Starting phenix.real_space_refine on Thu Jun 12 15:19:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a5p_15180/06_2025/8a5p_15180_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a5p_15180/06_2025/8a5p_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_15180/06_2025/8a5p_15180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a5p_15180/06_2025/8a5p_15180.map" model { file = "/net/cci-nas-00/data/ceres_data/8a5p_15180/06_2025/8a5p_15180_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a5p_15180/06_2025/8a5p_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-5710/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: 8.19, per 1000 atoms: 0.59 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: 3.40 Conformation dependent library (CDL) restraints added in 1.4 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: 5.57 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: 5.34 Time building geometry restraints manager: 4.06 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 37.360 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.131 14395 Z= 0.720 Angle : 1.651 21.811 19814 Z= 1.110 Chirality : 0.101 0.649 2150 Planarity : 0.022 0.239 2299 Dihedral : 17.868 85.625 5640 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.26 % Favored : 96.61 % Rotamer: Outliers : 0.90 % Allowed : 3.47 % Favored : 95.63 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.16485 ( 661) hydrogen bonds : angle 7.04637 ( 1717) covalent geometry : bond 0.01147 (14395) covalent geometry : angle 1.65104 (19814) *********************** 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 : 1.556 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: 0.3020 time to fit residues: 57.9212 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 : 1.415 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.055941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.038293 restraints weight = 60823.840| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 3.30 r_work: 0.2623 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 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= 0.148 Angle : 0.642 9.169 19814 Z= 0.347 Chirality : 0.042 0.162 2150 Planarity : 0.005 0.062 2299 Dihedral : 19.004 74.275 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 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 661) hydrogen bonds : angle 4.75439 ( 1717) covalent geometry : bond 0.00322 (14395) covalent geometry : angle 0.64200 (19814) *********************** 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 : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9223 (m-30) cc_final: 0.8876 (t0) REVERT: G 797 MET cc_start: 0.9397 (tmm) cc_final: 0.8947 (tmm) REVERT: U 182 ARG cc_start: 0.9345 (mtt180) cc_final: 0.9082 (mmt180) REVERT: U 184 ASN cc_start: 0.9348 (m110) cc_final: 0.9139 (m110) REVERT: U 194 ASP cc_start: 0.9196 (m-30) cc_final: 0.8940 (t0) REVERT: U 392 MET cc_start: 0.9414 (mtm) cc_final: 0.9002 (ttm) REVERT: U 396 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7145 (t0) REVERT: U 425 GLN cc_start: 0.8725 (tt0) cc_final: 0.8161 (tt0) REVERT: U 460 MET cc_start: 0.9365 (mtt) cc_final: 0.9089 (mtp) REVERT: U 507 MET cc_start: 0.9474 (mmm) cc_final: 0.9065 (mpp) REVERT: V 120 THR cc_start: 0.9345 (m) cc_final: 0.9029 (p) REVERT: V 305 MET cc_start: 0.9428 (mmm) cc_final: 0.9209 (mmm) REVERT: W 77 MET cc_start: 0.9444 (mmm) cc_final: 0.8546 (mmm) REVERT: W 82 MET cc_start: 0.8392 (mtm) cc_final: 0.8171 (mtt) REVERT: W 148 MET cc_start: 0.8919 (ttm) cc_final: 0.8402 (tpp) outliers start: 13 outliers final: 6 residues processed: 101 average time/residue: 0.3802 time to fit residues: 57.8720 Evaluate side-chains 85 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 396 ASN Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain W residue 20 GLU Chi-restraints excluded: chain W residue 438 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 15 