Starting phenix.real_space_refine on Wed Mar 4 13:47:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a5p_15180/03_2026/8a5p_15180_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a5p_15180/03_2026/8a5p_15180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a5p_15180/03_2026/8a5p_15180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a5p_15180/03_2026/8a5p_15180.map" model { file = "/net/cci-nas-00/data/ceres_data/8a5p_15180/03_2026/8a5p_15180_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a5p_15180/03_2026/8a5p_15180_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 81 5.49 5 Mg 3 5.21 5 S 61 5.16 5 C 8565 2.51 5 N 2464 2.21 5 O 2763 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13937 Number of models: 1 Model: "" Number of chains: 10 Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 831 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "K" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 739 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "L" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 737 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "U" Number of atoms: 4913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4913 Classifications: {'peptide': 605} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 576} 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: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 413 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 6, 'TRANS': 45} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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, 'ATP': 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, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.80, per 1000 atoms: 0.20 Number of scatterers: 13937 At special positions: 0 Unit cell: (96.48, 112.56, 155.44, 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 61 16.00 P 81 15.00 Mg 3 11.99 O 2763 8.00 N 2464 7.00 C 8565 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: 1.04 Conformation dependent library (CDL) restraints added in 391.1 milliseconds 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2904 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 19 sheets defined 48.8% alpha, 13.7% beta 32 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'G' and resid 724 through 741 Processing helix chain 'G' and resid 741 through 775 removed outlier: 3.508A pdb=" N LYS G 773 " --> pdb=" O SER G 769 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TRP G 775 " --> pdb=" O GLU G 771 " (cutoff:3.500A) Processing helix chain 'G' and resid 779 through 806 Processing helix chain 'U' and resid 7 through 13 removed outlier: 4.009A pdb=" N ALA U 11 " --> pdb=" O GLU U 7 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 68 removed outlier: 3.765A pdb=" N GLN U 55 " --> pdb=" O SER U 51 " (cutoff:3.500A) 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 162 Processing helix chain 'U' and resid 163 through 184 Processing helix chain 'U' and resid 191 through 203 removed outlier: 3.548A pdb=" N PHE U 199 " --> pdb=" O LEU U 195 " (cutoff:3.500A) Processing helix chain 'U' and resid 209 through 213 Processing helix chain 'U' and resid 237 through 242 Processing helix chain 'U' and resid 269 through 288 Processing helix chain 'U' and resid 293 through 299 removed outlier: 4.120A 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: 4.017A 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 396 Processing helix chain 'U' and resid 406 through 421 Processing helix chain 'U' and resid 453 through 458 Processing helix chain 'U' and resid 459 through 468 Proline residue: U 465 - end of helix Processing helix chain 'U' and resid 498 through 509 removed outlier: 3.590A pdb=" N VAL U 508 " --> pdb=" O ILE U 504 " (cutoff:3.500A) Processing helix chain 'U' and resid 620 through 630 Processing helix chain 'U' and resid 636 through 650 removed outlier: 3.518A pdb=" N HIS U 647 " --> pdb=" O THR U 643 " (cutoff:3.500A) Processing helix chain 'U' and resid 652 through 660 Processing helix chain 'U' and resid 667 through 672 Processing helix chain 'U' and resid 674 through 687 Processing helix chain 'U' and resid 688 through 691 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: 4.121A pdb=" N TYR U 740 " --> pdb=" O SER U 736 " (cutoff:3.500A) removed outlier: 3.788A 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 removed outlier: 4.066A pdb=" N LYS V 84 " --> pdb=" O ASP V 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 97 through 101 Processing helix chain 'V' and resid 112 through 126 removed outlier: 3.566A pdb=" N ARG V 116 " --> pdb=" O PRO V 112 " (cutoff:3.500A) removed outlier: 3.515A 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 181 through 197 Processing helix chain 'V' and resid 202 through 217 removed outlier: 4.416A pdb=" N ILE V 208 " --> pdb=" O ALA V 204 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP V 211 " --> pdb=" O GLU V 207 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS V 217 " --> pdb=" O LYS V 213 " (cutoff:3.500A) Processing helix chain 'V' and resid 222 through 231 removed outlier: 3.982A pdb=" N ALA V 231 " --> pdb=" O ILE V 227 " (cutoff:3.500A) 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 285 removed outlier: 3.586A pdb=" N CYS V 285 " --> pdb=" O SER V 281 " (cutoff:3.500A) Processing helix chain 'V' and resid 286 through 295 removed outlier: 3.517A pdb=" N ARG V 290 " --> pdb=" O ASP V 286 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LYS V 291 " --> pdb=" O VAL V 287 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP V 292 " --> pdb=" O ASP V 288 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 306 removed outlier: 4.054A pdb=" N TYR V 306 " --> pdb=" O THR V 303 " (cutoff:3.500A) Processing helix chain 'V' and resid 308 through 321 Processing helix chain 'V' and resid 337 through 347 Processing helix chain 'V' and resid 348 through 355 removed outlier: 6.262A pdb=" N THR V 351 " --> pdb=" O SER V 348 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN V 353 " --> pdb=" O SER V 350 " (cutoff:3.500A) Processing helix chain 'V' and resid 359 through 366 removed outlier: 4.052A pdb=" N GLU V 364 " --> pdb=" O GLN V 360 " (cutoff:3.500A) Processing helix chain 'V' and resid 368 through 374 removed outlier: 3.864A pdb=" N ARG V 372 " --> pdb=" O SER V 368 " (cutoff:3.500A) Processing helix chain 'W' and resid 61 through 65 removed outlier: 4.048A pdb=" N ILE W 65 " --> pdb=" O ASP W 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 98 Processing helix chain 'W' and resid 108 through 113 removed outlier: 3.787A pdb=" N ASN W 112 " --> pdb=" O ALA W 109 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY W 113 " --> pdb=" O SER W 110 " (cutoff:3.500A) Processing helix chain 'W' and resid 155 through 170 removed outlier: 3.532A pdb=" N TRP W 170 " --> pdb=" O VAL W 166 " (cutoff:3.500A) Processing helix chain 'W' and resid 180 through 188 Processing helix chain 'W' and resid 215 through 218 Processing helix chain 'W' and resid 224 through 237 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: 3.822A pdb=" N ARG W 285 " --> pdb=" O PHE W 281 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL W 286 " --> pdb=" O GLU W 282 " (cutoff:3.500A) Processing helix chain 'W' and resid 306 through 314 removed outlier: 4.231A pdb=" N GLU W 310 " --> pdb=" O ASN W 306 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASP W 311 " --> pdb=" O PRO W 307 " (cutoff:3.500A) Processing helix chain 'W' and resid 333 through 341 removed outlier: 3.601A pdb=" N ARG W 337 " --> pdb=" O GLU W 333 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA W 339 " --> pdb=" O ARG W 335 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY W 341 " --> pdb=" O ARG W 337 " (cutoff:3.500A) Processing helix chain 'W' and resid 342 through 343 No H-bonds generated for 'chain 'W' and resid 342 through 343' Processing helix chain 'W' and resid 344 through 348 Processing helix chain 'W' and resid 360 through 363 Processing helix chain 'W' and resid 364 through 375 Processing helix chain 'W' and resid 376 through 379 removed outlier: 5.863A pdb=" N ASP W 379 " --> pdb=" O VAL W 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 376 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 427 through 429 No H-bonds generated for 'chain 'W' and resid 427 through 429' Processing helix chain 'W' and resid 430 through 440 Processing helix chain 'W' and resid 441 through 448 removed outlier: 6.047A pdb=" N THR W 444 " --> pdb=" O SER W 441 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS W 446 " --> pdb=" O GLY W 443 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN W 447 " --> pdb=" O THR W 444 " (cutoff:3.500A) Processing helix chain 'W' and resid 452 through 459 Processing helix chain 'X' and resid 155 through 161 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 208 removed outlier: 3.578A pdb=" N ARG U 445 " --> pdb=" O LEU U 437 " (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 removed outlier: 8.063A pdb=" N MET U 664 " --> pdb=" O GLN U 348 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N CYS U 350 " --> pdb=" O MET U 664 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL U 666 " --> pdb=" O CYS U 350 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL U 352 " --> pdb=" O VAL U 666 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'V' and resid 29 through 32 removed outlier: 6.447A pdb=" N LEU V 8 " --> pdb=" O LEU V 104 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR V 106 " --> pdb=" O LEU V 8 " (cutoff:3.500A) removed outlier: 7.452A 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: 6.025A pdb=" N ILE V 151 " --> pdb=" O VAL V 298 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N SER V 300 " --> pdb=" O ILE V 151 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU V 153 " --> pdb=" O SER V 300 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE V 297 " --> pdb=" O ILE V 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'V' and resid 239 through 241 Processing sheet with id=AB4, first strand: chain 'W' and resid 45 through 48 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: 6.063A pdb=" N LEU W 194 " --> pdb=" O VAL W 389 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR W 391 " --> pdb=" O LEU W 194 " (cutoff:3.500A) removed outlier: 6.370A 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 254 removed outlier: 6.916A pdb=" N ARG W 266 " --> pdb=" O GLU W 252 " (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 179 587 hydrogen bonds defined for protein. 