 (mp0) REVERT: V 72 GLU cc_start: 0.8341 (tt0) cc_final: 0.8000 (mt-10) REVERT: V 93 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7732 (mm-30) REVERT: V 191 LYS cc_start: 0.7514 (tttt) cc_final: 0.7290 (ttpp) REVERT: V 210 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7764 (ttp-110) REVERT: V 241 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7928 (tm-30) REVERT: V 246 GLN cc_start: 0.7969 (pt0) cc_final: 0.6889 (tp40) REVERT: V 270 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7140 (mt-10) REVERT: V 288 ASP cc_start: 0.8316 (m-30) cc_final: 0.8041 (p0) REVERT: V 325 MET cc_start: 0.7928 (mmt) cc_final: 0.7675 (mmm) REVERT: V 358 SER cc_start: 0.8412 (t) cc_final: 0.8167 (p) REVERT: V 360 GLN cc_start: 0.7461 (mt0) cc_final: 0.7124 (mp10) REVERT: W 63 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6344 (mp0) REVERT: W 77 MET cc_start: 0.8306 (mmt) cc_final: 0.8055 (mmt) REVERT: W 94 GLU cc_start: 0.8443 (tp30) cc_final: 0.7636 (mt-10) REVERT: W 105 ARG cc_start: 0.7692 (mtt180) cc_final: 0.7241 (mpt-90) REVERT: W 167 MET cc_start: 0.8555 (mmt) cc_final: 0.8343 (mmt) REVERT: W 203 THR cc_start: 0.8781 (m) cc_final: 0.8466 (m) REVERT: W 215 LYS cc_start: 0.8248 (mttt) cc_final: 0.7801 (mtpt) REVERT: W 253 ASN cc_start: 0.7450 (m-40) cc_final: 0.6599 (p0) REVERT: W 264 ASP cc_start: 0.8179 (m-30) cc_final: 0.7743 (t70) REVERT: W 385 LEU cc_start: 0.8341 (mt) cc_final: 0.8090 (mm) outliers start: 20 outliers final: 9 residues processed: 194 average time/residue: 1.5802 time to fit residues: 328.8515 Evaluate side-chains 162 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 1.563 ------------------------------------------------------------------------------- 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 75 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 0.0370 chunk 92 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12501 Z= 0.295 Angle : 0.593 9.499 16947 Z= 0.310 Chirality : 0.046 0.156 1832 Planarity : 0.005 0.045 2185 Dihedral : 6.848 64.205 1728 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.30 % Allowed : 10.66 % Favored : 86.04 % 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: 1.39 (0.22), residues: 1501 helix: 1.53 (0.21), residues: 615 sheet: 0.44 (0.33), residues: 215 loop : 0.69 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 735 HIS 0.008 0.001 HIS V 235 PHE 0.025 0.002 PHE U 397 TYR 0.016 0.002 TYR V 69 ARG 0.005 0.000 ARG G 774 *********************** 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 201 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 1.600 Fit side-chains revert: symmetry clash REVERT: G 733 GLN cc_start: 0.7085 (tt0) cc_final: 0.6774 (tt0) REVERT: G 737 ASP cc_start: 0.7974 (m-30) cc_final: 0.7556 (m-30) REVERT: G 745 LYS cc_start: 0.6961 (mttt) cc_final: 0.6188 (tptp) REVERT: G 778 ARG cc_start: 0.7936 (mtt180) cc_final: 0.7703 (mtt180) REVERT: G 795 ARG cc_start: 0.7316 (mtt180) cc_final: 0.6996 (mtm110) REVERT: U 17 ARG cc_start: 0.6989 (ptt180) cc_final: 0.6579 (ptm160) REVERT: U 36 LYS cc_start: 0.8133 (tttt) cc_final: 0.7482 (mmpt) REVERT: U 60 ARG cc_start: 0.7902 (ttt180) cc_final: 0.7494 (mmt180) REVERT: U 127 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7638 (mtmt) REVERT: U 146 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7541 (pt0) REVERT: U 160 GLN cc_start: 0.7659 (mt0) cc_final: 0.7398 (tm-30) REVERT: U 193 LYS cc_start: 0.6054 (mmpt) cc_final: 0.5662 (mmmt) REVERT: U 218 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7870 (pm20) REVERT: U 224 LYS cc_start: 0.7026 (tttt) cc_final: 0.6788 (tttt) REVERT: U 266 ASP cc_start: 0.7849 (m-30) cc_final: 0.7597 (t0) REVERT: U 298 LYS cc_start: 0.7912 (pttt) cc_final: 0.7576 (mttp) REVERT: U 392 MET cc_start: 0.8008 (mtm) cc_final: 0.7395 (mmm) REVERT: U 401 ASP cc_start: 0.8445 (m-30) cc_final: 0.7962 (t0) REVERT: U 415 GLU cc_start: 0.7218 (tt0) cc_final: 0.6874 (tp30) REVERT: U 437 LEU cc_start: 0.8016 (tp) cc_final: 0.7739 (tt) REVERT: U 702 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8573 (mp0) REVERT: V 72 GLU cc_start: 0.8302 (tt0) cc_final: 0.7844 (mt-10) REVERT: V 93 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7704 (mm-30) REVERT: V 111 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.7994 (p0) REVERT: V 210 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7785 (ttp-110) REVERT: V 241 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8038 (tm-30) REVERT: V 246 GLN cc_start: 0.7916 (pt0) cc_final: 0.6861 (tp40) REVERT: V 288 ASP cc_start: 0.8354 (m-30) cc_final: 0.8057 (p0) REVERT: V 358 SER cc_start: 0.8630 (t) cc_final: 0.8349 (p) REVERT: V 360 GLN cc_start: 0.7563 (mt0) cc_final: 0.7193 (mp10) REVERT: W 63 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6308 (mp0) REVERT: W 94 GLU cc_start: 0.8501 (tp30) cc_final: 0.8230 (tm-30) REVERT: W 105 ARG cc_start: 0.7812 (mtt180) cc_final: 0.7370 (mpt-90) REVERT: W 203 THR cc_start: 0.8791 (m) cc_final: 0.8487 (m) REVERT: W 215 LYS cc_start: 0.8434 (mttt) cc_final: 0.7978 (mtpt) REVERT: W 264 ASP cc_start: 0.8211 (m-30) cc_final: 0.7868 (t70) REVERT: W 266 ARG cc_start: 0.7276 (ptt90) cc_final: 0.6792 (pmm-80) REVERT: W 385 LEU cc_start: 0.8378 (mt) cc_final: 0.8128 (mm) outliers start: 43 outliers final: 15 residues processed: 187 average time/residue: 1.6106 time to fit residues: 322.7375 Evaluate side-chains 164 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain U residue 127 LYS Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 685 ILE Chi-restraints excluded: chain U residue 692 ASP Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 111 ASN 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 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 325 ASP Chi-restraints excluded: chain W residue 426 SER Chi-restraints excluded: chain X residue 172 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.7980 chunk 102 optimal weight: 0.0470 chunk 70 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 0.0070 chunk 144 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 U 114 GLN ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12501 Z= 0.130 Angle : 0.494 6.853 16947 Z= 0.257 Chirality : 0.041 0.135 1832 Planarity : 0.004 0.047 2185 Dihedral : 6.247 60.049 1728 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.84 % Allowed : 12.73 % Favored : 85.43 % 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: 1.62 (0.22), residues: 1501 helix: 1.71 (0.21), residues: 633 sheet: 0.60 (0.34), residues: 211 loop : 0.79 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 735 HIS 0.004 0.001 HIS V 87 PHE 0.014 0.001 PHE U 397 TYR 0.011 0.001 TYR V 69 ARG 0.004 0.000 ARG U 117 *********************** 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 180 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 1.670 Fit side-chains revert: symmetry clash REVERT: G 733 GLN cc_start: 0.7086 (tt0) cc_final: 0.6785 (tt0) REVERT: G 737 ASP cc_start: 0.7957 (m-30) cc_final: 0.7551 (m-30) REVERT: G 745 LYS cc_start: 0.6931 (mttt) cc_final: 0.6114 (tptp) REVERT: G 795 ARG cc_start: 0.7312 (mtt180) cc_final: 0.6982 (mtm110) REVERT: U 17 ARG cc_start: 0.6805 (ptt180) cc_final: 0.6506 (ptm160) REVERT: U 36 LYS cc_start: 0.8094 (tttt) cc_final: 0.7432 (mmtt) REVERT: U 60 ARG cc_start: 0.7928 (ttt180) cc_final: 0.7506 (mmt180) REVERT: U 146 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7671 (pt0) REVERT: U 160 GLN cc_start: 0.7730 (mt0) cc_final: 0.7339 (tm-30) REVERT: U 193 LYS cc_start: 0.6086 (mmpt) cc_final: 0.5735 (mmmt) REVERT: U 218 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7829 (pm20) REVERT: U 224 LYS cc_start: 0.7114 (tttt) cc_final: 0.6873 (tttm) REVERT: U 266 ASP cc_start: 0.7734 (m-30) cc_final: 0.7525 (t0) REVERT: U 275 ASP cc_start: 0.7362 (m-30) cc_final: 0.7136 (m-30) REVERT: U 298 LYS cc_start: 0.7904 (pttt) cc_final: 0.7575 (mttp) REVERT: U 392 MET cc_start: 0.7917 (mtm) cc_final: 0.7408 (mmm) REVERT: U 401 ASP cc_start: 0.8369 (m-30) cc_final: 0.7869 (t0) REVERT: U 415 GLU cc_start: 0.7131 (tt0) cc_final: 0.6839 (tp30) REVERT: U 446 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7423 (ttmm) REVERT: U 702 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8589 (mp0) REVERT: V 72 GLU cc_start: 0.8280 (tt0) cc_final: 0.7876 (mt-10) REVERT: V 93 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7696 (mm-30) REVERT: V 210 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7914 (ttp-110) REVERT: V 241 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8061 (tm-30) REVERT: V 246 GLN cc_start: 0.8223 (pt0) cc_final: 0.7074 (tp40) REVERT: V 358 SER cc_start: 0.8600 (t) cc_final: 0.8274 (p) REVERT: V 360 GLN cc_start: 0.7504 (mt0) cc_final: 0.7166 (mp10) REVERT: W 63 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6342 (mp0) REVERT: W 94 GLU cc_start: 0.8501 (tp30) cc_final: 0.8235 (tm-30) REVERT: W 105 ARG cc_start: 0.7747 (mtt180) cc_final: 0.7301 (mpt-90) REVERT: W 215 LYS cc_start: 0.8409 (mttt) cc_final: 0.7960 (mtpt) REVERT: W 253 ASN cc_start: 0.7555 (m-40) cc_final: 0.7251 (m-40) REVERT: W 264 ASP cc_start: 0.8106 (m-30) cc_final: 0.7812 (t70) REVERT: W 266 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6684 (ptp-110) REVERT: W 284 GLU cc_start: 0.7278 (mt-10) cc_final: 0.7073 (mp0) REVERT: W 312 PHE cc_start: 0.7603 (t80) cc_final: 0.7265 (t80) REVERT: W 385 LEU cc_start: 0.8314 (mt) cc_final: 0.8085 (mm) REVERT: X 187 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8157 (mm-30) outliers start: 24 outliers final: 6 residues processed: 172 average time/residue: 1.6967 time to fit residues: 312.6458 Evaluate side-chains 151 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 210 ARG Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 266 ARG Chi-restraints excluded: chain W residue 320 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 130 optimal weight: 0.0040 chunk 36 optimal weight: 3.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 776 GLN ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12501 Z= 0.256 Angle : 0.531 8.110 16947 Z= 0.275 Chirality : 0.044 0.153 1832 Planarity : 0.004 0.044 2185 Dihedral : 6.283 61.606 1728 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.38 % Allowed : 13.42 % 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: 1.55 (0.22), residues: 1501 helix: 1.75 (0.21), residues: 627 sheet: 0.41 (0.33), residues: 220 loop : 0.70 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 340 HIS 0.008 0.001 HIS V 235 PHE 0.019 0.001 PHE U 397 TYR 0.012 0.001 TYR V 69 ARG 0.003 0.000 ARG U 475 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 1.590 Fit side-chains revert: symmetry clash REVERT: G 733 GLN cc_start: 0.7046 (tt0) cc_final: 0.6731 (tt0) REVERT: G 737 ASP cc_start: 0.8001 (m-30) cc_final: 0.7589 (m-30) REVERT: G 745 LYS cc_start: 0.6979 (mttt) cc_final: 0.6209 (tptp) REVERT: G 795 ARG cc_start: 0.7296 (mtt180) cc_final: 0.6972 (mtm110) REVERT: U 17 ARG cc_start: 0.6831 (ptt180) cc_final: 0.6514 (ptm160) REVERT: U 36 LYS cc_start: 0.8128 (tttt) cc_final: 0.7471 (mmtt) REVERT: U 60 ARG cc_start: 0.7882 (ttt180) cc_final: 0.7509 (mmt180) REVERT: U 146 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7649 (pt0) REVERT: U 160 GLN cc_start: 0.7819 (mt0) cc_final: 0.7423 (tm-30) REVERT: U 218 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7806 (pm20) REVERT: U 224 LYS cc_start: 0.7093 (tttt) cc_final: 0.6848 (tttm) REVERT: U 275 ASP cc_start: 0.7445 (m-30) cc_final: 0.7225 (m-30) REVERT: U 298 LYS cc_start: 0.7926 (pttt) cc_final: 0.7592 (mttp) REVERT: U 392 MET cc_start: 0.7909 (mtm) cc_final: 0.7681 (mmm) REVERT: U 401 ASP cc_start: 0.8402 (m-30) cc_final: 0.7885 (t0) REVERT: U 415 GLU cc_start: 0.7142 (tt0) cc_final: 0.6843 (tp30) REVERT: U 446 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7281 (tmmm) REVERT: U 702 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8608 (mp0) REVERT: V 72 GLU cc_start: 0.8295 (tt0) cc_final: 0.7902 (mt-10) REVERT: V 93 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7701 (mm-30) REVERT: V 111 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7801 (p0) REVERT: V 210 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7846 (ttp-110) REVERT: V 241 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8117 (tm-30) REVERT: V 246 GLN cc_start: 0.8199 (pt0) cc_final: 0.7105 (tp40) REVERT: V 288 ASP cc_start: 0.8299 (m-30) cc_final: 0.7939 (p0) REVERT: V 358 SER cc_start: 0.8671 (t) cc_final: 0.8289 (p) REVERT: V 360 GLN cc_start: 0.7566 (mt0) cc_final: 0.7102 (tt0) REVERT: W 63 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6360 (mp0) REVERT: W 94 GLU cc_start: 0.8485 (tp30) cc_final: 0.8179 (tm-30) REVERT: W 105 ARG cc_start: 0.7708 (mtt180) cc_final: 0.7269 (mpt-90) REVERT: W 215 LYS cc_start: 0.8493 (mttt) cc_final: 0.8044 (mtpt) REVERT: W 264 ASP cc_start: 0.8139 (m-30) cc_final: 0.7835 (t70) REVERT: W 266 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6740 (ptp-110) REVERT: W 284 