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 121 optimal weight: 0.0770 chunk 54 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.055116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.037423 restraints weight = 61888.805| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 3.37 r_work: 0.2605 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14395 Z= 0.155 Angle : 0.574 9.708 19814 Z= 0.307 Chirality : 0.040 0.151 2150 Planarity : 0.004 0.062 2299 Dihedral : 18.852 78.847 2583 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.39 % Rotamer: Outliers : 1.06 % Allowed : 8.29 % Favored : 90.66 % 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: 1.25 (0.22), residues: 1532 helix: 1.19 (0.21), residues: 642 sheet: 0.79 (0.37), residues: 205 loop : 0.69 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP W 433 HIS 0.011 0.001 HIS V 235 PHE 0.019 0.001 PHE U 235 TYR 0.017 0.001 TYR G 754 ARG 0.005 0.000 ARG X 196 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 661) hydrogen bonds : angle 4.40460 ( 1717) covalent geometry : bond 0.00338 (14395) covalent geometry : angle 0.57437 (19814) *********************** 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 91 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9218 (m-30) cc_final: 0.8822 (t0) REVERT: G 797 MET cc_start: 0.9454 (tmm) cc_final: 0.9055 (tmm) REVERT: G 805 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7821 (mm-30) REVERT: U 22 MET cc_start: 0.8679 (mmm) cc_final: 0.8469 (mmm) REVERT: U 181 MET cc_start: 0.9381 (ptm) cc_final: 0.9121 (ptt) REVERT: U 194 ASP cc_start: 0.9122 (m-30) cc_final: 0.8868 (t70) REVERT: U 392 MET cc_start: 0.9402 (mtm) cc_final: 0.8953 (ttm) REVERT: U 396 ASN cc_start: 0.7580 (OUTLIER) cc_final: 0.7065 (t0) REVERT: U 442 GLN cc_start: 0.9432 (OUTLIER) cc_final: 0.8636 (mp10) REVERT: U 507 MET cc_start: 0.9510 (mmm) cc_final: 0.9106 (mpp) REVERT: U 664 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8513 (ptm) REVERT: V 299 MET cc_start: 0.9094 (mmm) cc_final: 0.8887 (mmm) REVERT: W 77 MET cc_start: 0.9441 (mmm) cc_final: 0.8805 (mmm) REVERT: W 82 MET cc_start: 0.8455 (mtm) cc_final: 0.8033 (mtt) REVERT: W 148 MET cc_start: 0.8868 (ttm) cc_final: 0.8428 (tpp) REVERT: W 252 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.8932 (mm-30) REVERT: W 411 MET cc_start: 0.8717 (ptm) cc_final: 0.8338 (ptp) outliers start: 14 outliers final: 6 residues processed: 87 average time/residue: 0.3025 time to fit residues: 40.8890 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 : 1.858 ------------------------------------------------------------------------------- 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 U residue 664 MET Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain W residue 438 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 53 optimal weight: 8.9990 chunk 33 optimal weight: 0.5980 chunk 48 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 184 ASN ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.055256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.037561 restraints weight = 62026.936| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.35 r_work: 0.2613 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14395 Z= 0.134 Angle : 0.542 8.424 19814 Z= 0.287 Chirality : 0.040 0.138 2150 Planarity : 0.004 0.040 2299 Dihedral : 18.657 80.300 2583 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.35 % Favored : 97.58 % Rotamer: Outliers : 1.43 % Allowed : 8.29 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.57 (0.22), residues: 1532 helix: 1.62 (0.22), residues: 628 sheet: 0.60 (0.37), residues: 213 loop : 0.83 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP W 433 HIS 0.009 0.001 HIS V 235 PHE 0.010 0.001 PHE U 235 TYR 0.014 0.001 TYR G 754 ARG 0.004 0.000 ARG W 319 Details of bonding type rmsd hydrogen bonds : bond 0.03256 ( 661) hydrogen bonds : angle 4.11914 ( 1717) covalent