Starting phenix.real_space_refine on Mon Dec 30 21:35:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a5p_15180/12_2024/8a5p_15180_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a5p_15180/12_2024/8a5p_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_15180/12_2024/8a5p_15180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a5p_15180/12_2024/8a5p_15180.map" model { file = "/net/cci-nas-00/data/ceres_data/8a5p_15180/12_2024/8a5p_15180_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a5p_15180/12_2024/8a5p_15180_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 7.97, per 1000 atoms: 0.57 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: 3.46 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 5.73 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: 6.41 Time building geometry restraints manager: 4.13 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 38.050 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.400 ------------------------------------------------------------------------------- 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= 0.728 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (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 TRP 0.093 0.017 TRP V 340 HIS 0.020 0.005 HIS U 320 PHE 0.073 0.012 PHE U 716 TYR 0.079 0.016 TYR U 314 ARG 0.028 0.004 ARG U 17 *********************** 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 : 1.592 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 182 ARG cc_start: 0.9595 (mtt180) cc_final: 0.9222 (mmp-170) REVERT: U 194 ASP cc_start: 0.9414 (m-30) cc_final: 0.9179 (t70) REVERT: U 396 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.7962 (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: 0.3302 time to fit residues: 62.9392 Evaluate side-chains 78 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 1.570 ------------------------------------------------------------------------------- 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 134 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 14395 Z= 0.204 Angle : 0.642 9.169 19814 Z= 0.347 Chirality : 0.042 0.162 2150 Planarity : 0.005 0.062 2299 Dihedral : 19.004 74.278 2588 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.21), residues: 1532 helix: 0.60 (0.20), residues: 642 sheet: 1.03 (0.37), residues: 193 loop : 0.38 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP W 433 HIS 0.004 0.001 HIS V 235 PHE 0.012 0.002 PHE V 375 TYR 0.016 0.002 TYR U 463 ARG 0.008 0.000 ARG U 201 *********************** 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 : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9718 (m-30) cc_final: 0.9450 (t0) REVERT: G 797 MET cc_start: 0.9468 (tmm) cc_final: 0.8990 (tmm) REVERT: U 182 ARG cc_start: 0.9534 (mtt180) cc_final: 0.9266 (mmt180) REVERT: U 392 MET cc_start: 0.9504 (mtm) cc_final: 0.9136 (ttm) REVERT: U 396 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7200 (t0) REVERT: U 425 GLN cc_start: 0.9168 (tt0) cc_final: 0.8818 (tt0) REVERT: U 507 MET cc_start: 0.9485 (mmm) cc_final: 0.9256 (mpp) REVERT: V 120 THR cc_start: 0.9382 (m) cc_final: 0.9016 (p) REVERT: V 235 HIS cc_start: 0.8965 (OUTLIER) cc_final: 0.8657 (p-80) REVERT: W 77 MET cc_start: 0.9236 (mmm) cc_final: 0.8658 (mmm) REVERT: W 82 MET cc_start: 0.8796 (mtm) cc_final: 0.8373 (mtt) outliers start: 13 outliers final: 6 residues processed: 101 average time/residue: 0.2703 time to fit residues: 41.1732 Evaluate side-chains 84 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 V residue 235 HIS 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 80 optimal weight: 3.9990 chunk 44 optimal weight: 0.0370 chunk 120 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 144 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14395 Z= 0.173 Angle : 0.559 9.495 19814 Z= 0.300 Chirality : 0.040 0.152 2150 Planarity : 0.004 0.064 2299 Dihedral : 18.797 77.986 2583 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.68 % Favored : 97.26 % Rotamer: Outliers : 1.13 % Allowed : 7.91 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.22), residues: 1532 helix: 1.23 (0.21), residues: 643 sheet: 0.72 (0.37), residues: 207 loop : 0.76 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP W 433 HIS 0.003 0.001 HIS V 275 PHE 0.015 0.001 PHE U 235 TYR 0.015 0.001 TYR G 754 ARG 0.005 0.000 ARG U 201 *********************** 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 98 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9725 (m-30) cc_final: 0.9419 (t0) REVERT: G 797 MET cc_start: 0.9514 (tmm) cc_final: 0.9210 (tmm) REVERT: G 805 GLU cc_start: 0.9451 (mt-10) cc_final: 0.9047 (mm-30) REVERT: U 22 MET cc_start: 0.8633 (mmm) cc_final: 0.8417 (mmm) REVERT: U 182 ARG cc_start: 0.9567 (mtt180) cc_final: 0.9357 (mmt180) REVERT: U 392 MET cc_start: 0.9447 (mtm) cc_final: 0.9084 (ttm) REVERT: U 396 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.7233 (t0) REVERT: U 442 GLN cc_start: 0.9425 (OUTLIER) cc_final: 0.8809 (mp10) REVERT: U 507 MET cc_start: 0.9511 (mmm) cc_final: 0.9285 (mpp) REVERT: V 235 HIS cc_start: 0.8980 (OUTLIER) cc_final: 0.8595 (p-80) REVERT: W 77 MET cc_start: 0.9151 (mmm) cc_final: 0.8639 (mmm) REVERT: W 82 MET cc_start: 0.8816 (mtm) cc_final: 0.8322 (mtt) REVERT: W 148 MET cc_start: 0.8768 (tpp) cc_final: 0.8522 (tpp) REVERT: W 411 MET cc_start: 0.9409 (ptm) cc_final: 0.9154 (ptp) outliers start: 15 outliers final: 5 residues processed: 92 average time/residue: 0.2712 time to fit residues: 38.2297 Evaluate side-chains 80 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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 U residue 442 GLN Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain V residue 235 HIS 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 142 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 145 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14395 Z= 0.336 Angle : 0.610 9.490 19814 Z= 0.320 Chirality : 0.041 0.139 2150 Planarity : 0.004 0.041 2299 Dihedral : 18.799 80.424 2583 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 1.73 % Allowed : 7.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.22), residues: 1532 helix: 1.29 (0.21), residues: 648 sheet: 0.67 (0.36), residues: 209 loop : 0.71 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP W 433 HIS 0.004 0.001 HIS W 209 PHE 0.017 0.001 PHE U 235 TYR 0.018 0.002 TYR G 754 ARG 0.007 0.000 ARG W 268 *********************** 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 97 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9723 (m-30) cc_final: 0.9394 (t0) REVERT: G 797 MET cc_start: 0.9334 (tmm) cc_final: 0.9048 (tmm) REVERT: G 805 GLU cc_start: 0.9492 (mt-10) cc_final: 0.9162 (mm-30) REVERT: U 181 MET cc_start: 0.9537 (ptt) cc_final: 0.9312 (ttp) REVERT: U 216 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8706 (pm20) REVERT: U 396 ASN cc_start: 0.7771 (OUTLIER) cc_final: 0.7406 (t0) REVERT: U 442 GLN cc_start: 0.9471 (OUTLIER) cc_final: 0.9232 (mp10) REVERT: U 507 MET cc_start: 0.9491 (mmm) cc_final: 0.9255 (mpp) REVERT: W 77 MET cc_start: 0.9198 (mmm) cc_final: 0.8914 (mmm) REVERT: W 82 MET cc_start: 0.9017 (mtm) cc_final: 0.8458 (mtm) REVERT: W 148 MET cc_start: 0.8954 (tpp) cc_final: 0.8542 (tpp) REVERT: W 197 ASP cc_start: 0.9372 (t0) cc_final: 0.9112 (p0) REVERT: W 425 THR cc_start: 0.9326 (OUTLIER) cc_final: 0.9058 (p) outliers start: 23 outliers final: 10 residues processed: 91 average time/residue: 0.2670 time to fit residues: 37.4069 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 : 1.476 ------------------------------------------------------------------------------- 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 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 189 LEU Chi-restraints excluded: chain W residue 42 MET Chi-restraints excluded: chain W residue 116 VAL 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 87 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 425 GLN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14395 Z= 0.189 Angle : 0.546 7.406 19814 Z= 0.289 Chirality : 0.040 0.139 2150 Planarity : 0.004 0.045 2299 Dihedral : 18.705 80.995 2583 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.81 % Favored : 97.13 % Rotamer: Outliers : 0.83 % Allowed : 9.12 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.22), residues: 1532 helix: 1.56 (0.22), residues: 636 sheet: 0.65 (0.37), residues: 207 loop : 0.84 (0.25), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP W 433 HIS 0.004 0.001 HIS V 235 PHE 0.010 0.001 PHE U 235 TYR 0.014 0.001 TYR U 42 ARG 0.006 0.000 ARG U 182 *********************** 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 86 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 