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6936 (mp0) REVERT: W 312 PHE cc_start: 0.7609 (t80) cc_final: 0.7265 (t80) REVERT: W 385 LEU cc_start: 0.8333 (mt) cc_final: 0.8092 (mm) REVERT: X 187 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8132 (mm-30) outliers start: 31 outliers final: 18 residues processed: 162 average time/residue: 1.6316 time to fit residues: 283.2710 Evaluate side-chains 161 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain U residue 733 MET Chi-restraints excluded: chain V residue 111 ASN Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 208 ILE Chi-restraints excluded: chain V residue 210 ARG Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 246 VAL Chi-restraints excluded: chain W residue 266 ARG Chi-restraints excluded: chain W residue 276 ASP Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 325 ASP 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 48 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 chunk 139 optimal weight: 0.7980 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12501 Z= 0.232 Angle : 0.522 7.913 16947 Z= 0.268 Chirality : 0.043 0.142 1832 Planarity : 0.004 0.045 2185 Dihedral : 6.249 59.704 1728 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.07 % Allowed : 13.11 % Favored : 83.82 % 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: 1.53 (0.22), residues: 1501 helix: 1.79 (0.21), residues: 621 sheet: 0.45 (0.34), residues: 216 loop : 0.61 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 735 HIS 0.007 0.001 HIS V 235 PHE 0.017 0.001 PHE U 397 TYR 0.011 0.001 TYR V 69 ARG 0.003 0.000 ARG U 117 *********************** 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 184 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 1.549 Fit side-chains revert: symmetry clash REVERT: G 733 GLN cc_start: 0.7035 (tt0) cc_final: 0.6707 (tt0) REVERT: G 737 ASP cc_start: 0.8028 (m-30) cc_final: 0.7585 (m-30) REVERT: G 745 LYS cc_start: 0.6965 (mttt) cc_final: 0.6213 (tptp) REVERT: G 795 ARG cc_start: 0.7257 (mtt180) cc_final: 0.6910 (mtm110) REVERT: U 17 ARG cc_start: 0.6884 (ptt180) cc_final: 0.6516 (ptm160) REVERT: U 36 LYS cc_start: 0.8084 (tttt) cc_final: 0.7413 (mmtt) REVERT: U 60 ARG cc_start: 0.7923 (ttt180) cc_final: 0.7543 (mmt180) REVERT: U 101 MET cc_start: 0.5817 (OUTLIER) cc_final: 0.5498 (mtt) REVERT: U 146 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7633 (pt0) REVERT: U 160 GLN cc_start: 0.7847 (mt0) cc_final: 0.7441 (tm-30) REVERT: U 191 ASN cc_start: 0.5506 (p0) cc_final: 0.5084 (t0) REVERT: U 218 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7857 (pm20) REVERT: U 275 ASP cc_start: 0.7589 (m-30) cc_final: 0.7355 (m-30) REVERT: U 298 LYS cc_start: 0.7927 (pttt) cc_final: 0.7593 (mttp) REVERT: U 392 MET cc_start: 0.7857 (mtm) cc_final: 0.7586 (mmm) REVERT: U 401 ASP cc_start: 0.8405 (m-30) cc_final: 0.7884 (t0) REVERT: U 415 GLU cc_start: 0.7210 (tt0) cc_final: 0.6913 (tp30) REVERT: U 446 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7274 (tmmm) REVERT: U 702 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8634 (mp0) REVERT: V 72 GLU cc_start: 0.8211 (tt0) cc_final: 0.7823 (mt-10) REVERT: V 83 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: V 93 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7706 (mm-30) REVERT: V 111 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7821 (p0) REVERT: V 210 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7818 (ttp-110) REVERT: V 241 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8123 (tm-30) REVERT: V 246 GLN cc_start: 0.8175 (pt0) cc_final: 0.7110 (tp40) REVERT: V 288 ASP cc_start: 0.8334 (m-30) cc_final: 0.7964 (p0) REVERT: V 358 SER cc_start: 0.8651 (t) cc_final: 0.8259 (p) REVERT: V 360 GLN cc_start: 0.7660 (mt0) cc_final: 0.7124 (tt0) REVERT: W 63 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6389 (mp0) REVERT: W 94 GLU cc_start: 0.8484 (tp30) cc_final: 0.8199 (tm-30) REVERT: W 105 ARG cc_start: 0.7723 (mtt180) cc_final: 0.7248 (mpt-90) REVERT: W 253 ASN cc_start: 0.7493 (m-40) cc_final: 0.7176 (m-40) REVERT: W 264 ASP cc_start: 0.8098 (m-30) cc_final: 0.7838 (t70) REVERT: W 266 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6664 (ptp-110) REVERT: W 284 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6963 (mp0) REVERT: W 312 PHE cc_start: 0.7560 (t80) cc_final: 