Starting phenix.real_space_refine on Fri Jul 3 06:57:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a5o_15179/07_2026/8a5o_15179_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a5o_15179/07_2026/8a5o_15179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8a5o_15179/07_2026/8a5o_15179_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a5o_15179/07_2026/8a5o_15179_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8a5o_15179/07_2026/8a5o_15179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a5o_15179/07_2026/8a5o_15179.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 50 5.16 5 C 7968 2.51 5 N 2128 2.21 5 O 2413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12571 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 882 Classifications: {'peptide': 103} Link IDs: {'TRANS': 102} Chain: "U" Number of atoms: 5060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5060 Classifications: {'peptide': 626} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 594} Chain: "V" Number of atoms: 2824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2824 Classifications: {'peptide': 361} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 Chain: "W" Number of atoms: 3422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3422 Classifications: {'peptide': 431} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 409} Chain breaks: 1 Chain: "X" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 287 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.70, per 1000 atoms: 0.21 Number of scatterers: 12571 At special positions: 0 Unit cell: (98.487, 135.552, 137.67, 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 50 16.00 P 9 15.00 Mg 3 11.99 O 2413 8.00 N 2128 7.00 C 7968 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: 0.99 Conformation dependent library (CDL) restraints added in 575.5 milliseconds 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2954 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 20 sheets defined 52.7% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'G' and resid 458 through 483 Processing helix chain 'G' and resid 483 through 518 removed outlier: 4.360A pdb=" N LYS G 487 " --> pdb=" O LYS G 483 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN G 518 " --> pdb=" O ALA G 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 521 through 559 Processing helix chain 'U' and resid 300 through 302 No H-bonds generated for 'chain 'U' and resid 300 through 302' Processing helix chain 'U' and resid 303 through 307 Processing helix chain 'U' and resid 320 through 341 removed outlier: 3.887A pdb=" N ASN U 324 " --> pdb=" O SER U 320 " (cutoff:3.500A) Processing helix chain 'U' and resid 348 through 360 removed outlier: 3.540A pdb=" N PHE U 356 " --> pdb=" O GLN U 352 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN U 359 " --> pdb=" O SER U 355 " (cutoff:3.500A) Processing helix chain 'U' and resid 387 through 391 Processing helix chain 'U' and resid 417 through 434 Processing helix chain 'U' and resid 441 through 448 removed outlier: 3.712A pdb=" N PHE U 445 " --> pdb=" O PRO U 442 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ASN U 446 " --> pdb=" O THR U 443 " (cutoff:3.500A) Processing helix chain 'U' and resid 459 through 473 Processing helix chain 'U' and resid 484 through 493 Processing helix chain 'U' and resid 520 through 523 Processing helix chain 'U' and resid 531 through 544 Processing helix chain 'U' and resid 555 through 570 Processing helix chain 'U' and resid 573 through 577 Processing helix chain 'U' and resid 602 through 610 Proline residue: U 608 - end of helix Processing helix chain 'U' and resid 611 through 613 No H-bonds generated for 'chain 'U' and resid 611 through 613' Processing helix chain 'U' and resid 614 through 620 removed outlier: 3.521A pdb=" N ILE U 620 " --> pdb=" O ILE U 616 " (cutoff:3.500A) Processing helix chain 