1.612 Fit side-chains revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9695 (m-30) cc_final: 0.9374 (t0) REVERT: G 805 GLU cc_start: 0.9457 (mt-10) cc_final: 0.9181 (mm-30) REVERT: U 396 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.7289 (t0) REVERT: U 418 MET cc_start: 0.9544 (mmt) cc_final: 0.9336 (mmt) REVERT: U 507 MET cc_start: 0.9454 (mmm) cc_final: 0.9168 (mpp) REVERT: U 664 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8299 (ptm) REVERT: W 77 MET cc_start: 0.9131 (mmm) cc_final: 0.8897 (mmm) REVERT: W 82 MET cc_start: 0.8952 (mtm) cc_final: 0.8417 (mtt) REVERT: W 148 MET cc_start: 0.8908 (tpp) cc_final: 0.8623 (tpp) REVERT: W 167 MET cc_start: 0.8780 (mmm) cc_final: 0.8452 (mmm) REVERT: W 197 ASP cc_start: 0.9340 (t0) cc_final: 0.9084 (p0) REVERT: W 411 MET cc_start: 0.9390 (ptm) cc_final: 0.9150 (ptp) outliers start: 11 outliers final: 7 residues processed: 83 average time/residue: 0.2607 time to fit residues: 33.7403 Evaluate side-chains 78 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 1.549 ------------------------------------------------------------------------------- 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 U residue 664 MET Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain V residue 189 LEU 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 138 optimal weight: 0.0870 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14395 Z= 0.145 Angle : 0.526 7.450 19814 Z= 0.277 Chirality : 0.039 0.169 2150 Planarity : 0.004 0.043 2299 Dihedral : 18.434 79.444 2583 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.28 % Favored : 97.65 % Rotamer: Outliers : 1.36 % Allowed : 9.12 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.22), residues: 1532 helix: 1.63 (0.22), residues: 638 sheet: 0.66 (0.37), residues: 204 loop : 0.89 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 433 HIS 0.004 0.001 HIS V 235 PHE 0.008 0.001 PHE W 249 TYR 0.019 0.001 TYR U 42 ARG 0.006 0.000 ARG U 182 *********************** 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 98 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9690 (m-30) cc_final: 0.9381 (t0) REVERT: G 797 MET cc_start: 0.9164 (tmm) cc_final: 0.8894 (tmm) REVERT: G 805 GLU cc_start: 0.9449 (mt-10) cc_final: 0.9196 (mm-30) REVERT: U 216 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8764 (pm20) REVERT: U 396 ASN cc_start: 0.7370 (OUTLIER) cc_final: 0.7168 (t0) REVERT: U 664 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8374 (ptm) REVERT: W 77 MET cc_start: 0.9111 (mmm) cc_final: 0.8891 (mmm) REVERT: W 82 MET cc_start: 0.8902 (mtm) cc_final: 0.8402 (mtt) REVERT: W 148 MET cc_start: 0.8797 (tpp) cc_final: 0.8450 (tpp) REVERT: W 167 MET cc_start: 0.8620 (mmm) cc_final: 0.8289 (mmm) REVERT: W 197 ASP cc_start: 0.9321 (t0) cc_final: 0.9049 (p0) REVERT: W 411 MET cc_start: 0.9327 (ptm) cc_final: 0.9079 (ptp) REVERT: W 425 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.9046 (p) outliers start: 18 outliers final: 10 residues processed: 94 average time/residue: 0.2472 time to fit residues: 36.3516 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 : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 404 LEU 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 189 LEU Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 393 SER Chi-restraints excluded: chain W residue 425 THR 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 17 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 153 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 24 GLN U 431 GLN U 646 GLN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14395 Z= 0.367 Angle : 0.616 7.421 19814 Z= 0.320 Chirality : 0.041 0.165 2150 Planarity : 0.004 0.065 2299 Dihedral : 18.640 79.787 2583 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.26 % Favored : 96.67 % Rotamer: Outliers : 1.58 % Allowed : 9.