geometry : bond 0.00296 (14395) covalent geometry : angle 0.54219 (19814) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9230 (m-30) cc_final: 0.8839 (t0) REVERT: G 797 MET cc_start: 0.9376 (tmm) cc_final: 0.8847 (tmm) REVERT: G 798 MET cc_start: 0.9537 (OUTLIER) cc_final: 0.9132 (mmm) REVERT: U 43 MET cc_start: 0.9255 (mtp) cc_final: 0.8886 (mtp) REVERT: U 181 MET cc_start: 0.9259 (ptm) cc_final: 0.8873 (ptt) REVERT: U 194 ASP cc_start: 0.9059 (m-30) cc_final: 0.8763 (t0) REVERT: U 216 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8727 (pm20) REVERT: U 507 MET cc_start: 0.9495 (mmm) cc_final: 0.9113 (mpp) REVERT: W 77 MET cc_start: 0.9460 (mmm) cc_final: 0.8850 (mmm) REVERT: W 82 MET cc_start: 0.8531 (mtm) cc_final: 0.8103 (mtt) REVERT: W 148 MET cc_start: 0.8891 (ttm) cc_final: 0.8614 (tpp) REVERT: W 197 ASP cc_start: 0.8549 (t0) cc_final: 0.8166 (p0) REVERT: W 252 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.8960 (mm-30) REVERT: X 151 GLN cc_start: 0.8484 (tp-100) cc_final: 0.8143 (tp40) outliers start: 19 outliers final: 6 residues processed: 95 average time/residue: 0.2378 time to fit residues: 35.6811 Evaluate side-chains 81 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain G residue 798 MET Chi-restraints excluded: chain U residue 216 GLN Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain W residue 438 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 46 optimal weight: 10.0000 chunk 138 optimal weight: 0.0970 chunk 70 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 86 optimal weight: 0.1980 chunk 12 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.054977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.037396 restraints weight = 62054.800| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.35 r_work: 0.2611 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14395 Z= 0.131 Angle : 0.540 9.777 19814 Z= 0.284 Chirality : 0.039 0.131 2150 Planarity : 0.004 0.040 2299 Dihedral : 18.547 80.350 2581 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.35 % Favored : 97.58 % Rotamer: Outliers : 1.06 % Allowed : 8.74 % Favored : 90.20 % 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: 1.65 (0.22), residues: 635 sheet: 0.60 (0.37), residues: 209 loop : 0.89 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 433 HIS 0.012 0.001 HIS V 235 PHE 0.012 0.001 PHE U 235 TYR 0.015 0.001 TYR G 754 ARG 0.003 0.000 ARG U 150 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 661) hydrogen bonds : angle 4.04861 ( 1717) covalent geometry : bond 0.00284 (14395) covalent geometry : angle 0.53979 (19814) *********************** 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 92 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 2.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9219 (m-30) cc_final: 0.8863 (t0) REVERT: U 43 MET cc_start: 0.9248 (mtp) cc_final: 0.8888 (mtp) REVERT: U 181 MET cc_start: 0.9311 (ptm) cc_final: 0.9030 (ptt) REVERT: U 194 ASP cc_start: 0.9044 (m-30) cc_final: 0.8741 (t70) REVERT: U 216 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8722 (pm20) REVERT: U 418 MET cc_start: 0.9043 (mmt) cc_final: 0.8789 (mmt) REVERT: U 442 GLN cc_start: 0.9447 (OUTLIER) cc_final: 0.9168 (mt0) REVERT: U 507 MET cc_start: 0.9486 (mmm) cc_final: 0.9106 (mmm) REVERT: W 77 MET cc_start: 0.9462 (mmm) cc_final: 0.8857 (mmm) REVERT: W 82 MET cc_start: 0.8521 (mtm) cc_final: 0.8117 (mtt) REVERT: W 148 MET cc_start: 0.8842 (ttm) cc_final: 0.8622 (tpp) REVERT: W 197 ASP cc_start: 0.8524 (t0) cc_final: 0.8176 (p0) REVERT: W 252 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.8962 (mm-30) REVERT: W 411 MET cc_start: 0.8638 (ptm) cc_final: 0.8290 (ptp) REVERT: X 151 GLN cc_start: 0.8537 (tp-100) cc_final: 0.8188 (tp40) outliers start: 14 outliers final: 7 residues processed: 89 average time/residue: 0.3099 time to fit residues: 43.4791 Evaluate side-chains 83 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 