'U' and resid 627 through 634 Processing helix chain 'U' and resid 650 through 659 Processing helix chain 'U' and resid 661 through 665 Processing helix chain 'U' and resid 667 through 688 removed outlier: 5.734A pdb=" N HIS U 679 " --> pdb=" O ILE U 675 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASN U 680 " --> pdb=" O LEU U 676 " (cutoff:3.500A) Processing helix chain 'U' and resid 702 through 716 Processing helix chain 'U' and resid 719 through 721 No H-bonds generated for 'chain 'U' and resid 719 through 721' Processing helix chain 'U' and resid 722 through 728 removed outlier: 3.513A pdb=" N TYR U 727 " --> pdb=" O MET U 723 " (cutoff:3.500A) Processing helix chain 'U' and resid 734 through 739 removed outlier: 3.538A pdb=" N ILE U 739 " --> pdb=" O SER U 736 " (cutoff:3.500A) Processing helix chain 'U' and resid 741 through 754 removed outlier: 3.627A pdb=" N ILE U 745 " --> pdb=" O ALA U 741 " (cutoff:3.500A) Processing helix chain 'U' and resid 755 through 760 removed outlier: 3.510A pdb=" N SER U 760 " --> pdb=" O SER U 756 " (cutoff:3.500A) Processing helix chain 'U' and resid 762 through 781 Processing helix chain 'U' and resid 788 through 816 removed outlier: 4.043A pdb=" N ASN U 792 " --> pdb=" O THR U 788 " (cutoff:3.500A) Processing helix chain 'U' and resid 832 through 836 removed outlier: 4.202A pdb=" N ASP U 835 " --> pdb=" O PRO U 832 " (cutoff:3.500A) Processing helix chain 'U' and resid 840 through 850 Processing helix chain 'U' and resid 851 through 858 removed outlier: 6.542A pdb=" N LEU U 854 " --> pdb=" O GLN U 851 " (cutoff:3.500A) Processing helix chain 'U' and resid 862 through 869 Processing helix chain 'U' and resid 870 through 875 Processing helix chain 'V' and resid 55 through 61 Processing helix chain 'V' and resid 78 through 92 removed outlier: 3.866A 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 Processing helix chain 'V' and resid 137 through 144 Processing helix chain 'V' and resid 172 through 175 Processing helix chain 'V' and resid 181 through 196 Processing helix chain 'V' and resid 202 through 217 removed outlier: 3.629A pdb=" N ILE V 208 " --> pdb=" O ALA V 204 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP V 211 " --> pdb=" O GLU V 207 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS V 217 " --> pdb=" O LYS V 213 " (cutoff:3.500A) Processing helix chain 'V' and resid 222 through 233 Processing helix chain 'V' and resid 234 through 237 Processing helix chain 'V' and resid 252 through 260 Proline residue: V 258 - end of helix Processing helix chain 'V' and resid 261 through 262 No H-bonds generated for 'chain 'V' and resid 261 through 262' Processing helix chain 'V' and resid 263 through 268 Processing helix chain 'V' and resid 273 through 283 Processing helix chain 'V' and resid 286 through 288 No H-bonds generated for 'chain 'V' and resid 286 through 288' Processing helix chain 'V' and resid 289 through 295 Processing helix chain 'V' and resid 301 through 306 removed outlier: 4.045A pdb=" N PHE V 306 " --> pdb=" O THR V 303 " (cutoff:3.500A) Processing helix chain 'V' and resid 308 through 321 removed outlier: 3.513A pdb=" N LEU V 320 " --> pdb=" O GLU V 316 " (cutoff:3.500A) Processing helix chain 'V' and resid 337 through 348 Processing helix chain 'V' and resid 349 through 355 removed outlier: 3.744A pdb=" N GLN V 353 " --> pdb=" O THR V 350 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN V 354 " --> pdb=" O THR V 351 " (cutoff:3.500A) Processing helix chain 'V' and resid 359 through 366 Processing helix chain 'V' and resid 369 through 374 Processing helix chain 'W' and resid 58 through 63 removed outlier: 4.785A pdb=" N GLY W 63 " --> pdb=" O GLU W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 97 Processing helix chain 'W' and resid 117 through 130 removed outlier: 3.602A pdb=" N LEU W 125 " --> pdb=" O ARG W 121 " (cutoff:3.500A) Processing