0.7212 (t80) REVERT: W 385 LEU cc_start: 0.8324 (mt) cc_final: 0.8068 (mm) REVERT: X 187 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8154 (mm-30) outliers start: 40 outliers final: 20 residues processed: 167 average time/residue: 1.6055 time to fit residues: 287.4713 Evaluate side-chains 164 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain U residue 101 MET Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 494 ASP Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain U residue 733 MET Chi-restraints excluded: chain V residue 83 GLU Chi-restraints excluded: chain V residue 111 ASN Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 208 ILE Chi-restraints excluded: chain V residue 210 ARG Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 163 ILE Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 246 VAL Chi-restraints excluded: chain W residue 266 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 122 optimal weight: 0.0970 chunk 81 optimal weight: 0.5980 chunk 144 optimal weight: 0.0980 chunk 90 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12501 Z= 0.252 Angle : 0.532 8.045 16947 Z= 0.272 Chirality : 0.043 0.144 1832 Planarity : 0.004 0.044 2185 Dihedral : 6.241 58.862 1728 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.84 % Allowed : 13.96 % 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: 1.47 (0.22), residues: 1501 helix: 1.78 (0.21), residues: 621 sheet: 0.35 (0.34), residues: 218 loop : 0.57 (0.24), residues: 662 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 0.016 0.001 PHE U 397 TYR 0.010 0.001 TYR W 304 ARG 0.004 0.000 ARG W 466 *********************** 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 180 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 1.696 Fit side-chains revert: symmetry clash REVERT: G 733 GLN cc_start: 0.7037 (tt0) cc_final: 0.6725 (tt0) REVERT: G 737 ASP cc_start: 0.8026 (m-30) cc_final: 0.7599 (m-30) REVERT: G 745 LYS cc_start: 0.6967 (mttt) cc_final: 0.6213 (tptp) REVERT: G 795 ARG cc_start: 0.7244 (mtt180) cc_final: 0.6911 (mtm110) REVERT: U 17 ARG cc_start: 0.6888 (ptt180) cc_final: 0.6532 (ptm160) REVERT: U 36 LYS cc_start: 0.8081 (tttt) cc_final: 0.7416 (mmpt) REVERT: U 60 ARG cc_start: 0.7952 (ttt180) cc_final: 0.7560 (mmt180) REVERT: U 146 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7616 (pt0) REVERT: U 160 GLN cc_start: 0.7765 (mt0) cc_final: 0.7423 (tm-30) REVERT: U 191 ASN cc_start: 0.5567 (p0) cc_final: 0.5168 (t0) REVERT: U 218 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7870 (pm20) REVERT: U 232 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.7129 (mt0) REVERT: U 275 ASP cc_start: 0.7398 (m-30) cc_final: 0.7161 (m-30) REVERT: U 298 LYS cc_start: 0.7927 (pttt) cc_final: 0.7593 (mttp) REVERT: U 401 ASP cc_start: 0.8455 (m-30) cc_final: 0.7900 (t0) REVERT: U 415 GLU cc_start: 0.7227 (tt0) cc_final: 0.6921 (tp30) REVERT: U 446 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7267 (tmmm) REVERT: U 702 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8621 (mp0) REVERT: V 72 GLU cc_start: 0.8213 (tt0) cc_final: 0.7828 (mt-10) REVERT: V 93 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7658 (mm-30) REVERT: V 111 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7851 (p0) REVERT: V 210 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7813 (ttp-110) REVERT: V 241 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8125 (tm-30) REVERT: V 246 GLN cc_start: 0.8154 (pt0) cc_final: 0.7075 (tp40) REVERT: V 288 ASP cc_start: 0.8330 (m-30) cc_final: 0.7951 (p0) REVERT: V 358 SER cc_start: 0.8733 (t) cc_final: 0.8347 (p) REVERT: V 360 GLN cc_start: 0.7665 (mt0) cc_final: 0.7130 (tt0) REVERT: W 63 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6412 (mp0) REVERT: W 94 GLU cc_start: 0.8482 (tp30) cc_final: 0.8197 (tm-30) REVERT: W 105 ARG cc_start: 0.7721 (mtt180) cc_final: 0.7280 (mmp80) REVERT: W 253 ASN cc_start: 0.7511 (m-40) cc_final: 0.7203 (m-40) REVERT: W 264 ASP cc_start: 0.8071 (m-30) cc_final: 0.7831 (t70) REVERT: W 266 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6689 (ptp-110) REVERT: W 312 PHE cc_start: 0.7569 (t80) cc_final: 0.7219 (t80) REVERT: W 385 LEU cc_start: 0.8328 (mt) cc_final: 0.8068 (mm) REVERT: X 187 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8169 (mm-30) outliers start: 37 