Starting phenix.real_space_refine on Sat Sep 12 05:42:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a5p_15180/09_2026/8a5p_15180_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a5p_15180/09_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_15180/09_2026/8a5p_15180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a5p_15180/09_2026/8a5p_15180.map" model { file = "/net/cci-nas-00/data/ceres_data/8a5p_15180/09_2026/8a5p_15180_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a5p_15180/09_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-2.2.1-6174/lib/python3.11/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: 3.06, per 1000 atoms: 0.22 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: 1.12 Conformation dependent library (CDL) restraints added in 613.9 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: 1.84 Creating SS restraints... Processing helix chain 'G' and resid 724 through 741 Processing helix chain 'G' and resid 741 through 775 removed outlier: 3.508A 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: 2.77 Time building geometry restraints manager: 1.54 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: 19465 4.36 - 8.72: 337 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 - 0.132: 1793 0.132 - 0.264: 292 0.264 - 0.396: 63 0.396 - 0.527: 0 0.527 - 0.659: 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 2.34 -2.99 -0.66 2.00e-01 2.50e+01 1.09e+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 2.34 -2.94 -0.60 2.00e-01 2.50e+01 9.07e+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 2.34 -2.69 -0.36 2.00e-01 2.50e+01 3.18e+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: 0.680 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.200 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 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 : 0.012 0.131 14395 Z= 0.764 Angle : 1.660 21.811 19814 Z= 1.160 Chirality : 0.103 0.659 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/Z covalent geometry : bond 0.01158 / 0.76 (14395) covalent geometry : angle 1.65974 / 1.16 (19814) hydrogen bonds : bond 0.16485 / 11.18 ( 661) hydrogen bonds : angle 7.04637 / 6.95 ( 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 : 0.548 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: 0.1298 time to fit residues: 25.2852 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 : 0.433 ------------------------------------------------------------------------------- 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: 40.0000 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... U 110 HIS U 184 ASN U 425 GLN V 275 HIS W 458 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.055961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.038227 restraints weight = 61043.431| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 3.30 r_work: 0.2616 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14395 Z= 0.156 Angle : 0.718 9.640 19814 Z= 0.390 Chirality : 0.047 0.273 2150 Planarity : 0.005 0.051 2299 Dihedral : 19.103 78.822 2588 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.35 % Favored : 97.52 % Rotamer: Outliers : 1.13 % Allowed : 6.41 % Favored : 92.46 % 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: 0.40 (0.21), residues: 1532 helix: 0.35 (0.20), residues: 644 sheet: 0.76 (0.36), residues: 193 loop : 0.23 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG V 290 TYR 0.022 0.002 TYR G 754 PHE 0.012 0.002 PHE U 397 TRP 0.031 0.002 TRP W 433 HIS 0.008 0.001 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 (14395) covalent geometry : angle 0.71806 / 0.39 (19814) hydrogen bonds : bond 0.04926 / 3.24 ( 661) hydrogen bonds : angle 4.93837 / 4.91 ( 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 103 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9218 (m-30) cc_final: 0.8875 (t0) REVERT: G 797 MET cc_start: 0.9378 (tmm) cc_final: 0.8946 (tmm) REVERT: G 798 MET cc_start: 0.9249 (mmt) cc_final: 0.9041 (mmt) REVERT: U 144 MET cc_start: 0.9360 (mtp) cc_final: 0.9017 (mtm) REVERT: U 182 ARG cc_start: 0.9323 (mtt180) cc_final: 0.9008 (mmt180) REVERT: U 184 ASN cc_start: 0.9365 (m110) cc_final: 0.8968 (m110) REVERT: U 194 ASP cc_start: 0.9211 (m-30) cc_final: 0.8969 (t0) REVERT: U 392 MET cc_start: 0.9414 (mtm) cc_final: 0.8902 (ttm) REVERT: U 396 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.7724 (t0) REVERT: U 425 GLN cc_start: 0.8674 (tt0) cc_final: 0.8078 (tt0) REVERT: U 507 MET cc_start: 0.9467 (mmm) cc_final: 0.9070 (mpp) REVERT: U 664 MET cc_start: 0.8961 (ttt) cc_final: 0.8462 (ptm) REVERT: V 305 MET cc_start: 0.9377 (mmm) cc_final: 0.9152 (mmm) REVERT: V 313 MET cc_start: 0.9521 (tpp) cc_final: 0.9217 (tpp) REVERT: W 77 MET cc_start: 0.9479 (mmm) cc_final: 0.8528 (mmm) REVERT: W 82 MET cc_start: 0.8410 (mtm) cc_final: 0.8199 (mtm) REVERT: W 148 MET cc_start: 0.8857 (ttm) cc_final: 0.8313 (tpp) outliers start: 15 outliers final: 4 residues processed: 99 average time/residue: 0.1151 time to fit residues: 17.2736 Evaluate side-chains 80 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 139 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 396 ASN ** 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 = 0.3344 r_free = 0.3344 target = 0.055093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.037406 restraints weight = 61847.035| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.29 r_work: 0.2600 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14395 Z= 0.169 Angle : 0.620 8.488 19814 Z= 0.336 Chirality : 0.043 0.150 2150 Planarity : 0.004 0.059 2299 Dihedral : 19.321 77.191 2583 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.87 % Favored : 97.06 % Rotamer: Outliers : 1.13 % Allowed : 7.31 % Favored : 91.56 % 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: 0.99 (0.22), residues: 1532 helix: 0.95 (0.21), residues: 640 sheet: 0.83 (0.37), residues: 193 loop : 0.51 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG W 452 TYR 0.018 0.002 TYR G 754 PHE 0.010 0.001 PHE U 235 TRP 0.018 0.001 TRP W 433 HIS 0.012 0.001 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (14395) covalent geometry : angle 0.61991 / 0.34 (19814) hydrogen bonds : bond 0.04294 / 2.86 ( 661) hydrogen bonds : angle 4.57473 / 4.47 ( 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 94 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9218 (m-30) cc_final: 0.8842 (t0) REVERT: G 797 MET cc_start: 0.9418 (tmm) cc_final: 0.8950 (tmm) REVERT: G 805 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7707 (mm-30) REVERT: U 144 MET cc_start: 0.9278 (mtp) cc_final: 0.8881 (mtm) REVERT: U 181 MET cc_start: 0.9621 (ttp) cc_final: 0.9295 (ptt) REVERT: U 182 ARG cc_start: 0.9346 (mtt180) cc_final: 0.9044 (mmt180) REVERT: U 194 ASP cc_start: 0.9193 (m-30) cc_final: 0.8929 (t0) REVERT: U 392 MET cc_start: 0.9424 (OUTLIER) cc_final: 0.8950 (ttm) REVERT: U 396 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7240 (t0) REVERT: U 442 GLN cc_start: 0.9470 (OUTLIER) cc_final: 0.8736 (mp10) REVERT: U 507 MET cc_start: 0.9475 (mmm) cc_final: 0.9071 (mpp) REVERT: U 664 MET cc_start: 0.9040 (ttt) cc_final: 0.8708 (ptm) REVERT: V 235 HIS cc_start: 0.7830 (p-80) cc_final: 0.7592 (p-80) REVERT: V 313 MET cc_start: 0.9493 (tpp) cc_final: 