helix chain 'W' and resid 142 through 151 removed outlier: 3.542A pdb=" N PHE W 148 " --> pdb=" O THR W 144 " (cutoff:3.500A) Processing helix chain 'W' and resid 186 through 197 Processing helix chain 'W' and resid 205 through 207 No H-bonds generated for 'chain 'W' and resid 205 through 207' Processing helix chain 'W' and resid 226 through 236 removed outlier: 3.702A pdb=" N TYR W 230 " --> pdb=" O ASP W 226 " (cutoff:3.500A) Processing helix chain 'W' and resid 237 through 246 Processing helix chain 'W' and resid 254 through 265 removed outlier: 5.257A pdb=" N THR W 260 " --> pdb=" O GLU W 256 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLU W 261 " --> pdb=" O GLU W 257 " (cutoff:3.500A) Processing helix chain 'W' and resid 281 through 291 removed outlier: 4.059A pdb=" N ALA W 289 " --> pdb=" O ARG W 285 " (cutoff:3.500A) Processing helix chain 'W' and resid 384 through 395 Processing helix chain 'W' and resid 400 through 406 Processing helix chain 'W' and resid 412 through 417 removed outlier: 3.968A pdb=" N SER W 416 " --> pdb=" O GLY W 413 " (cutoff:3.500A) Processing helix chain 'W' and resid 419 through 432 Processing helix chain 'W' and resid 446 through 462 removed outlier: 3.840A pdb=" N TYR W 450 " --> pdb=" O ILE W 446 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER W 452 " --> pdb=" O ARG W 448 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TRP W 453 " --> pdb=" O GLN W 449 " (cutoff:3.500A) Processing helix chain 'W' and resid 463 through 469 removed outlier: 4.511A pdb=" N GLN W 467 " --> pdb=" O THR W 464 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP W 469 " --> pdb=" O HIS W 466 " (cutoff:3.500A) Processing helix chain 'W' and resid 472 through 479 Processing helix chain 'W' and resid 479 through 487 removed outlier: 3.846A pdb=" N ASN W 485 " --> pdb=" O GLU W 481 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'U' and resid 289 through 292 Processing sheet with id=AA2, first strand: chain 'U' and resid 384 through 385 Processing sheet with id=AA3, first strand: chain 'U' and resid 363 through 365 removed outlier: 3.707A pdb=" N THR U 593 " --> pdb=" O ILE U 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'U' and resid 403 through 404 Processing sheet with id=AA5, first strand: chain 'U' and resid 517 through 518 Processing sheet with id=AA6, first strand: chain 'U' and resid 517 through 518 removed outlier: 6.419A pdb=" N CYS U 499 " --> pdb=" O LEU U 731 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL U 733 " --> pdb=" O CYS U 499 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL U 501 " --> pdb=" O VAL U 733 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE U 730 " --> pdb=" O ILE U 830 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'V' and resid 29 through 32 removed outlier: 6.455A pdb=" N LEU V 8 " --> pdb=" O LEU V 104 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR V 106 " --> pdb=" O LEU V 8 " (cutoff:3.500A) removed outlier: 7.558A 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: 5.875A pdb=" N ILE V 151 " --> pdb=" O VAL V 298 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N SER V 300 " --> pdb=" O ILE V 151 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU V 153 " --> pdb=" O SER V 300 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE V 297 " --> pdb=" O ILE V 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'V' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'W' and resid 38 through 41 Processing sheet with id=AB5, first strand: chain 'W' and resid 55 through 56 Processing sheet with id=AB6, first strand: chain 'W' and resid 75 through 76 Processing sheet with id=AB7, first strand: chain 'W' and resid 174 through 175 Processing sheet with id=AB8, first strand: chain 'W' and resid 174 through 175 removed outlier: 5.970A pdb=" N LEU W 156 " --> pdb=" O VAL W 409 