1.756 ------------------------------------------------------------------------------- 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 132 PHE 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 14 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 0.4980 chunk 132 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.054913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.037321 restraints weight = 63328.817| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 3.41 r_work: 0.2604 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14395 Z= 0.132 Angle : 0.533 8.881 19814 Z= 0.279 Chirality : 0.039 0.161 2150 Planarity : 0.004 0.044 2299 Dihedral : 18.451 79.112 2581 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.42 % Favored : 97.52 % Rotamer: Outliers : 0.98 % Allowed : 8.97 % 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: 1.72 (0.22), residues: 1532 helix: 1.77 (0.22), residues: 631 sheet: 0.49 (0.35), residues: 221 loop : 0.96 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 433 HIS 0.011 0.001 HIS V 235 PHE 0.011 0.001 PHE U 397 TYR 0.013 0.001 TYR G 754 ARG 0.003 0.000 ARG U 150 Details of bonding type rmsd hydrogen bonds : bond 0.03074 ( 661) hydrogen bonds : angle 3.97699 ( 1717) covalent geometry : bond 0.00287 (14395) covalent geometry : angle 0.53263 (19814) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9222 (m-30) cc_final: 0.8862 (t0) REVERT: U 181 MET cc_start: 0.9247 (ptm) cc_final: 0.9008 (ptt) REVERT: U 194 ASP cc_start: 0.9104 (m-30) cc_final: 0.8801 (t70) REVERT: U 216 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8703 (pm20) REVERT: U 391 MET cc_start: 0.8773 (mtm) cc_final: 0.8364 (ptp) REVERT: U 418 MET cc_start: 0.9066 (mmt) cc_final: 0.8832 (mmt) REVERT: U 442 GLN cc_start: 0.9414 (OUTLIER) cc_final: 0.9082 (mp10) REVERT: U 507 MET cc_start: 0.9489 (mmm) cc_final: 0.9095 (mmm) REVERT: U 733 MET cc_start: 0.9493 (mmm) cc_final: 0.9162 (mmm) REVERT: W 77 MET cc_start: 0.9466 (mmm) cc_final: 0.8859 (mmm) REVERT: W 82 MET cc_start: 0.8546 (mtm) cc_final: 0.8126 (mtt) REVERT: W 148 MET cc_start: 0.8941 (ttm) cc_final: 0.8717 (tpp) REVERT: W 197 ASP cc_start: 0.8545 (t0) cc_final: 0.8146 (p0) REVERT: W 252 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8975 (mm-30) REVERT: W 411 MET cc_start: 0.8567 (ptm) cc_final: 0.8209 (ptp) REVERT: X 151 GLN cc_start: 0.8637 (tp-100) cc_final: 0.8301 (tp40) REVERT: X 198 LYS cc_start: 0.8673 (mmmt) cc_final: 0.8450 (tppt) outliers start: 13 outliers final: 10 residues processed: 89 average time/residue: 0.2939 time to fit residues: 41.6467 Evaluate side-chains 84 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 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 298 LYS Chi-restraints excluded: chain U residue 404 LEU Chi-restraints excluded: chain U residue 442 GLN Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 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 138 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 59 optimal weight: 0.1980 chunk 56 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.054797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.037230 restraints weight = 63026.138| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 3.41 r_work: 0.2606 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14395 Z= 0.127 Angle : 0.521 7.399 19814 Z= 0.274 Chirality : 0.039 0.144 2150 Planarity : 0.004 0.044 2299 Dihedral : 18.373 78.241 2581 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.74 % Favored : 97.19 % Rotamer: Outliers : 1.06 % Allowed : 9.50 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.76 (0.22), residues: 633 sheet: 0.51 (0.35), residues: 224 loop : 1.02 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 86 HIS 0.008 0.001 HIS V 235 PHE 0.008 0.001 PHE U 235 TYR 0.012 0.001 TYR G 754 ARG 0.002 0.000 ARG U 483 Details of bonding type rmsd hydrogen bonds : bond 0.03025 ( 661) hydrogen