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.22), residues: 1532 helix: 1.43 (0.21), residues: 649 sheet: 0.52 (0.36), residues: 208 loop : 0.80 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP W 449 HIS 0.004 0.001 HIS V 235 PHE 0.013 0.001 PHE U 235 TYR 0.017 0.001 TYR G 754 ARG 0.005 0.001 ARG W 452 *********************** 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 88 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9712 (m-30) cc_final: 0.9365 (t0) REVERT: G 805 GLU cc_start: 0.9487 (mt-10) cc_final: 0.9212 (mm-30) REVERT: U 216 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8730 (pm20) REVERT: U 396 ASN cc_start: 0.7485 (OUTLIER) cc_final: 0.7258 (t0) REVERT: U 507 MET cc_start: 0.9410 (mpp) cc_final: 0.9102 (mtm) REVERT: U 664 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8561 (ptm) REVERT: W 77 MET cc_start: 0.9171 (mmm) cc_final: 0.8862 (mmm) REVERT: W 82 MET cc_start: 0.9012 (mtm) cc_final: 0.8442 (mtt) REVERT: W 148 MET cc_start: 0.8959 (tpp) cc_final: 0.8548 (tpp) REVERT: W 197 ASP cc_start: 0.9365 (t0) cc_final: 0.9065 (p0) REVERT: W 411 MET cc_start: 0.9348 (ptm) cc_final: 0.9105 (ptp) REVERT: W 425 THR cc_start: 0.9380 (OUTLIER) cc_final: 0.9123 (p) outliers start: 21 outliers final: 11 residues processed: 84 average time/residue: 0.2155 time to fit residues: 29.0049 Evaluate side-chains 80 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 1.514 ------------------------------------------------------------------------------- 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 V residue 189 LEU Chi-restraints excluded: chain V residue 235 HIS Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 425 THR Chi-restraints excluded: chain W residue 438 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 0.0370 chunk 29 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 139 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 overall best weight: 2.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 646 GLN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14395 Z= 0.223 Angle : 0.555 8.191 19814 Z= 0.291 Chirality : 0.041 0.359 2150 Planarity : 0.004 0.045 2299 Dihedral : 18.638 80.695 2583 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.94 % Favored : 97.00 % Rotamer: Outliers : 1.28 % Allowed : 9.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.22), residues: 1532 helix: 1.67 (0.22), residues: 638 sheet: 0.53 (0.36), residues: 208 loop : 0.88 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 433 HIS 0.004 0.001 HIS V 235 PHE 0.011 0.001 PHE V 375 TYR 0.013 0.001 TYR G 754 ARG 0.004 0.000 ARG U 182 *********************** 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 85 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9687 (m-30) cc_final: 0.9342 (t0) REVERT: G 805 GLU cc_start: 0.9465 (mt-10) cc_final: 0.9189 (mm-30) REVERT: U 216 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8702 (pm20) REVERT: U 507 MET cc_start: 0.9293 (mpp) cc_final: 0.8895 (mtm) REVERT: U 703 MET cc_start: 0.8148 (mtp) cc_final: 0.7701 (mtp) REVERT: W 77 MET cc_start: 0.9096 (mmm) cc_final: 0.8878 (mmm) REVERT: W 82 MET cc_start: 0.8962 (mtm) cc_final: 0.8419 (mtt) REVERT: W 148 MET cc_start: 0.8959 (tpp) cc_final: 0.8691 (tpp) REVERT: W 411 MET cc_start: 0.9328 (ptm) cc_final: 0.9071 (ptp) REVERT: W 425 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9106 (p) outliers start: 17 outliers final: 12 residues processed: 82 average time/residue: 0.2559 time to fit residues: 33.3537 Evaluate side-chains 82 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 1.555 ------------------------------------------------------------------------------- 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 217 VAL Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 235 HIS Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 425 THR 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 133 optimal weight: 0.5980 chunk 142 optimal weight: 8.9990 chunk 146 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 135 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 646 GLN W 154 ASN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14395 Z= 0.240 Angle : 0.569 8.554 19814 Z= 0.295 Chirality : 0.040 0.293 2150 Planarity : 0.004 0.045 2299 Dihedral : 18.590 80.187 2581 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.48 % Rotamer: Outliers : 1.13 % Allowed : 10.