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N THR W 411 " --> pdb=" O LEU W 156 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL W 158 " --> pdb=" O THR W 411 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'W' and resid 209 through 211 removed outlier: 6.955A pdb=" N ILE W 217 " --> pdb=" O LYS W 210 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'W' and resid 269 through 271 Processing sheet with id=AC2, first strand: chain 'X' and resid 41 through 51 removed outlier: 6.775A pdb=" N LYS X 44 " --> pdb=" O ILE X 64 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE X 64 " --> pdb=" O LYS X 44 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS X 46 " --> pdb=" O GLY X 62 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLY X 62 " --> pdb=" O LYS X 46 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1698 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.34: 3920 1.34 - 1.53: 6323 1.53 - 1.71: 2526 1.71 - 1.89: 76 1.89 - 2.07: 1 Bond restraints: 12846 Sorted by residual: bond pdb=" C ILE U 510 " pdb=" O ILE U 510 " ideal model delta sigma weight residual 1.237 1.312 -0.075 1.07e-02 8.73e+03 4.95e+01 bond pdb=" PG AGS U 900 " pdb=" S1G AGS U 900 " ideal model delta sigma weight residual 1.936 2.074 -0.138 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C LYS U 459 " pdb=" O LYS U 459 " ideal model delta sigma weight residual 1.236 1.318 -0.082 1.22e-02 6.72e+03 4.50e+01 bond pdb=" C ILE W 160 " pdb=" O ILE W 160 " ideal model delta sigma weight residual 1.236 1.311 -0.075 1.14e-02 7.69e+03 4.36e+01 bond pdb=" C PRO W 36 " pdb=" O PRO W 36 " ideal model delta sigma weight residual 1.233 1.162 0.071 1.10e-02 8.26e+03 4.20e+01 ... (remaining 12841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 15130 2.79 - 5.58: 2149 5.58 - 8.36: 124 8.36 - 11.15: 7 11.15 - 13.94: 3 Bond angle restraints: 17413 Sorted by residual: angle pdb=" CA GLY W 412 " pdb=" C GLY W 412 " pdb=" O GLY W 412 " ideal model delta sigma weight residual 121.88 116.71 5.17 7.80e-01 1.64e+00 4.40e+01 angle pdb=" CA ASP V 275 " pdb=" CB ASP V 275 " pdb=" CG ASP V 275 " ideal model delta sigma weight residual 112.60 119.00 -6.40 1.00e+00 1.00e+00 4.09e+01 angle pdb=" CA ASP G 552 " pdb=" CB ASP G 552 " pdb=" CG ASP G 552 " ideal model delta sigma weight residual 112.60 118.98 -6.38 1.00e+00 1.00e+00 4.07e+01 angle pdb=" N ARG W 212 " pdb=" CA ARG W 212 " pdb=" CB ARG W 212 " ideal model delta sigma weight residual 111.00 102.56 8.44 1.33e+00 5.65e-01 4.03e+01 angle pdb=" CG ARG U 754 " pdb=" CD ARG U 754 " pdb=" NE ARG U 754 " ideal model delta sigma weight residual 112.00 98.06 13.94 2.20e+00 2.07e-01 4.01e+01 ... (remaining 17408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 7658 35.88 - 71.76: 154 71.76 - 107.64: 31 107.64 - 143.51: 1 143.51 - 179.39: 3 Dihedral angle restraints: 7847 sinusoidal: 3293 harmonic: 4554 Sorted by residual: dihedral pdb=" CA GLY W 32 " pdb=" C GLY W 32 " pdb=" N SER W 33 " pdb=" CA SER W 33 " ideal model delta harmonic sigma weight residual 180.00 154.08 25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA SER U 522 " pdb=" C SER U 522 " pdb=" N ALA U 523 " pdb=" CA ALA U 523 " ideal model delta harmonic sigma weight residual -180.00 -154.45 -25.55 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA VAL W 158 " pdb=" C VAL W 158 " pdb=" N ASP W 159 " pdb=" CA ASP W 159 " ideal model delta harmonic sigma weight residual -180.00 -155.62 -24.38 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 7844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1162 0.080 - 0.161: 592 0.161 - 0.241: 125 0.241 - 0.322: 35 0.322 - 0.402: 6 Chirality restraints: 1920 Sorted by residual: chirality pdb=" CA ILE U 510 " pdb=" N ILE U 510 " pdb=" C ILE U 510 " pdb=" CB ILE U 510 " both_signs ideal model delta sigma weight residual False 2.43 2.84 -0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" C4' AGS