0.9123 (tpp) REVERT: W 77 MET cc_start: 0.9459 (mmm) cc_final: 0.8791 (mmm) REVERT: W 82 MET cc_start: 0.8423 (mtm) cc_final: 0.8215 (mtm) REVERT: W 148 MET cc_start: 0.8895 (ttm) cc_final: 0.8416 (tpp) REVERT: W 197 ASP cc_start: 0.8699 (t0) cc_final: 0.8421 (p0) REVERT: W 252 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.8897 (mm-30) REVERT: W 425 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8884 (p) REVERT: W 448 MET cc_start: 0.9352 (mmm) cc_final: 0.8659 (mmt) outliers start: 15 outliers final: 5 residues processed: 91 average time/residue: 0.1083 time to fit residues: 15.1912 Evaluate side-chains 84 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 392 MET Chi-restraints excluded: chain U residue 396 ASN Chi-restraints excluded: chain U residue 442 GLN Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain W residue 425 THR 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: 8.9990 chunk 152 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 425 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 = 0.3317 r_free = 0.3317 target = 0.053818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.036173 restraints weight = 64205.376| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.30 r_work: 0.2561 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14395 Z= 0.251 Angle : 0.639 9.239 19814 Z= 0.339 Chirality : 0.042 0.142 2150 Planarity : 0.004 0.040 2299 Dihedral : 19.478 82.035 2583 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.07 % Favored : 96.87 % Rotamer: Outliers : 1.66 % Allowed : 8.36 % Favored : 89.98 % 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: 1.09 (0.22), residues: 1532 helix: 1.12 (0.21), residues: 643 sheet: 0.50 (0.37), residues: 203 loop : 0.59 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG W 381 TYR 0.019 0.002 TYR G 754 PHE 0.015 0.001 PHE U 235 TRP 0.015 0.002 TRP W 433 HIS 0.009 0.001 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.25 (14395) covalent geometry : angle 0.63887 / 0.34 (19814) hydrogen bonds : bond 0.04374 / 2.93 ( 661) hydrogen bonds : angle 4.52244 / 4.42 ( 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 95 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9247 (m-30) cc_final: 0.8823 (t0) REVERT: G 797 MET cc_start: 0.9456 (tmm) cc_final: 0.8927 (tmm) REVERT: G 798 MET cc_start: 0.9486 (mmt) cc_final: 0.9133 (mmm) REVERT: U 43 MET cc_start: 0.9246 (mtp) cc_final: 0.8866 (mtp) REVERT: U 181 MET cc_start: 0.9540 (ttp) cc_final: 0.8995 (ptm) REVERT: U 182 ARG cc_start: 0.9444 (mtt180) cc_final: 0.9215 (mmp-170) REVERT: U 194 ASP cc_start: 0.9087 (m-30) cc_final: 0.8780 (t70) REVERT: U 279 MET cc_start: 0.8941 (tpp) cc_final: 0.8325 (tpp) REVERT: U 392 MET cc_start: 0.9424 (OUTLIER) cc_final: 0.8932 (ttm) REVERT: U 396 ASN cc_start: 0.7734 (OUTLIER) cc_final: 0.7176 (t0) REVERT: U 442 GLN cc_start: 0.9470 (OUTLIER) cc_final: 0.8603 (mp10) REVERT: U 507 MET cc_start: 0.9473 (mmm) cc_final: 0.9037 (mpp) REVERT: U 664 MET cc_start: 0.9028 (ttt) cc_final: 0.8794 (ptm) REVERT: V 313 MET cc_start: 0.9475 (tpp) cc_final: 0.9216 (tpp) REVERT: W 77 MET cc_start: 0.9462 (mmm) cc_final: 0.8809 (mmm) REVERT: W 82 MET cc_start: 0.8581 (mtm) cc_final: 0.8322 (mtm) REVERT: W 148 MET cc_start: 0.8913 (ttm) cc_final: 0.8444 (tpp) REVERT: W 197 ASP cc_start: 0.8763 (t0) cc_final: 0.8377 (p0) REVERT: W 252 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.8963 (mm-30) REVERT: W 411 MET cc_start: 0.8792 (ptm) cc_final: 0.8429 (ptp) REVERT: W 425 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8956 (p) outliers start: 22 outliers final: 9 residues processed: 91 average