outliers final: 22 residues processed: 167 average time/residue: 1.6255 time to fit residues: 291.2218 Evaluate side-chains 167 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 232 GLN 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 U residue 733 MET Chi-restraints excluded: chain V residue 111 ASN Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 135 SER Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 208 ILE Chi-restraints excluded: chain V residue 210 ARG Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain V residue 269 LEU Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 246 VAL Chi-restraints excluded: chain W residue 266 ARG Chi-restraints excluded: chain W residue 276 ASP Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 411 MET Chi-restraints excluded: chain W residue 426 SER Chi-restraints excluded: chain X residue 172 THR Chi-restraints excluded: chain X residue 175 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 98 optimal weight: 0.0980 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 235 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12501 Z= 0.165 Angle : 0.498 7.220 16947 Z= 0.254 Chirality : 0.042 0.135 1832 Planarity : 0.004 0.044 2185 Dihedral : 6.052 55.406 1728 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.61 % Allowed : 15.11 % Favored : 83.28 % 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: 1.56 (0.22), residues: 1501 helix: 1.82 (0.21), residues: 627 sheet: 0.42 (0.34), residues: 218 loop : 0.64 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 735 HIS 0.004 0.001 HIS V 235 PHE 0.013 0.001 PHE U 397 TYR 0.008 0.001 TYR V 69 ARG 0.004 0.000 ARG W 466 *********************** 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 164 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 1.614 Fit side-chains revert: symmetry clash REVERT: G 733 GLN cc_start: 0.7088 (tt0) cc_final: 0.6775 (tt0) REVERT: G 737 ASP cc_start: 0.8041 (m-30) cc_final: 0.7635 (m-30) REVERT: G 745 LYS cc_start: 0.6956 (mttt) cc_final: 0.6197 (tptp) REVERT: G 795 ARG cc_start: 0.7280 (mtt180) cc_final: 0.6864 (mtm110) REVERT: U 17 ARG cc_start: 0.6840 (ptt180) cc_final: 0.6530 (ptm160) REVERT: U 36 LYS cc_start: 0.8079 (tttt) cc_final: 0.7415 (mmpt) REVERT: U 60 ARG cc_start: 0.7986 (ttt180) cc_final: 0.7584 (mmt180) REVERT: U 146 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7620 (pt0) REVERT: U 160 GLN cc_start: 0.7729 (mt0) cc_final: 0.7338 (tm-30) REVERT: U 191 ASN cc_start: 0.5701 (p0) cc_final: 0.5356 (t0) REVERT: U 218 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7754 (pm20) REVERT: U 275 ASP cc_start: 0.7385 (m-30) cc_final: 0.7129 (m-30) REVERT: U 298 LYS cc_start: 0.7919 (pttt) cc_final: 0.7589 (mttp) REVERT: U 401 ASP cc_start: 0.8435 (m-30) cc_final: 0.7880 (t0) REVERT: U 415 GLU cc_start: 0.7223 (tt0) cc_final: 0.6919 (tp30) REVERT: U 446 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7256 (tmmm) REVERT: U 702 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8662 (mp0) REVERT: V 72 GLU cc_start: 0.8212 (tt0) cc_final: 0.7807 (mt-10) REVERT: V 93 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7661 (mm-30) REVERT: V 241 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8109 (tm-30) REVERT: V 246 GLN cc_start: 0.8155 (pt0) cc_final: 0.7067 (tp40) REVERT: V 288 ASP cc_start: 0.8349 (m-30) cc_final: 0.7964 (p0) REVERT: V 358 SER cc_start: 0.8624 (t) cc_final: 0.8217 (p) REVERT: V 360 GLN cc_start: 0.7643 (mt0) cc_final: 0.7118 (tt0) REVERT: W 63 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6432 (mp0) REVERT: W 94 GLU cc_start: 0.8481 (tp30) cc_final: 0.8195 (tm-30) REVERT: W 105 ARG cc_start: 0.7738 (mtt180) cc_final: 0.7297 (mmp80) REVERT: W 253 ASN cc_start: 0.7507 (m-40) cc_final: 0.7214 (m-40) REVERT: W 264 ASP cc_start: 0.8079 (m-30) cc_final: 0.7122 (p0) REVERT: W 266 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6739 (ptp-110) REVERT: W 312 PHE cc_start: 0.7579 (t80) cc_final: 0.7244 (t80) REVERT: W 385 LEU cc_start: 0.8316 (mt) cc_final: 0.8069 (mm) REVERT: X 187 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8157 (mm-30) outliers start: 21 outliers final: 14 residues processed: 159 average time/residue: 1.6439 time to fit residues: 280.1689 Evaluate side-chains 154 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 246 VAL Chi-restraints