bonds : angle 3.94670 ( 1717) covalent geometry : bond 0.00275 (14395) covalent geometry : angle 0.52139 (19814) *********************** 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 91 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9207 (m-30) cc_final: 0.8784 (t0) REVERT: U 194 ASP cc_start: 0.9073 (m-30) cc_final: 0.8793 (t70) REVERT: U 216 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8669 (pm20) REVERT: U 336 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8130 (pm20) REVERT: U 418 MET cc_start: 0.9077 (mmt) cc_final: 0.8870 (mmt) REVERT: U 442 GLN cc_start: 0.9401 (OUTLIER) cc_final: 0.9068 (mp10) REVERT: U 507 MET cc_start: 0.9480 (mmm) cc_final: 0.9098 (mmm) REVERT: U 733 MET cc_start: 0.9524 (mmm) cc_final: 0.9283 (mmm) REVERT: W 77 MET cc_start: 0.9468 (mmm) cc_final: 0.8862 (mmm) REVERT: W 82 MET cc_start: 0.8560 (mtm) cc_final: 0.8140 (mtt) REVERT: W 148 MET cc_start: 0.8929 (ttm) cc_final: 0.8707 (tpp) REVERT: W 197 ASP cc_start: 0.8535 (t0) cc_final: 0.8117 (p0) REVERT: W 252 GLU cc_start: 0.9282 (OUTLIER) cc_final: 0.8980 (mm-30) REVERT: W 411 MET cc_start: 0.8502 (ptm) cc_final: 0.8192 (ptp) REVERT: X 151 GLN cc_start: 0.8639 (tp-100) cc_final: 0.8303 (tp40) outliers start: 14 outliers final: 8 residues processed: 89 average time/residue: 0.2449 time to fit residues: 34.3418 Evaluate side-chains 83 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 1.582 ------------------------------------------------------------------------------- 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 404 LEU Chi-restraints excluded: chain U residue 442 GLN Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain W residue 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 20 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 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 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 646 GLN W 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.054618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.037091 restraints weight = 62936.337| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.40 r_work: 0.2604 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14395 Z= 0.138 Angle : 0.542 9.165 19814 Z= 0.283 Chirality : 0.040 0.302 2150 Planarity : 0.004 0.045 2299 Dihedral : 18.363 78.209 2581 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.68 % Favored : 97.26 % Rotamer: Outliers : 1.13 % Allowed : 9.72 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.23), residues: 1532 helix: 1.77 (0.22), residues: 634 sheet: 0.50 (0.35), residues: 224 loop : 1.06 (0.26), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 433 HIS 0.008 0.001 HIS V 235 PHE 0.009 0.001 PHE U 235 TYR 0.012 0.001 TYR G 754 ARG 0.004 0.000 ARG G 806 Details of bonding type rmsd hydrogen bonds : bond 0.03062 ( 661) hydrogen bonds : angle 3.92433 ( 1717) covalent geometry : bond 0.00301 (14395) covalent geometry : angle 0.54217 (19814) *********************** 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 90 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9187 (m-30) cc_final: 0.8759 (t0) REVERT: U 194 ASP cc_start: 0.9039 (m-30) cc_final: 0.8761 (t70) REVERT: U 216 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8678 (pm20) REVERT: U 336 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8191 (pm20) REVERT: U 418 MET cc_start: 0.9108 (mmt) cc_final: 0.8902 (mmt) REVERT: U 442 GLN cc_start: 0.9410 (OUTLIER) cc_final: 0.9069 (mp10) REVERT: U 507 MET cc_start: 0.9469 (mmm) cc_final: 0.9082 (mmm) REVERT: U 703 MET cc_start: 0.8468 (mtp) cc_final: 0.8147 (ptm) REVERT: U 733 MET cc_start: 0.9529 (mmm) cc_final: 0.9306 (mmm) REVERT: W 77 MET cc_start: 0.9465 (mmm) cc_final: 0.8860 (mmm) REVERT: W 82 MET cc_start: 0.8572 (mtm) cc_final: 0.8235 (mtt) REVERT: W 148 MET cc_start: 0.8938 (ttm) cc_final: 0.8706 (tpp) REVERT: W 197 ASP cc_start: 0.8538 (t0) cc_final: 0.8110 (p0) REVERT: W 252 GLU