time/residue: 0.1050 time to fit residues: 14.9638 Evaluate side-chains 85 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 392 MET Chi-restraints excluded: chain U residue 396 ASN 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 V residue 202 THR Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain W residue 425 THR 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: 3.9990 chunk 82 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 158 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.054750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.037130 restraints weight = 62512.030| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 3.37 r_work: 0.2598 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14395 Z= 0.124 Angle : 0.559 10.281 19814 Z= 0.300 Chirality : 0.041 0.145 2150 Planarity : 0.004 0.042 2299 Dihedral : 19.301 82.020 2583 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 0.98 % Allowed : 9.19 % Favored : 89.83 % 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: 1.37 (0.22), residues: 1532 helix: 1.44 (0.22), residues: 642 sheet: 0.54 (0.37), residues: 203 loop : 0.69 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG W 452 TYR 0.013 0.001 TYR G 754 PHE 0.009 0.001 PHE U 235 TRP 0.015 0.001 TRP W 433 HIS 0.014 0.001 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (14395) covalent geometry : angle 0.55925 / 0.30 (19814) hydrogen bonds : bond 0.03581 / 2.38 ( 661) hydrogen bonds : angle 4.25191 / 4.16 ( 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: 13 poor density : 76 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9239 (m-30) cc_final: 0.8821 (t0) REVERT: G 797 MET cc_start: 0.9431 (tmm) cc_final: 0.8860 (tmm) REVERT: U 35 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8343 (pt0) REVERT: U 181 MET cc_start: 0.9514 (ttp) cc_final: 0.8925 (ptm) REVERT: U 182 ARG cc_start: 0.9454 (mtt180) cc_final: 0.9169 (mmp-170) REVERT: U 194 ASP cc_start: 0.9079 (m-30) cc_final: 0.8768 (t70) REVERT: U 279 MET cc_start: 0.8917 (tpp) cc_final: 0.8316 (tpp) REVERT: U 392 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.8935 (ttm) REVERT: U 396 ASN cc_start: 0.7465 (OUTLIER) cc_final: 0.7165 (t0) REVERT: U 507 MET cc_start: 0.9490 (mmm) cc_final: 0.9089 (mpp) REVERT: U 733 MET cc_start: 0.9537 (mmm) cc_final: 0.9267 (mmm) REVERT: V 313 MET cc_start: 0.9474 (tpp) cc_final: 0.9250 (tpp) REVERT: W 77 MET cc_start: 0.9457 (mmm) cc_final: 0.8825 (mmm) REVERT: W 82 MET cc_start: 0.8549 (mtm) cc_final: 0.8092 (mtt) REVERT: W 148 MET cc_start: 0.8872 (ttm) cc_final: 0.8529 (tpp) REVERT: W 197 ASP cc_start: 0.8642 (t0) cc_final: 0.8280 (p0) REVERT: W 252 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8955 (mm-30) outliers start: 13 outliers final: 7 residues processed: 87 average time/residue: 0.1040 time to fit residues: 14.1998 Evaluate side-chains 80 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 35 GLN Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 392 MET Chi-restraints excluded: chain U residue 396 ASN 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 158 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 121 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.053790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.036253 restraints weight = 63439.429| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.26 r_work: 0.2571 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14395 Z= 0.209 Angle : 0.585 7.661 19814 Z= 0.310 Chirality : 0.041 0.147 2150 Planarity : 0.004 0.042 2299 Dihedral : 19.277 84.139 2583 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.13 % Favored : 96.80 % Rotamer: Outliers : 1.73 % Allowed : 9.34 % Favored : 88.92 % 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: 1.33 (0.22), residues: 1532 helix: 1.42 (0.22), residues: 643 sheet: 0.43 (0.37), residues: 203 loop : 0.69 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 483 TYR 0.016 0.001 TYR G 754 PHE 0.012 0.001 PHE U 235 TRP 0.012 0.001 TRP W 433 HIS 0.012 0.001 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.21 (14395) covalent geometry : angle 0.58492 / 0.31 (19814) hydrogen bonds : bond 0.04010 / 2.69 ( 661) hydrogen bonds : angle 4.27482 / 4.23 ( 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 93 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9226 (m-30) cc_final: 0.8819 (t0) REVERT: U 181 MET cc_start: 0.9476 (ttp) cc_final: 0.8942 (ptm) REVERT: U 182 ARG cc_start: 0.9453 (mtt180) cc_final: 0.9110 (mmt180) REVERT: U 194 ASP cc_start: 0.9027 (m-30) cc_final: 0.8702 (t0) REVERT: U 279 MET cc_start: 0.8933 (tpp) cc_final: 0.8306 (tpp) REVERT: U 442 GLN cc_start: 0.9459 (OUTLIER) cc_final: 0.8442 (mp10) REVERT: U 507 MET cc_start: 0.9495 (mmm) cc_final: 0.9157 (mmm) REVERT: V 313 MET cc_start: 0.9480 (tpp) cc_final: 0.9225 (tpp) REVERT: W 77 MET cc_start: 0.9460 (mmm) cc_final: 0.8846 (mmm) REVERT: W 82 MET cc_start: 0.8582 (mtm) cc_final: 0.8163 (mtm) REVERT: W 148 MET cc_start: 0.8933 (ttm) cc_final: 0.8625 (tpp) REVERT: W 197 ASP cc_start: 0.8659 (t0) cc_final: 0.8260 (p0) REVERT: W 252 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.8976 (mm-30) REVERT: W 411 MET cc_start: 0.8687 (ptm) cc_final: 0.8369 (ptp) outliers start: 23 outliers final: 10 residues processed: 88 average time/residue: 0.1055 time to fit residues: 14.6221 Evaluate side-chains 81 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 U residue 664 MET Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain V residue 134 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 48 optimal weight: 0.0870 chunk 71 optimal weight: 0.1980 chunk 90 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 40 optimal weight: 0.0670 chunk 96 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.054826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.037247 restraints weight = 62386.794| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.36 r_work: 0.2604 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14395 Z= 0.110 Angle : 0.545 7.683 19814 Z= 0.291 Chirality : 0.040 0.170 2150 Planarity : 0.004 0.044 2299 Dihedral : 19.148 82.553 2581 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.28 % Favored : 97.65 % Rotamer: Outliers : 0.90 % Allowed : 9.87 % Favored : 89.22 % 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: 1.48 (0.22), residues: 1532 helix: 1.58 (0.22), residues: 637 sheet: 0.41 (0.36), residues: 211 loop : 0.79 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG W 452 TYR 0.012 0.001 TYR G 754 PHE 0.007 0.001 PHE V 132 TRP 0.014 0.001 TRP W 433 HIS 0.008 0.001 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (14395) covalent geometry : angle 0.54504 / 0.29 (19814) hydrogen bonds : bond 0.03360 / 2.23 ( 661) hydrogen bonds : angle 4.12375 / 4.06 ( 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 89 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9205 (m-30) cc_final: 0.8794 (t0) REVERT: U 181 MET cc_start: 0.9522 (ttp) cc_final: 0.9267 (tpp) REVERT: U 182 ARG cc_start: 0.9456 (mtt180) cc_final: 0.9140 (mmp-170) REVERT: U 194 ASP cc_start: 0.8998 (m-30) cc_final: 0.8674 (t0) REVERT: U 279 MET cc_start: 0.8948 (tpp) cc_final: 0.8250 (tpp) REVERT: U 442 GLN cc_start: 0.9444 (OUTLIER) cc_final: 0.8560 (mp10) REVERT: U 460 