1557 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 3373 1.34 - 1.49: 5000 1.49 - 1.64: 5914 1.64 - 1.79: 14 1.79 - 1.93: 94 Bond restraints: 14395 Sorted by residual: bond pdb=" CE1 HIS V 371 " pdb=" NE2 HIS V 371 " ideal model delta sigma weight residual 1.321 1.395 -0.074 1.00e-02 1.00e+04 5.44e+01 bond pdb=" CE1 HIS U 320 " pdb=" NE2 HIS U 320 " ideal model delta sigma weight residual 1.321 1.391 -0.070 1.00e-02 1.00e+04 4.92e+01 bond pdb=" CE1 HIS U 746 " pdb=" NE2 HIS U 746 " ideal model delta sigma weight residual 1.321 1.379 -0.058 1.00e-02 1.00e+04 3.40e+01 bond pdb=" CE1 HIS U 408 " pdb=" NE2 HIS U 408 " ideal model delta sigma weight residual 1.321 1.376 -0.055 1.00e-02 1.00e+04 2.99e+01 bond pdb=" CG MET V 355 " pdb=" SD MET V 355 " ideal model delta sigma weight residual 1.803 1.934 -0.131 2.50e-02 1.60e+03 2.75e+01 ... (remaining 14390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.36: 19471 4.36 - 8.72: 331 8.72 - 13.09: 6 13.09 - 17.45: 3 17.45 - 21.81: 3 Bond angle restraints: 19814 Sorted by residual: angle pdb=" PB ATP U 900 " pdb=" O3B ATP U 900 " pdb=" PG ATP U 900 " ideal model delta sigma weight residual 139.87 118.06 21.81 1.00e+00 1.00e+00 4.76e+02 angle pdb=" PA ATP V 500 " pdb=" O3A ATP V 500 " pdb=" PB ATP V 500 " ideal model delta sigma weight residual 136.83 117.10 19.73 1.00e+00 1.00e+00 3.89e+02 angle pdb=" PA ATP U 900 " pdb=" O3A ATP U 900 " pdb=" PB ATP U 900 " ideal model delta sigma weight residual 136.83 117.99 18.84 1.00e+00 1.00e+00 3.55e+02 angle pdb=" PB ATP V 500 " pdb=" O3B ATP V 500 " pdb=" PG ATP V 500 " ideal model delta sigma weight residual 139.87 122.61 17.26 1.00e+00 1.00e+00 2.98e+02 angle pdb=" PA ATP W 500 " pdb=" O3A ATP W 500 " pdb=" PB ATP W 500 " ideal model delta sigma weight residual 136.83 119.62 17.21 1.00e+00 1.00e+00 2.96e+02 ... (remaining 19809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 7307 17.13 - 34.25: 792 34.25 - 51.38: 295 51.38 - 68.50: 126 68.50 - 85.62: 24 Dihedral angle restraints: 8544 sinusoidal: 4046 harmonic: 4498 Sorted by residual: dihedral pdb=" CA ARG V 372 " pdb=" C ARG V 372 " pdb=" N LYS V 373 " pdb=" CA LYS V 373 " ideal model delta harmonic sigma weight residual -180.00 -149.23 -30.77 0 5.00e+00 4.00e-02 3.79e+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 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA LEU V 65 " pdb=" C LEU V 65 " pdb=" N THR V 66 " pdb=" CA THR V 66 " ideal model delta harmonic sigma weight residual 180.00 153.90 26.10 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 8541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 1780 0.130 - 0.260: 309 0.260 - 0.389: 59 0.389 - 0.519: 0 0.519 - 0.649: 2 Chirality restraints: 2150 Sorted by residual: chirality pdb=" P DC K 75 " pdb=" OP1 DC K 75 " pdb=" OP2 DC K 75 " pdb=" O5' DC K 75 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P DC L-110 " pdb=" OP1 DC L-110 " pdb=" OP2 DC L-110 " pdb=" O5' DC L-110 " both_signs ideal model delta sigma weight residual True 2.35 -2.94 -0.59 2.00e-01 2.50e+01 8.77e+00 chirality pdb=" P DC K 89 " pdb=" OP1 DC K 89 " pdb=" OP2 DC K 89 " pdb=" O5' DC K 89 " both_signs ideal model delta sigma weight residual True 2.35 -2.69 -0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 2147 not shown) Planarity restraints: 2299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT K 82 " -0.105 2.00e-02 2.50e+03 4.84e-02 5.86e+01 pdb=" N1 DT K 82 " 0.023 2.00e-02 2.50e+03 pdb=" C2 DT K 82 " 0.034 2.00e-02 2.50e+03 pdb=" O2 DT K 82 " 0.042 2.00e-02 2.50e+03 pdb=" N3 DT K 82 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DT K 82 " -0.019 2.00e-02 2.50e+03 pdb=" O4 DT K 82 " -0.075 2.00e-02 2.50e+03 pdb=" C5 DT K 82 " 0.030 2.00e-02 2.50e+03 pdb=" C7 DT K 82 " 0.024 2.00e-02 2.50e+03 pdb=" C6 DT K 82 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP V 340 " 0.093 2.00e-02 2.50e+03 4.40e-02 4.83e+01 pdb=" CG TRP V 340 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP V 340 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP V 340 " -0.036 2.00e-02 2.50e+03 pdb=" NE1 TRP V 340 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP V 340 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP V 340 " -0.038 2.00e-02 2.50e+03 pdb=" CZ2 TRP V 340 " 0.039 2.00e-02 2.50e+03 pdb=" CZ3 TRP V 340 " -0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP V 340 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT L -76 " -0.091 2.00e-02 2.50e+03 4.39e-02 4.82e+01 pdb=" N1 DT L -76 " 0.027 2.00e-02 2.50e+03 pdb=" C2 DT L -76 " 0.032 2.00e-02 2.50e+03 pdb=" O2 DT L -76 " 0.047 2.00e-02 2.50e+03 pdb=" N3 DT L -76 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT L -76 " -0.020 2.00e-02 2.50e+03 pdb=" O4 DT L -76 " -0.066 2.00e-02 2.50e+03 pdb=" C5 DT L -76 " 0.016 2.00e-02 2.50e+03 pdb=" C7 DT L -76 " 0.044 2.00e-02 2.50e+03 pdb=" C6 DT L -76 " 0.010 2.00e-02 2.50e+03 ... (remaining 2296 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 12 2.43 - 3.05: 8343 3.05 - 3.67: 20702 3.67 - 4.28: 33021 4.28 - 4.90: 52749 Nonbonded interactions: 114827 Sorted by model distance: nonbonded pdb=" O1B ATP W 500 " pdb="MG MG W 501 " model vdw 1.816 2.170 nonbonded pdb=" O2B ATP V 500 " pdb="MG MG V 501 " model vdw 1.851 2.170 nonbonded pdb=" O2G ATP W 500 " pdb="MG MG W 501 " model vdw 1.943 2.170 nonbonded pdb=" O2G ATP V 500 " pdb="MG MG V 501 " model vdw 2.048 2.170 nonbonded pdb=" O1B ATP U 900 " pdb="MG MG U 901 " model vdw 2.048 2.170 ... (remaining 114822 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: 0.410 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: 0.180 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 13.710 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 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 : 0.011 0.131 14395 Z= 0.720 Angle : 1.651 21.811 19814 Z= 1.110 Chirality : 0.101 0.649 2150 Planarity : 0.022 0.239 2299 Dihedral : 17.868 85.625 