cc_start: 0.9284 (OUTLIER) cc_final: 0.8980 (mm-30) REVERT: W 411 MET cc_start: 0.8513 (ptm) cc_final: 0.8204 (ptp) REVERT: X 151 GLN cc_start: 0.8641 (tp-100) cc_final: 0.8305 (tp40) outliers start: 15 outliers final: 10 residues processed: 88 average time/residue: 0.2373 time to fit residues: 33.2463 Evaluate side-chains 84 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 216 GLN Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 404 LEU Chi-restraints excluded: chain U residue 442 GLN Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 252 GLU 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 123 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 24 GLN ** U 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 396 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.054915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.037413 restraints weight = 62895.002| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 3.40 r_work: 0.2616 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14395 Z= 0.115 Angle : 0.533 8.812 19814 Z= 0.278 Chirality : 0.039 0.297 2150 Planarity : 0.004 0.046 2299 Dihedral : 18.290 77.441 2581 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.74 % Favored : 97.19 % 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: 1.82 (0.23), residues: 1532 helix: 1.80 (0.22), residues: 632 sheet: 0.48 (0.35), residues: 222 loop : 1.10 (0.26), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 433 HIS 0.006 0.001 HIS V 235 PHE 0.008 0.001 PHE V 132 TYR 0.011 0.001 TYR G 754 ARG 0.006 0.000 ARG W 452 Details of bonding type rmsd hydrogen bonds : bond 0.02925 ( 661) hydrogen bonds : angle 3.88299 ( 1717) covalent geometry : bond 0.00250 (14395) covalent geometry : angle 0.53302 (19814) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9199 (m-30) cc_final: 0.8761 (t0) REVERT: U 194 ASP cc_start: 0.9122 (m-30) cc_final: 0.8843 (t0) REVERT: U 216 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8660 (pm20) REVERT: U 391 MET cc_start: 0.8736 (mtm) cc_final: 0.8381 (ptp) REVERT: U 396 ASN cc_start: 0.7304 (OUTLIER) cc_final: 0.6719 (t0) REVERT: U 418 MET cc_start: 0.9077 (mmt) cc_final: 0.8866 (mmt) REVERT: U 442 GLN cc_start: 0.9388 (OUTLIER) cc_final: 0.9047 (mp10) REVERT: U 460 MET cc_start: 0.9425 (mtt) cc_final: 0.9179 (mtp) REVERT: U 507 MET cc_start: 0.9467 (mmm) cc_final: 0.9090 (mmm) REVERT: U 703 MET cc_start: 0.8515 (mtp) cc_final: 0.8255 (ptm) REVERT: U 733 MET cc_start: 0.9509 (mmm) cc_final: 0.9285 (mmm) REVERT: V 305 MET cc_start: 0.9456 (mmm) cc_final: 0.9131 (mmm) REVERT: W 77 MET cc_start: 0.9453 (mmm) cc_final: 0.8873 (mmm) REVERT: W 82 MET cc_start: 0.8544 (mtm) cc_final: 0.8231 (mtt) REVERT: W 197 ASP cc_start: 0.8544 (t0) cc_final: 0.8081 (p0) REVERT: W 252 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.8975 (mm-30) REVERT: W 411 MET cc_start: 0.8473 (ptm) cc_final: 0.8150 (ptp) REVERT: W 448 MET cc_start: 0.9213 (tpt) cc_final: 0.8775 (tpp) REVERT: X 151 GLN cc_start: 0.8623 (tp-100) cc_final: 0.8286 (tp40) outliers start: 15 outliers final: 10 residues processed: 86 average time/residue: 0.2858 time to fit residues: 39.0538 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 : 2.595 ------------------------------------------------------------------------------- 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 404 LEU Chi-restraints excluded: chain U residue 442 GLN Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 252 GLU 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 24 optimal weight: 0.8980 chunk 61 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 396 ASN W 446 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.055126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.037714 restraints weight = 62971.918| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 3.31 r_work: 0.2631 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14395 Z= 0.108 Angle : 0.534 8.361 19814 