MET cc_start: 0.9420 (mtt) cc_final: 0.9185 (mtp) REVERT: U 507 MET cc_start: 0.9469 (mmm) cc_final: 0.9080 (mpp) REVERT: V 82 MET cc_start: 0.9683 (tpt) cc_final: 0.9333 (tmm) REVERT: V 313 MET cc_start: 0.9434 (tpp) cc_final: 0.9177 (tpp) REVERT: W 77 MET cc_start: 0.9445 (mmm) cc_final: 0.8837 (mmm) REVERT: W 82 MET cc_start: 0.8506 (mtm) cc_final: 0.8102 (mtt) REVERT: W 148 MET cc_start: 0.8850 (ttm) cc_final: 0.8614 (tpp) REVERT: W 197 ASP cc_start: 0.8646 (t0) cc_final: 0.8227 (p0) REVERT: W 252 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.8956 (mm-30) REVERT: W 411 MET cc_start: 0.8635 (ptm) cc_final: 0.8329 (ptp) outliers start: 12 outliers final: 8 residues processed: 88 average time/residue: 0.1032 time to fit residues: 14.1406 Evaluate side-chains 82 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 35 GLN Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 442 GLN 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 158 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 113 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 100 optimal weight: 0.0060 chunk 45 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.054854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.037265 restraints weight = 62581.614| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 3.38 r_work: 0.2613 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14395 Z= 0.108 Angle : 0.540 8.022 19814 Z= 0.287 Chirality : 0.041 0.325 2150 Planarity : 0.004 0.043 2299 Dihedral : 19.055 83.211 2581 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.81 % Favored : 97.13 % Rotamer: Outliers : 0.98 % Allowed : 9.87 % 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: 1.46 (0.22), residues: 1532 helix: 1.54 (0.22), residues: 643 sheet: 0.33 (0.35), residues: 222 loop : 0.83 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 150 TYR 0.012 0.001 TYR G 754 PHE 0.008 0.001 PHE V 375 TRP 0.012 0.001 TRP W 433 HIS 0.008 0.001 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.11 (14395) covalent geometry : angle 0.54008 / 0.29 (19814) hydrogen bonds : bond 0.03332 / 2.22 ( 661) hydrogen bonds : angle 4.07867 / 4.02 ( 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 88 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9204 (m-30) cc_final: 0.8811 (t0) REVERT: G 794 MET cc_start: 0.9312 (ttt) cc_final: 0.9055 (ttm) REVERT: U 35 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8551 (pt0) REVERT: U 181 MET cc_start: 0.9521 (ttp) cc_final: 0.9266 (tpp) REVERT: U 182 ARG cc_start: 0.9453 (mtt180) cc_final: 0.9142 (mmp-170) REVERT: U 194 ASP cc_start: 0.9115 (m-30) cc_final: 0.8807 (t0) REVERT: U 279 MET cc_start: 0.8950 (tpp) cc_final: 0.8286 (tpp) REVERT: U 391 MET cc_start: 0.8803 (mtm) cc_final: 0.8349 (ptp) REVERT: U 442 GLN cc_start: 0.9423 (OUTLIER) cc_final: 0.9165 (mt0) REVERT: U 507 MET cc_start: 0.9466 (mmm) cc_final: 0.9088 (mpp) REVERT: V 82 MET cc_start: 0.9683 (tpt) cc_final: 0.9413 (mmm) REVERT: V 313 MET cc_start: 0.9436 (tpp) cc_final: 0.9162 (tpp) REVERT: W 77 MET cc_start: 0.9440 (mmm) cc_final: 0.8831 (mmm) REVERT: W 82 MET cc_start: 0.8495 (mtm) cc_final: 0.8101 (mtt) REVERT: W 148 MET cc_start: 0.8884 (ttm) cc_final: 0.8671 (tpp) REVERT: W 197 ASP cc_start: 0.8646 (t0) cc_final: 0.8248 (p0) REVERT: W 252 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8949 (mm-30) outliers start: 13 outliers final: 9 residues processed: 87 average time/residue: 0.1039 time to fit residues: 14.3185 Evaluate side-chains 85 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 35 GLN Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 442 