excluded: chain W residue 266 ARG Chi-restraints excluded: chain W residue 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.8980 chunk 138 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2904 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= 0.242 Angle : 0.538 8.050 16947 Z= 0.272 Chirality : 0.043 0.139 1832 Planarity : 0.004 0.044 2185 Dihedral : 6.151 56.142 1728 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.22 % Allowed : 14.57 % 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: 1.45 (0.22), residues: 1501 helix: 1.73 (0.21), residues: 627 sheet: 0.35 (0.34), residues: 216 loop : 0.58 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 340 HIS 0.015 0.001 HIS V 235 PHE 0.016 0.001 PHE U 397 TYR 0.010 0.001 TYR U 379 ARG 0.003 0.000 ARG W 466 *********************** 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 168 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 1.552 Fit side-chains revert: symmetry clash REVERT: G 733 GLN cc_start: 0.7049 (tt0) cc_final: 0.6727 (tt0) REVERT: G 737 ASP cc_start: 0.8036 (m-30) cc_final: 0.7613 (m-30) REVERT: G 745 LYS cc_start: 0.6944 (mttt) cc_final: 0.6173 (tptp) REVERT: G 795 ARG cc_start: 0.7250 (mtt180) cc_final: 0.6867 (mtm110) REVERT: U 17 ARG cc_start: 0.6882 (ptt180) cc_final: 0.6526 (ptm160) REVERT: U 36 LYS cc_start: 0.8079 (tttt) cc_final: 0.7406 (mmtt) REVERT: U 60 ARG cc_start: 0.7991 (ttt180) cc_final: 0.7603 (mtt90) REVERT: U 146 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7593 (pt0) REVERT: U 160 GLN cc_start: 0.7832 (mt0) cc_final: 0.7393 (tm-30) REVERT: U 191 ASN cc_start: 0.5747 (p0) cc_final: 0.5444 (t0) REVERT: U 218 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7799 (pm20) REVERT: U 232 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.7131 (mt0) REVERT: U 250 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7155 (tptm) REVERT: U 298 LYS cc_start: 0.7936 (pttt) cc_final: 0.7611 (mttp) REVERT: U 401 ASP cc_start: 0.8491 (m-30) cc_final: 0.7923 (t0) REVERT: U 415 GLU cc_start: 0.7226 (tt0) cc_final: 0.6921 (tp30) REVERT: U 446 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7267 (tmmm) REVERT: U 702 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8674 (mp0) REVERT: V 72 GLU cc_start: 0.8211 (tt0) cc_final: 0.7814 (mt-10) REVERT: V 93 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7691 (mm-30) REVERT: V 241 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8279 (tm-30) REVERT: V 246 GLN cc_start: 0.8150 (pt0) cc_final: 0.7112 (tp40) REVERT: V 288 ASP cc_start: 0.8364 (m-30) cc_final: 0.7975 (p0) REVERT: V 325 MET cc_start: 0.7669 (mmm) cc_final: 0.7414 (mmm) REVERT: V 360 GLN cc_start: 0.7664 (mt0) cc_final: 0.7173 (tt0) REVERT: W 63 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6404 (mp0) REVERT: W 94 GLU cc_start: 0.8474 (tp30) cc_final: 0.8182 (tm-30) REVERT: W 105 ARG cc_start: 0.7725 (mtt180) cc_final: 0.7300 (mmp80) REVERT: W 157 LYS cc_start: 0.7871 (mttt) cc_final: 0.7602 (mppt) REVERT: W 253 ASN cc_start: 0.7548 (m-40) cc_final: 0.7241 (m-40) REVERT: W 264 ASP cc_start: 0.8091 (m-30) cc_final: 0.7137 (p0) REVERT: W 266 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6723 (ptp-110) REVERT: W 385 LEU cc_start: 0.8328 (mt) cc_final: 0.8072 (mm) REVERT: X 187 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8166 (mm-30) outliers start: 29 outliers final: 18 residues processed: 160 average time/residue: 1.6702 time to fit residues: 285.6315 Evaluate side-chains 155 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain U residue 232 GLN Chi-restraints excluded: chain U residue 250 LYS Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 695 LEU Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain U residue 733 MET Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 135 SER Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 208 ILE Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain V residue 269 LEU Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 246 VAL Chi-restraints excluded: chain W residue 266 ARG Chi-restraints excluded: chain W residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 chunk 149 optimal weight: 0.0020 chunk 137 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 126 optimal weight: 0.0670 chunk 36 optimal weight: 3.9990 overall best weight: 