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.22), residues: 1532 helix: 1.67 (0.22), residues: 638 sheet: 0.51 (0.36), residues: 208 loop : 0.90 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 449 HIS 0.004 0.001 HIS V 235 PHE 0.009 0.001 PHE U 235 TYR 0.014 0.001 TYR G 754 ARG 0.004 0.000 ARG U 182 *********************** 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 85 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9690 (m-30) cc_final: 0.9327 (t0) REVERT: G 805 GLU cc_start: 0.9449 (mt-10) cc_final: 0.9182 (mm-30) REVERT: U 216 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8766 (pm20) REVERT: U 507 MET cc_start: 0.9283 (mpp) cc_final: 0.8887 (mtm) REVERT: U 703 MET cc_start: 0.8225 (mtp) cc_final: 0.7765 (mtp) REVERT: W 77 MET cc_start: 0.9103 (mmm) cc_final: 0.8884 (mmm) REVERT: W 82 MET cc_start: 0.8977 (mtm) cc_final: 0.8488 (mtt) REVERT: W 148 MET cc_start: 0.8970 (tpp) cc_final: 0.8721 (tpp) REVERT: W 411 MET cc_start: 0.9331 (ptm) cc_final: 0.9071 (ptp) REVERT: W 425 THR cc_start: 0.9351 (OUTLIER) cc_final: 0.9118 (p) outliers start: 15 outliers final: 12 residues processed: 83 average time/residue: 0.2536 time to fit residues: 33.2978 Evaluate side-chains 82 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 1.644 ------------------------------------------------------------------------------- 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 V residue 189 LEU Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 425 THR 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 92 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 158 optimal weight: 0.4980 chunk 145 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 chunk 13 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 100 optimal weight: 0.0020 chunk 134 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14395 Z= 0.143 Angle : 0.541 8.340 19814 Z= 0.281 Chirality : 0.039 0.271 2150 Planarity : 0.004 0.044 2299 Dihedral : 18.442 79.483 2581 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.68 % Favored : 97.26 % Rotamer: Outliers : 1.28 % Allowed : 10.10 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.23), residues: 1532 helix: 1.71 (0.22), residues: 645 sheet: 0.66 (0.36), residues: 204 loop : 0.98 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 340 HIS 0.004 0.001 HIS V 235 PHE 0.008 0.001 PHE V 132 TYR 0.012 0.001 TYR U 42 ARG 0.005 0.000 ARG G 795 ********************** 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 87 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9668 (m-30) cc_final: 0.9309 (t0) REVERT: G 797 MET cc_start: 0.9066 (tmm) cc_final: 0.8846 (tmm) REVERT: G 805 GLU cc_start: 0.9432 (mt-10) cc_final: 0.9169 (mm-30) REVERT: U 507 MET cc_start: 0.9242 (mpp) cc_final: 0.9010 (mtm) REVERT: W 77 MET cc_start: 0.9070 (mmm) cc_final: 0.8846 (mmm) REVERT: W 82 MET cc_start: 0.8924 (mtm) cc_final: 0.8412 (mtt) REVERT: W 148 MET cc_start: 0.8921 (tpp) cc_final: 0.8654 (tpp) REVERT: W 411 MET cc_start: 0.9304 (ptm) cc_final: 0.9028 (ptp) REVERT: W 425 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.9085 (p) outliers start: 17 outliers final: 12 residues processed: 83 average time/residue: 0.2449 time to fit residues: 32.4672 Evaluate side-chains 81 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 1.726 ------------------------------------------------------------------------------- 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 V residue 235 HIS Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 425 THR 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 38 optimal weight: 4.9990 chunk 116 optimal weight: 0.0070 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 126 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 446 HIS ** X 155 ASN ** 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 = 0.3357 r_free = 0.3357 target = 0.054926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.037543 restraints weight = 62345.406| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 3.36 r_work: 0.2631 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14395 Z= 0.143 Angle : 0.535 8.404 19814 Z= 0.277 Chirality : 0.039 0.262 2150 Planarity : 0.004 0.043 2299 Dihedral : 18.333 78.073 2581 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.87 % Favored : 97.06 % Rotamer: Outliers : 1.13 % Allowed : 9.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.22), residues: 1532 helix: 1.74 (0.22), residues: 645 sheet: 0.65 (0.37), residues: 205 loop : 1.00 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 433 HIS 0.005 0.001 HIS V 88 PHE 0.008 0.001 PHE W 249 TYR 0.010 0.001 TYR U 42 ARG 0.004 0.000 ARG U 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2344.44 seconds wall clock time: 44 minutes 43.27 seconds (2683.27 seconds total)