GLN Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain V residue 134 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 143 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 24 GLN ** U 35 GLN ** 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 = 0.3326 r_free = 0.3326 target = 0.054093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.036541 restraints weight = 63773.145| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 3.31 r_work: 0.2585 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14395 Z= 0.184 Angle : 0.569 8.088 19814 Z= 0.299 Chirality : 0.041 0.292 2150 Planarity : 0.004 0.045 2299 Dihedral : 19.069 83.013 2581 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.13 % Favored : 96.80 % Rotamer: Outliers : 0.98 % Allowed : 10.02 % Favored : 89.00 % 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: 1.46 (0.23), residues: 1532 helix: 1.59 (0.22), residues: 644 sheet: 0.32 (0.36), residues: 223 loop : 0.76 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 242 TYR 0.014 0.001 TYR G 754 PHE 0.011 0.001 PHE V 255 TRP 0.010 0.001 TRP W 449 HIS 0.008 0.001 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (14395) covalent geometry : angle 0.56946 / 0.30 (19814) hydrogen bonds : bond 0.03573 / 2.40 ( 661) hydrogen bonds : angle 4.10536 / 4.05 ( 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 86 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9218 (m-30) cc_final: 0.8816 (t0) REVERT: U 181 MET cc_start: 0.9507 (ttp) cc_final: 0.9248 (tpp) REVERT: U 182 ARG cc_start: 0.9457 (mtt180) cc_final: 0.9145 (mmp-170) REVERT: U 194 ASP cc_start: 0.9032 (m-30) cc_final: 0.8680 (t0) REVERT: U 279 MET cc_start: 0.8972 (tpp) cc_final: 0.8312 (tpp) REVERT: U 442 GLN cc_start: 0.9411 (OUTLIER) cc_final: 0.8391 (mp10) REVERT: U 507 MET cc_start: 0.9486 (mmm) cc_final: 0.9098 (mmm) REVERT: V 82 MET cc_start: 0.9694 (tpt) cc_final: 0.9407 (mmm) REVERT: V 313 MET cc_start: 0.9447 (tpp) cc_final: 0.9164 (tpp) REVERT: V 325 MET cc_start: 0.8842 (mmt) cc_final: 0.8440 (mmm) REVERT: W 77 MET cc_start: 0.9456 (mmm) cc_final: 0.8845 (mmm) REVERT: W 82 MET cc_start: 0.8545 (mtm) cc_final: 0.8108 (mtt) REVERT: W 148 MET cc_start: 0.8865 (ttm) cc_final: 0.8614 (tpp) REVERT: W 197 ASP cc_start: 0.8683 (t0) cc_final: 0.8312 (p0) REVERT: W 252 GLU cc_start: 0.9275 (OUTLIER) cc_final: 0.8968 (mm-30) outliers start: 13 outliers final: 9 residues processed: 85 average time/residue: 0.1025 time to fit residues: 13.5810 Evaluate side-chains 84 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 132 PHE Chi-restraints excluded: chain V residue 134 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 4 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 70 optimal weight: 0.0670 chunk 10 optimal weight: 50.0000 chunk 86 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 overall best weight: 1.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... W 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.054605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.037095 restraints weight = 62679.116| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 3.37 r_work: 0.2608 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14395 Z= 0.118 Angle : 0.546 8.184 19814 Z= 0.288 Chirality : 0.040 0.271 2150 Planarity : 0.004 0.045 2299 Dihedral : 18.996 82.076 2581 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.68 % Favored : 97.26 % Rotamer: Outliers : 0.90 % Allowed : 10.25 % Favored : 88.85 % 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: 1.56 (0.23), residues: 1532 helix: 1.64 (0.22), residues: 639 sheet: 0.40 (0.36), residues: 223 loop : 0.85 