5640 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.26 % Favored : 96.61 % Rotamer: Outliers : 0.90 % Allowed : 3.47 % Favored : 95.63 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.20), residues: 1532 helix: -1.25 (0.18), residues: 634 sheet: 0.38 (0.36), residues: 195 loop : -0.38 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.004 ARG U 17 TYR 0.079 0.016 TYR U 314 PHE 0.073 0.012 PHE U 716 TRP 0.093 0.017 TRP V 340 HIS 0.020 0.005 HIS U 320 Details of bonding type rmsd covalent geometry : bond 0.01147 (14395) covalent geometry : angle 1.65104 (19814) hydrogen bonds : bond 0.16485 ( 661) hydrogen bonds : angle 7.04637 ( 1717) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 797 MET cc_start: 0.9492 (tmm) cc_final: 0.9213 (tmm) REVERT: U 43 MET cc_start: 0.9378 (mtp) cc_final: 0.9163 (mtp) REVERT: U 144 MET cc_start: 0.9687 (mtp) cc_final: 0.9477 (mtm) REVERT: U 181 MET cc_start: 0.9627 (ptm) cc_final: 0.9426 (ptt) REVERT: U 182 ARG cc_start: 0.9595 (mtt180) cc_final: 0.9209 (mmt180) REVERT: U 194 ASP cc_start: 0.9414 (m-30) cc_final: 0.9179 (t70) REVERT: U 242 ARG cc_start: 0.9443 (mmm160) cc_final: 0.9184 (ttt-90) REVERT: U 396 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.7963 (t0) REVERT: U 397 PHE cc_start: 0.9421 (t80) cc_final: 0.9178 (t80) REVERT: V 132 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.8768 (t80) REVERT: W 77 MET cc_start: 0.9327 (mmm) cc_final: 0.8702 (mmm) REVERT: W 82 MET cc_start: 0.9081 (mtm) cc_final: 0.8541 (mtm) REVERT: W 250 MET cc_start: 0.9480 (mtp) cc_final: 0.9271 (mtp) REVERT: W 448 MET cc_start: 0.8713 (mmm) cc_final: 0.8414 (mmt) REVERT: W 466 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7394 (mmt-90) outliers start: 12 outliers final: 1 residues processed: 135 average time/residue: 0.1345 time to fit residues: 25.7714 Evaluate side-chains 79 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 396 ASN Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain W residue 390 VAL Chi-restraints excluded: chain W residue 466 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 110 HIS U 184 ASN U 396 ASN U 425 GLN V 275 HIS W 458 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.055979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.038295 restraints weight = 61258.613| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 3.31 r_work: 0.2622 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 14395 Z= 0.149 Angle : 0.658 9.923 19814 Z= 0.353 Chirality : 0.043 0.177 2150 Planarity : 0.005 0.064 2299 Dihedral : 18.958 73.483 2588 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.48 % Favored : 97.45 % Rotamer: Outliers : 0.98 % Allowed : 6.33 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.21), residues: 1532 helix: 0.55 (0.20), residues: 642 sheet: 1.02 (0.37), residues: 193 loop : 0.36 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 201 TYR 0.017 0.002 TYR G 727 PHE 0.012 0.001 PHE V 375 TRP 0.022 0.002 TRP W 433 HIS 0.003 0.001 HIS V 235 Details of bonding type rmsd covalent geometry : bond 0.00329 (14395) covalent geometry : angle 0.65780 (19814) hydrogen bonds : bond 0.04285 ( 661) hydrogen bonds : angle 4.78364 ( 1717) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9217 (m-30) cc_final: 0.8877 (t0) REVERT: G 797 MET cc_start: 0.9401 (tmm) cc_final: 0.8959 (tmm) REVERT: U 144 MET cc_start: 0.9293 (mtp) cc_final: 0.8942 (mtm) REVERT: U 182 ARG cc_start: 0.9347 (mtt180) cc_final: 0.9043 (mmt180) REVERT: U 194 ASP cc_start: 0.9202 (m-30) cc_final: 0.8944 (t0) REVERT: U 392 MET cc_start: 0.9420 (mtm) cc_final: 0.8996 (ttm) REVERT: U 396 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7234 (t0) REVERT: U 460 MET cc_start: 0.9382 (mtt) cc_final: 0.9118 (mtp) REVERT: U 507 MET cc_start: 0.9480 (mmm) cc_final: 0.9068 (mpp) REVERT: V 305 MET cc_start: 0.9418 (mmm) cc_final: 0.9198 (mmm) REVERT: W 77 MET cc_start: 0.9449 (mmm) cc_final: 0.8545 (mmm) REVERT: W 82 MET cc_start: 0.8384 (mtm) cc_final: 0.8094 (mtm) REVERT: W 148 MET cc_start: 0.8821 (ttm) cc_final: 0.8357 (tpp) outliers start: 13 outliers final: 6 residues processed: 101 average time/residue: 0.1157 time to fit residues: 17.1321 Evaluate side-chains 82 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 396 ASN Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain W residue 20 GLU Chi-restraints excluded: chain W residue 438 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 139 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 152 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 157 optimal weight: 0.8980 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.053198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.035677 restraints weight = 63573.870| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 3.35 r_work: 0.2548 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 14395 Z= 0.274 Angle : 0.662 9.481 19814 Z= 0.349 Chirality : 0.043 0.149 2150 Planarity : 0.005 0.055 2299 Dihedral : 19.123 82.047 2583 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.81 % Favored : 97.13 % Rotamer: Outliers : 1.66 % Allowed : 7.76 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.22), residues: 1532 helix: 1.01 (0.21), residues: 642 sheet: 0.69 (0.37), residues: 203 loop : 0.52 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG W 452 TYR 0.022 0.002 TYR G 754 PHE 0.018 0.001 PHE U 235 TRP 0.020 0.002 TRP W 449 HIS 0.015 0.002 HIS V 235 Details of bonding type rmsd covalent geometry : bond 0.00595 (14395) covalent geometry : angle 0.66163 (19814) hydrogen bonds : bond 0.04475 ( 661) hydrogen bonds : angle 4.63265 ( 1717) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9252 (m-30) cc_final: 0.8833 (t0) REVERT: G 797 MET cc_start: 0.9416 (tmm) cc_final: 0.8835 (tmm) REVERT: G 798 MET cc_start: 0.9512 (mmt) cc_final: 0.9012 (mmm) REVERT: G 805 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7788 (mm-30) REVERT: U 182 ARG cc_start: 0.9428 (mtt180) cc_final: 0.9179 (mmt180) REVERT: U 194 ASP cc_start: 0.9040 (m-30) cc_final: 0.8714 (t70) REVERT: U 216 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8727 (pm20) REVERT: U 392 MET cc_start: 0.9426 (OUTLIER) cc_final: 0.8920 (ttm) REVERT: U 396 ASN cc_start: 0.7411 (OUTLIER) cc_final: 0.7151 (t0) REVERT: U 442 GLN cc_start: 0.9468 (OUTLIER) cc_final: 0.8975 (mt0) REVERT: U 507 MET cc_start: 0.9522 (mmm) cc_final: 0.9104 (mpp) REVERT: U 664 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8764 (ptm) REVERT: V 120 THR cc_start: 0.9547 (OUTLIER) cc_final: 0.9162 (p) REVERT: W 77 MET cc_start: 0.9453 (mmm) cc_final: 0.8834 (mmm) REVERT: W 82 MET cc_start: 0.8592 (mtm) cc_final: 0.8354 (mtm) REVERT: W 148 MET cc_start: 0.8933 (ttm) cc_final: 0.8468 (tpp) REVERT: W 252 GLU cc_start: 0.9218 (OUTLIER) cc_final: 0.8841 (mm-30) REVERT: W 411 MET cc_start: 0.8767 (ptm) cc_final: 0.8380 (ptp) REVERT: X 151 GLN cc_start: 0.8514 (tp-100) cc_final: 0.8247 (tp-100) outliers start: 22 outliers final: 6 residues processed: 90 average time/residue: 0.1128 time to fit residues: 15.4171 Evaluate side-chains 84 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 216 GLN Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 364 VAL Chi-restraints excluded: chain U residue 392 MET Chi-restraints excluded: chain U residue 396 ASN Chi-restraints excluded: chain U residue 442 GLN Chi-restraints excluded: chain U residue 664 MET Chi-restraints excluded: chain V residue 120 THR Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain W residue 438 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 84 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 425 GLN ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.053913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.036410 restraints weight = 63258.816| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.36 r_work: 0.2576 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14395 Z= 0.168 Angle : 0.573 9.492 19814 Z= 0.301 Chirality : 0.040 0.139 2150 Planarity : 0.004 0.039 2299 Dihedral : 18.978 81.671 2583 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.68 % Favored : 97.26 % Rotamer: Outliers : 1.66 % Allowed : 8.06 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.22), residues: 1532 helix: 1.43 (0.22), residues: 641 sheet: 0.62 (0.37), residues: 203 loop : 0.67 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 242 TYR 0.015 0.001 TYR G 754 PHE 0.013 0.001 PHE U 235 TRP 0.016 0.001 TRP W 433 HIS 0.009 0.001 HIS V 235 Details of bonding type rmsd covalent geometry : bond 0.00367 (14395) covalent geometry : angle 0.57280 (19814) hydrogen bonds : bond 0.03485 ( 661) hydrogen bonds : angle 4.25407 ( 1717) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9240 (m-30) cc_final: 0.8803 (t0) REVERT: G 805 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7920 (mm-30) REVERT: U 181 MET cc_start: 0.9591 (ttp) cc_final: 0.9165 (ptt) REVERT: U 182 ARG cc_start: 0.9377 (mtt180) cc_final: 0.9150 (mmt180) REVERT: U 194 ASP cc_start: 0.9026 (m-30) cc_final: 0.8728 (t70) REVERT: U 216 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8755 (pm20) REVERT: U 392 MET cc_start: 0.9427 (mtm) cc_final: 0.9226 (ttm) REVERT: U 396 ASN cc_start: 0.7506 (OUTLIER) cc_final: 0.7256 (t0) REVERT: U 442 GLN cc_start: 0.9439 (OUTLIER) cc_final: 0.8823 (mt0) REVERT: U 507 MET cc_start: 0.9488 (mmm) cc_final: 0.9113 (mpp) REVERT: U 664 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8640 (ptm) REVERT: V 235 HIS cc_start: 0.7809 (p-80) cc_final: 0.7550 (p-80) REVERT: W 77 MET cc_start: 0.9444 (mmm) cc_final: 0.8862 (mmm) REVERT: W 82 MET cc_start: 0.8557 (mtm) cc_final: 0.8117 (mtt) REVERT: W 148 MET cc_start: 0.8915 (ttm) cc_final: 0.8518 (tpp) REVERT: W 197 ASP cc_start: 0.8555 (t0) cc_final: 0.8180 (p0) REVERT: W 252 GLU cc_start: 0.9273 (OUTLIER) cc_final: 0.8983 (mm-30) REVERT: W 411 MET cc_start: 0.8657 (ptm) cc_final: 0.8298 (ptp) REVERT: X 151 GLN cc_start: 0.8403 (tp-100) cc_final: 0.8158 (tp-100) outliers start: 22 outliers final: 7 residues processed: 98 average time/residue: 0.1060 time to fit residues: 15.9872 Evaluate side-chains 83 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 216 GLN Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 396 ASN Chi-restraints excluded: chain U residue 442 GLN Chi-restraints excluded: chain U residue 664 MET Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain W residue 438 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 100 optimal weight: 0.2980 chunk 5 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.054702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.037130 restraints weight = 62767.696| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 3.26 r_work: 0.2607 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14395 Z= 0.120 Angle : 0.538 7.569 19814 Z= 0.285 Chirality : 0.040 0.139 2150 Planarity : 0.004 0.041 2299 Dihedral : 18.727 81.556 2583 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 0.90 % Allowed : 8.74 