Z= 0.277 Chirality : 0.039 0.272 2150 Planarity : 0.004 0.044 2299 Dihedral : 18.228 76.534 2581 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 0.90 % Allowed : 10.40 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.83 (0.23), residues: 1532 helix: 1.83 (0.22), residues: 632 sheet: 0.51 (0.35), residues: 221 loop : 1.06 (0.26), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 433 HIS 0.006 0.001 HIS V 235 PHE 0.009 0.001 PHE U 397 TYR 0.012 0.001 TYR W 455 ARG 0.002 0.000 ARG W 452 Details of bonding type rmsd hydrogen bonds : bond 0.02888 ( 661) hydrogen bonds : angle 3.85886 ( 1717) covalent geometry : bond 0.00233 (14395) covalent geometry : angle 0.53351 (19814) ********************** 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: 12 poor density : 75 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9155 (m-30) cc_final: 0.8722 (t0) REVERT: U 194 ASP cc_start: 0.9116 (m-30) cc_final: 0.8846 (t70) REVERT: U 216 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8661 (pm20) REVERT: U 391 MET cc_start: 0.8717 (mtm) cc_final: 0.8403 (ptp) REVERT: U 396 ASN cc_start: 0.7617 (OUTLIER) cc_final: 0.7071 (t0) REVERT: U 418 MET cc_start: 0.9079 (mmt) cc_final: 0.8873 (mmt) REVERT: U 442 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.9036 (mp10) REVERT: U 460 MET cc_start: 0.9417 (mtt) cc_final: 0.9160 (mtp) REVERT: U 507 MET cc_start: 0.9452 (mmm) cc_final: 0.9094 (mmm) REVERT: U 703 MET cc_start: 0.8472 (mtp) cc_final: 0.8241 (ptm) REVERT: U 733 MET cc_start: 0.9492 (mmm) cc_final: 0.9266 (mmm) REVERT: V 305 MET cc_start: 0.9440 (mmm) cc_final: 0.9110 (mmm) REVERT: W 77 MET cc_start: 0.9454 (mmm) cc_final: 0.8768 (mmm) REVERT: W 82 MET cc_start: 0.8555 (mtm) cc_final: 0.8192 (mtt) REVERT: W 148 MET cc_start: 0.8690 (tpp) cc_final: 0.8197 (tpp) REVERT: W 197 ASP cc_start: 0.8464 (t0) cc_final: 0.8068 (p0) REVERT: W 252 GLU cc_start: 0.9292 (OUTLIER) cc_final: 0.8978 (mm-30) REVERT: W 411 MET cc_start: 0.8465 (ptm) cc_final: 0.8137 (ptp) REVERT: W 448 MET cc_start: 0.9242 (tpt) cc_final: 0.8751 (tpp) REVERT: X 151 GLN cc_start: 0.8630 (tp-100) cc_final: 0.8301 (tp-100) outliers start: 12 outliers final: 7 residues processed: 85 average time/residue: 0.2464 time to fit residues: 33.4318 Evaluate side-chains 82 residues out of total 1327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 442 GLN Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain W residue 438 ILE 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 58 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 0.0070 chunk 95 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 140 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 184 ASN ** U 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 396 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.054781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.037377 restraints weight = 63928.366| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 3.36 r_work: 0.2619 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14395 Z= 0.128 Angle : 0.537 8.552 19814 Z= 0.277 Chirality : 0.039 0.268 2150 Planarity : 0.004 0.043 2299 Dihedral : 18.223 76.247 2581 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.81 % Favored : 97.13 % Rotamer: Outliers : 1.06 % Allowed : 10.25 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.86 (0.23), residues: 1532 helix: 1.83 (0.22), residues: 635 sheet: 0.51 (0.35), residues: 223 loop : 1.10 (0.26), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 433 HIS 0.007 0.001 HIS V 235 PHE 0.009 0.001 PHE V 375 TYR 0.011 0.001 TYR W 455 ARG 0.003 0.000 ARG W 452 Details of bonding type rmsd hydrogen bonds : bond 0.02960 ( 661) hydrogen bonds : angle 3.86857 ( 1717) covalent geometry : bond 0.00278 (14395) covalent geometry : angle 0.53716 (19814) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6386.73 seconds wall clock time: 115 minutes 33.30 seconds (6933.30 seconds total)