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 283 TYR 0.012 0.001 TYR U 420 PHE 0.008 0.001 PHE V 375 TRP 0.012 0.001 TRP W 433 HIS 0.007 0.001 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (14395) covalent geometry : angle 0.54640 / 0.29 (19814) hydrogen bonds : bond 0.03232 / 2.16 ( 661) hydrogen bonds : angle 4.02769 / 3.97 ( 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 85 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9197 (m-30) cc_final: 0.8829 (t0) REVERT: G 794 MET cc_start: 0.9347 (ttt) cc_final: 0.9128 (ttm) REVERT: U 22 MET cc_start: 0.8724 (mmm) cc_final: 0.8378 (mmm) REVERT: U 43 MET cc_start: 0.9334 (mtp) cc_final: 0.8895 (mtp) REVERT: U 181 MET cc_start: 0.9509 (ttp) cc_final: 0.9249 (tpp) REVERT: U 182 ARG cc_start: 0.9445 (mtt180) cc_final: 0.9131 (mmp-170) REVERT: U 194 ASP cc_start: 0.9067 (m-30) cc_final: 0.8719 (t0) REVERT: U 279 MET cc_start: 0.8976 (tpp) cc_final: 0.8340 (tpp) REVERT: U 391 MET cc_start: 0.8770 (mtm) cc_final: 0.8401 (ptp) REVERT: U 442 GLN cc_start: 0.9398 (OUTLIER) cc_final: 0.9101 (mt0) REVERT: U 460 MET cc_start: 0.9439 (mtt) cc_final: 0.9229 (mtp) REVERT: U 507 MET cc_start: 0.9467 (mmm) cc_final: 0.9098 (mmm) REVERT: V 82 MET cc_start: 0.9684 (tpt) cc_final: 0.9429 (mmm) REVERT: V 313 MET cc_start: 0.9429 (tpp) cc_final: 0.9147 (tpp) REVERT: W 77 MET cc_start: 0.9461 (mmm) cc_final: 0.8856 (mmm) REVERT: W 82 MET cc_start: 0.8539 (mtm) cc_final: 0.8223 (mtt) REVERT: W 197 ASP cc_start: 0.8642 (t0) cc_final: 0.8271 (p0) REVERT: W 252 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.8952 (mm-30) REVERT: W 411 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8434 (ptm) REVERT: W 448 MET cc_start: 0.9285 (tpt) cc_final: 0.8803 (tpp) outliers start: 12 outliers final: 9 residues processed: 82 average time/residue: 0.1061 time to fit residues: 13.6786 Evaluate side-chains 85 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 132 PHE 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 411 MET Chi-restraints excluded: chain W residue 438 ILE Chi-restraints excluded: chain X residue 148 LYS Chi-restraints excluded: chain X residue 158 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 18 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 30 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** W 410 ASN ** 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 = 0.3336 r_free = 0.3336 target = 0.054372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.036922 restraints weight = 62661.634| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.37 r_work: 0.2605 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 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 0.040 14395 Z= 0.129 Angle : 0.552 10.403 19814 Z= 0.289 Chirality : 0.040 0.265 2150 Planarity : 0.004 0.045 2299 Dihedral : 18.943 82.512 2581 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.87 % Favored : 97.06 % Rotamer: Outliers : 0.90 % Allowed : 10.32 % Favored : 88.77 % 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: 1.62 (0.23), residues: 1532 helix: 1.71 (0.22), residues: 639 sheet: 0.38 (0.35), residues: 223 loop : 0.89 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 283 TYR 0.012 0.001 TYR G 754 PHE 0.008 0.001 PHE V 255 TRP 0.012 0.001 TRP X 186 HIS 0.008 0.001 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (14395) covalent geometry : angle 0.55211 / 0.29 (19814) hydrogen bonds : bond 0.03304 / 2.22 ( 661) hydrogen bonds : angle 4.02406 / 4.00 ( 1717) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2671.61 seconds wall clock time: 46 minutes 47.58 seconds (2807.58 seconds total)