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.22), residues: 1532 helix: 1.63 (0.22), residues: 636 sheet: 0.46 (0.36), residues: 217 loop : 0.84 (0.25), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 150 TYR 0.013 0.001 TYR G 754 PHE 0.010 0.001 PHE U 235 TRP 0.013 0.001 TRP W 433 HIS 0.007 0.001 HIS V 235 Details of bonding type rmsd covalent geometry : bond 0.00253 (14395) covalent geometry : angle 0.53829 (19814) hydrogen bonds : bond 0.03154 ( 661) hydrogen bonds : angle 4.11220 ( 1717) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9185 (m-30) cc_final: 0.8696 (t0) REVERT: G 805 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7896 (mm-30) REVERT: U 181 MET cc_start: 0.9645 (ttp) cc_final: 0.9169 (ptt) REVERT: U 182 ARG cc_start: 0.9367 (mtt180) cc_final: 0.9152 (mmt180) REVERT: U 194 ASP cc_start: 0.9015 (m-30) cc_final: 0.8700 (t70) REVERT: U 460 MET cc_start: 0.9443 (mtt) cc_final: 0.9156 (mtp) REVERT: U 507 MET cc_start: 0.9472 (mmm) cc_final: 0.9043 (mpp) REVERT: U 703 MET cc_start: 0.8586 (mtp) cc_final: 0.8206 (mtp) REVERT: V 235 HIS cc_start: 0.7851 (p-80) cc_final: 0.7611 (p-80) REVERT: W 77 MET cc_start: 0.9432 (mmm) cc_final: 0.8848 (mmm) REVERT: W 82 MET cc_start: 0.8442 (mtm) cc_final: 0.8069 (mtt) REVERT: W 148 MET cc_start: 0.8874 (ttm) cc_final: 0.8608 (tpp) REVERT: W 197 ASP cc_start: 0.8528 (t0) cc_final: 0.8142 (p0) REVERT: W 252 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.8968 (mm-30) REVERT: X 151 GLN cc_start: 0.8345 (tp-100) cc_final: 0.8076 (tp40) outliers start: 12 outliers final: 6 residues processed: 86 average time/residue: 0.1023 time to fit residues: 13.8628 Evaluate side-chains 78 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain W residue 438 ILE Chi-restraints excluded: chain X residue 182 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 121 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 154 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 24 GLN ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.053468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.035961 restraints weight = 63606.086| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.35 r_work: 0.2564 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14395 Z= 0.211 Angle : 0.575 7.508 19814 Z= 0.302 Chirality : 0.040 0.158 2150 Planarity : 0.004 0.043 2299 Dihedral : 18.733 81.189 2581 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.61 % Rotamer: Outliers : 1.28 % Allowed : 9.04 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.22), residues: 1532 helix: 1.56 (0.22), residues: 645 sheet: 0.37 (0.35), residues: 223 loop : 0.80 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 202 TYR 0.015 0.001 TYR G 754 PHE 0.013 0.001 PHE U 235 TRP 0.015 0.001 TRP U 219 HIS 0.008 0.001 HIS V 235 Details of bonding type rmsd covalent geometry : bond 0.00460 (14395) covalent geometry : angle 0.57507 (19814) hydrogen bonds : bond 0.03634 ( 661) hydrogen bonds : angle 4.18693 ( 1717) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9240 (m-30) cc_final: 0.8791 (t0) REVERT: U 181 MET cc_start: 0.9654 (ttp) cc_final: 0.9136 (ptt) REVERT: U 182 ARG cc_start: 0.9403 (mtt180) cc_final: 0.9155 (mmt180) REVERT: U 194 ASP cc_start: 0.9014 (m-30) cc_final: 0.8652 (t0) REVERT: U 442 GLN cc_start: 0.9399 (OUTLIER) cc_final: 0.9041 (mp10) REVERT: U 507 MET cc_start: 0.9498 (mmm) cc_final: 0.9114 (mmm) REVERT: V 235 HIS cc_start: 0.7914 (p-80) cc_final: 0.7702 (p-80) REVERT: W 77 MET cc_start: 0.9428 (mmm) cc_final: 0.8842 (mmm) REVERT: W 82 MET cc_start: 0.8587 (mtm) cc_final: 0.8126 (mtt) REVERT: W 148 MET cc_start: 0.8970 (ttm) cc_final: 0.8661 (tpt) REVERT: W 252 GLU cc_start: 0.9295 (OUTLIER) cc_final: 0.8996 (mm-30) REVERT: W 411 MET cc_start: 0.8770 (ptm) cc_final: 0.8422 (ptp) REVERT: X 198 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8480 (tppt) outliers start: 17 outliers final: 12 residues processed: 86 average time/residue: 0.1035 time to fit residues: 13.5840 Evaluate side-chains 84 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 364 VAL Chi-restraints excluded: chain U residue 442 GLN Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain W residue 42 MET Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain W residue 438 ILE Chi-restraints excluded: chain X residue 158 LEU Chi-restraints excluded: chain X residue 182 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 28 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 48 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 118 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 96 optimal weight: 0.0570 overall best weight: 1.2702 ------------------------------------------------------------------------------- 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 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.053977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.037081 restraints weight = 62946.975| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.36 r_work: 0.2593 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14395 Z= 0.120 Angle : 0.538 8.794 19814 Z= 0.282 Chirality : 0.039 0.177 2150 Planarity : 0.004 0.044 2299 Dihedral : 18.602 81.346 2581 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.94 % Favored : 97.00 % Rotamer: Outliers : 1.13 % Allowed : 9.42 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.22), residues: 1532 helix: 1.65 (0.22), residues: 646 sheet: 0.42 (0.35), residues: 222 loop : 0.89 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 