0.4526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12501 Z= 0.137 Angle : 0.492 7.756 16947 Z= 0.249 Chirality : 0.041 0.134 1832 Planarity : 0.004 0.047 2185 Dihedral : 5.910 51.916 1728 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.92 % Allowed : 14.95 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.22), residues: 1501 helix: 1.87 (0.21), residues: 631 sheet: 0.51 (0.34), residues: 214 loop : 0.71 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 170 HIS 0.011 0.001 HIS V 235 PHE 0.011 0.001 PHE W 249 TYR 0.009 0.001 TYR W 412 ARG 0.004 0.000 ARG W 466 ********************** 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 162 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 737 ASP cc_start: 0.8023 (m-30) cc_final: 0.7646 (m-30) REVERT: G 745 LYS cc_start: 0.6945 (mttt) cc_final: 0.6187 (tptp) REVERT: G 795 ARG cc_start: 0.7302 (mtt180) cc_final: 0.6873 (mtm110) REVERT: U 36 LYS cc_start: 0.8103 (tttt) cc_final: 0.7466 (mmpt) REVERT: U 60 ARG cc_start: 0.7931 (ttt180) cc_final: 0.7563 (mpt180) REVERT: U 146 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7615 (pt0) REVERT: U 160 GLN cc_start: 0.7779 (mt0) cc_final: 0.7419 (tm-30) REVERT: U 191 ASN cc_start: 0.5668 (p0) cc_final: 0.5403 (t0) REVERT: U 298 LYS cc_start: 0.7913 (pttt) cc_final: 0.7595 (mttp) REVERT: U 401 ASP cc_start: 0.8424 (m-30) cc_final: 0.7882 (t0) REVERT: U 415 GLU cc_start: 0.7201 (tt0) cc_final: 0.6910 (tp30) REVERT: U 446 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7249 (tmmm) REVERT: U 702 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8678 (mp0) REVERT: V 72 GLU cc_start: 0.8214 (tt0) cc_final: 0.7820 (mt-10) REVERT: V 93 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7676 (mm-30) REVERT: V 241 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8185 (tm-30) REVERT: V 246 GLN cc_start: 0.8192 (pt0) cc_final: 0.7116 (tp40) REVERT: V 270 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6822 (mt-10) REVERT: V 360 GLN cc_start: 0.7630 (mt0) cc_final: 0.7153 (tt0) REVERT: W 63 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6248 (mp0) REVERT: W 94 GLU cc_start: 0.8470 (tp30) cc_final: 0.8180 (tm-30) REVERT: W 105 ARG cc_start: 0.7724 (mtt180) cc_final: 0.7295 (mmp80) REVERT: W 253 ASN cc_start: 0.7463 (m-40) cc_final: 0.7191 (m-40) REVERT: W 264 ASP cc_start: 0.8009 (m-30) cc_final: 0.7066 (p0) REVERT: W 266 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6784 (ptp-110) REVERT: W 312 PHE cc_start: 0.7582 (t80) cc_final: 0.7278 (t80) REVERT: W 385 LEU cc_start: 0.8290 (mt) cc_final: 0.8071 (mm) REVERT: X 187 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8133 (mm-30) outliers start: 25 outliers final: 13 residues processed: 157 average time/residue: 1.5699 time to fit residues: 264.2337 Evaluate side-chains 149 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 695 LEU Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 135 SER Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain V residue 269 LEU Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 266 ARG Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 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 109 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 119 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 122 optimal weight: 0.0970 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 145 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.140222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.117182 restraints weight = 14930.026| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.64 r_work: 0.3325 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12501 Z= 0.159 Angle : 0.509 8.901 16947 Z= 0.256 Chirality : 0.042 0.136 1832 Planarity : 0.004 0.047 2185 Dihedral : 5.869 53.075 1728 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.84 % Allowed : 15.49 % Favored : 82.67 % 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: 1.68 (0.22), residues: 1501 helix: 1.87 (0.21), residues: 632 sheet: 0.50 (0.34), residues: 214 loop : 0.74 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 79 HIS 0.010 0.001 HIS V 235 PHE 0.012 0.001 PHE U 397 TYR 0.009 0.001 TYR W 412 ARG 0.006 0.000 ARG U 475 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5070.86 seconds wall clock time: 91 minutes 4.35 seconds (5464.35 seconds total)