242 TYR 0.012 0.001 TYR G 754 PHE 0.010 0.001 PHE V 375 TRP 0.013 0.001 TRP U 219 HIS 0.007 0.001 HIS V 235 Details of bonding type rmsd covalent geometry : bond 0.00261 (14395) covalent geometry : angle 0.53830 (19814) hydrogen bonds : bond 0.03029 ( 661) hydrogen bonds : angle 4.01029 ( 1717) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9202 (m-30) cc_final: 0.8695 (t0) REVERT: G 794 MET cc_start: 0.9362 (ttt) cc_final: 0.9143 (ttm) REVERT: U 181 MET cc_start: 0.9657 (ttp) cc_final: 0.9192 (ptt) REVERT: U 194 ASP cc_start: 0.8988 (m-30) cc_final: 0.8669 (t0) REVERT: U 391 MET cc_start: 0.8783 (mtm) cc_final: 0.8410 (ptp) REVERT: U 442 GLN cc_start: 0.9377 (OUTLIER) cc_final: 0.8285 (mp10) REVERT: U 507 MET cc_start: 0.9477 (mmm) cc_final: 0.9136 (mpp) REVERT: V 235 HIS cc_start: 0.7902 (p-80) cc_final: 0.7695 (p-80) REVERT: W 77 MET cc_start: 0.9369 (mmm) cc_final: 0.8786 (mmm) REVERT: W 82 MET cc_start: 0.8533 (mtm) cc_final: 0.8232 (mtt) REVERT: W 148 MET cc_start: 0.8994 (ttm) cc_final: 0.8784 (tpp) REVERT: W 252 GLU cc_start: 0.9296 (OUTLIER) cc_final: 0.8983 (mm-30) REVERT: W 411 MET cc_start: 0.8697 (ptm) cc_final: 0.8345 (ptp) REVERT: X 198 LYS cc_start: 0.8739 (mmmt) cc_final: 0.8469 (tppt) outliers start: 15 outliers final: 11 residues processed: 90 average time/residue: 0.0970 time to fit residues: 13.8328 Evaluate side-chains 83 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 442 GLN Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain W residue 265 CYS Chi-restraints excluded: chain W residue 438 ILE Chi-restraints excluded: chain X residue 158 LEU Chi-restraints excluded: chain X residue 182 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 113 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 151 optimal weight: 0.1980 chunk 93 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 646 GLN ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.054559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.037054 restraints weight = 62826.062| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 3.38 r_work: 0.2607 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14395 Z= 0.113 Angle : 0.536 8.283 19814 Z= 0.280 Chirality : 0.039 0.146 2150 Planarity : 0.004 0.051 2299 Dihedral : 18.477 79.747 2581 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.94 % Favored : 97.00 % Rotamer: Outliers : 1.13 % Allowed : 9.72 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.23), residues: 1532 helix: 1.76 (0.22), residues: 640 sheet: 0.47 (0.35), residues: 224 loop : 0.96 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG U 182 TYR 0.011 0.001 TYR G 754 PHE 0.011 0.001 PHE V 375 TRP 0.013 0.001 TRP U 219 HIS 0.006 0.001 HIS V 235 Details of bonding type rmsd covalent geometry : bond 0.00245 (14395) covalent geometry : angle 0.53560 (19814) hydrogen bonds : bond 0.02963 ( 661) hydrogen bonds : angle 3.93868 ( 1717) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9181 (m-30) cc_final: 0.8681 (t0) REVERT: U 181 MET cc_start: 0.9667 (ttp) cc_final: 0.9013 (ptt) REVERT: U 194 ASP cc_start: 0.9040 (m-30) cc_final: 0.8737 (t0) REVERT: U 442 GLN cc_start: 0.9385 (OUTLIER) cc_final: 0.8334 (mp10) REVERT: U 507 MET cc_start: 0.9459 (mmm) cc_final: 0.9134 (mpp) REVERT: U 703 MET cc_start: 0.8718 (ptm) cc_final: 0.8441 (ptt) REVERT: V 235 HIS cc_start: 0.7849 (p-80) cc_final: 0.7637 (p-80) REVERT: W 77 MET cc_start: 0.9417 (mmm) cc_final: 0.8844 (mmm) REVERT: W 82 MET cc_start: 0.8559 (mtm) cc_final: 0.8230 (mtt) REVERT: W 143 GLU cc_start: 0.9295 (OUTLIER) cc_final: 0.8936 (pm20) REVERT: W 197 ASP cc_start: 0.8535 (t0) cc_final: 0.8103 (p0) REVERT: W 252 GLU cc_start: 0.9275 (OUTLIER) cc_final: 0.8965 (mm-30) REVERT: W 411 MET cc_start: 0.8715 (ptm) cc_final: 0.8371 (ptp) outliers start: 15 outliers final: 11 residues processed: 85 average time/residue: 0.1046 time to fit residues: 14.0612 Evaluate side-chains 83 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 404 LEU Chi-restraints excluded: chain U residue 442 GLN Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 143 GLU Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain W residue 265 CYS Chi-restraints excluded: chain W residue 438 ILE Chi-restraints excluded: chain X residue 158 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 143 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 147 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.053922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.036585 restraints weight = 63324.837| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 3.38 r_work: 0.2588 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14395 Z= 0.145 Angle : 0.550 8.642 19814 Z= 0.285 Chirality : 0.040 0.334 2150 Planarity : 0.004 0.045 2299 Dihedral : 18.460 78.651 2581 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.26 % Favored : 96.67 % Rotamer: Outliers : 1.28 % Allowed : 9.34 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.23), residues: 1532 helix: 1.84 (0.22), residues: 640 sheet: 0.48 (0.36), residues: 222 loop : 1.00 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 242 TYR 0.011 0.001 TYR G 754 PHE 0.013 0.001 PHE V 375 TRP 0.013 0.001 TRP U 219 HIS 0.007 0.001 HIS V 235 Details of bonding type rmsd covalent geometry : bond 0.00318 (14395) covalent geometry : angle 0.55017 (19814) hydrogen bonds : bond 0.03093 ( 661) hydrogen bonds : angle 3.93912 ( 1717) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9204 (m-30) cc_final: 0.8683 (t0) REVERT: U 181 MET cc_start: 0.9649 (ttp) cc_final: 0.9066 (ptt) REVERT: U 194 ASP cc_start: 0.9038 (m-30) cc_final: 0.8737 (t0) REVERT: U 216 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8500 (pm20) REVERT: U 218 GLU cc_start: 0.9378 (mt-10) cc_final: 0.9094 (mm-30) REVERT: U 442 GLN cc_start: 0.9401 (OUTLIER) cc_final: 0.9068 (mp10) REVERT: U 507 MET cc_start: 0.9463 (mmm) cc_final: 0.9118 (mmm) REVERT: V 235 HIS cc_start: 0.7753 (p-80) cc_final: 0.7536 (p-80) REVERT: W 77 MET cc_start: 0.9375 (mmm) cc_final: 0.8783 (mmm) REVERT: W 82 MET cc_start: 0.8605 (mtm) cc_final: 0.8245 (mtt) REVERT: W 143 GLU cc_start: 0.9310 (OUTLIER) cc_final: 0.8965 (pm20) REVERT: W 148 MET cc_start: 0.8772 (tpp) cc_final: 0.8266 (tpp) REVERT: W 197 ASP cc_start: 0.8552 (t0) cc_final: 0.8106 (p0) REVERT: W 252 GLU cc_start: 0.9300 (OUTLIER) cc_final: 0.8980 (mm-30) REVERT: W 411 MET cc_start: 0.8617 (ptm) cc_final: 0.8279 (ptp) outliers start: 17 outliers final: 12 residues processed: 87 average time/residue: 0.0979 time to fit residues: 13.5484 Evaluate side-chains 87 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 216 GLN Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 404 LEU Chi-restraints excluded: chain U residue 442 GLN Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 143 GLU Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain W residue 265 CYS Chi-restraints excluded: chain W residue 438 ILE Chi-restraints excluded: chain X residue 158 LEU Chi-restraints excluded: chain X residue 182 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 4 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 154 optimal weight: 6.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.053940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.036617 restraints weight = 63348.476| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.40 r_work: 0.2590 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14395 Z= 0.140 Angle : 0.553 9.132 19814 Z= 0.286 Chirality : 0.040 0.316 2150 Planarity : 0.004 0.045 2299 Dihedral : 18.459 77.949 2581 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.93 % Rotamer: Outliers : 1.28 % Allowed : 9.65 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.23), residues: 1532 helix: 1.83 (0.22), residues: 640 sheet: 0.46 (0.36), residues: 222 loop : 1.00 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 17 TYR 0.011 0.001 TYR G 754 PHE 0.013 0.001 PHE V 375 TRP 0.013 0.001 TRP U 219 HIS 0.006 0.001 HIS V 235 Details of bonding type rmsd covalent geometry : bond 0.00307 (14395) covalent geometry : angle 0.55316 (19814) hydrogen bonds : bond 0.03064 ( 661) hydrogen bonds : angle 3.93230 ( 1717) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9200 (m-30) cc_final: 0.8681 (t0) REVERT: U 181 MET cc_start: 0.9634 (ttp) cc_final: 0.9035 (ptt) REVERT: U 194 ASP cc_start: 0.9039 (m-30) cc_final: 0.8734 (t0) REVERT: U 216 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8494 (pm20) REVERT: U 218 GLU cc_start: 0.9344 (mt-10) cc_final: 0.9077 (mm-30) REVERT: U 391 MET cc_start: 0.8769 (mtm) cc_final: 0.8384 (ptp) REVERT: U 442 GLN cc_start: 0.9402 (OUTLIER) cc_final: 0.9077 (mp10) REVERT: U 507 MET cc_start: 0.9459 (mmm) cc_final: 0.9112 (mmm) REVERT: W 77 MET cc_start: 0.9366 (mmm) cc_final: 0.8781 (mmm) REVERT: W 82 MET cc_start: 0.8615 (mtm) cc_final: 0.8242 (mtt) REVERT: W 143 GLU cc_start: 0.9333 (OUTLIER) cc_final: 0.9011 (pm20) REVERT: W 148 MET cc_start: 0.8719 (tpp) cc_final: 0.8342 (tpp) REVERT: W 252 GLU cc_start: 0.9300 (OUTLIER) cc_final: 0.8988 (mm-30) REVERT: W 411 MET cc_start: 0.8600 (ptm) cc_final: 0.8235 (ptp) outliers start: 17 outliers final: 12 residues processed: 87 average time/residue: 0.0949 time to fit residues: 13.2737 Evaluate side-chains 86 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 216 GLN Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 404 LEU Chi-restraints excluded: chain U residue 442 GLN Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 143 GLU Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain W residue 265 CYS Chi-restraints excluded: chain W residue 438 ILE Chi-restraints excluded: chain X residue 158 LEU Chi-restraints excluded: chain X residue 182 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 18 optimal weight: 0.4980 chunk 122 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.054287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.036947 restraints weight = 62987.662| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.40 r_work: 0.2602 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14395 Z= 0.120 Angle : 0.547 9.193 19814 Z= 0.283 Chirality : 0.040 0.291 2150 Planarity : 0.004 0.044 2299 Dihedral : 18.413 77.616 2581 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.74 % Favored : 97.19 % Rotamer: Outliers : 1.28 % Allowed : 10.02 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.22), residues: 1532 helix: 1.80 (0.22), residues: 645 sheet: 0.45 (0.35), residues: 223 loop : 1.02 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 803 TYR 0.010 0.001 TYR G 754 PHE 0.013 0.001 PHE V 375 TRP 0.011 0.001 TRP W 433 HIS 0.014 0.001 HIS V 235 Details of bonding type rmsd covalent geometry : bond 0.00262 (14395) covalent geometry : angle 0.54700 (19814) hydrogen bonds : bond 0.02919 ( 661) hydrogen bonds : angle 3.87851 ( 1717) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2542.33 seconds wall clock time: 44 minutes 28.21 seconds (2668.21 seconds total)