W 500 " pdb=" C3' AGS W 500 " pdb=" C5' AGS W 500 " pdb=" O4' AGS W 500 " both_signs ideal model delta sigma weight residual False -2.41 -2.80 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CA VAL U 451 " pdb=" N VAL U 451 " pdb=" C VAL U 451 " pdb=" CB VAL U 451 " both_signs ideal model delta sigma weight residual False 2.44 2.81 -0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 1917 not shown) Planarity restraints: 2229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR W 450 " -0.087 2.00e-02 2.50e+03 5.05e-02 5.11e+01 pdb=" CG TYR W 450 " 0.098 2.00e-02 2.50e+03 pdb=" CD1 TYR W 450 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR W 450 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR W 450 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR W 450 " 0.026 2.00e-02 2.50e+03 pdb=" CZ TYR W 450 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR W 450 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS W 162 " -0.062 2.00e-02 2.50e+03 5.23e-02 4.10e+01 pdb=" CG HIS W 162 " 0.105 2.00e-02 2.50e+03 pdb=" ND1 HIS W 162 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 HIS W 162 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 HIS W 162 " -0.034 2.00e-02 2.50e+03 pdb=" NE2 HIS W 162 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP W 469 " 0.079 2.00e-02 2.50e+03 3.84e-02 3.70e+01 pdb=" CG TRP W 469 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP W 469 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP W 469 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP W 469 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP W 469 " 0.022 2.00e-02 2.50e+03 pdb=" CE3 TRP W 469 " -0.022 2.00e-02 2.50e+03 pdb=" CZ2 TRP W 469 " 0.029 2.00e-02 2.50e+03 pdb=" CZ3 TRP W 469 " -0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP W 469 " 0.013 2.00e-02 2.50e+03 ... (remaining 2226 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 17 2.57 - 3.15: 9703 3.15 - 3.73: 18005 3.73 - 4.32: 27207 4.32 - 4.90: 45111 Nonbonded interactions: 100043 Sorted by model distance: nonbonded pdb=" O2G AGS W 500 " pdb="MG MG W 501 " model vdw 1.981 2.170 nonbonded pdb=" OD1 ASP U 531 " pdb=" O3' AGS U 900 " model vdw 1.989 3.040 nonbonded pdb=" O2G AGS V 500 " pdb="MG MG V 501 " model vdw 2.087 2.170 nonbonded pdb=" O2B AGS U 900 " pdb="MG MG U 901 " model vdw 2.230 2.170 nonbonded pdb=" O3G AGS U 900 " pdb="MG MG U 901 " model vdw 2.266 2.170 ... (remaining 100038 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: 1.030 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.860 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.138 12846 Z= 1.174 Angle : 1.868 13.939 17413 Z= 1.307 Chirality : 0.098 0.402 1920 Planarity : 0.010 0.052 2229 Dihedral : 16.437 179.393 4893 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.76 % Favored : 96.04 % Rotamer: Outliers : 0.72 % Allowed : 3.38 % Favored : 95.90 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.20), residues: 1541 helix: -1.33 (0.16), residues: 694 sheet: 0.88 (0.38), residues: 179 loop : -0.35 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG V 116 TYR 0.098 0.013 TYR W 450 PHE 0.070 0.013 PHE U 572 TRP 0.079 0.014 TRP W 469 HIS 0.039 0.006 HIS W 162 Details of bonding type rmsd/Z covalent geometry : bond 0.01625 / 1.17 (12846) covalent geometry : angle 1.86806 / 1.31 (17413) hydrogen bonds : bond 0.17728 / 12.31 ( 630) hydrogen bonds : angle 6.96085 / 5.22 ( 1698) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 288 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: G 457 MET cc_start: 0.6300 (tpp) cc_final: 0.6021 (tpt) REVERT: G 490 ARG cc_start: 0.5695 (mtt180) cc_final: 0.5300 (ptt-90) REVERT: G 524 GLN cc_start: 0.6742 (mt0) cc_final: 0.6517 (mt0) REVERT: G 545 LYS cc_start: 0.7951 (mttt) cc_final: 0.7553 (tppt) REVERT: U 286 ASP cc_start: 0.7792 (m-30) cc_final: 0.7336 (p0) REVERT: U 287 HIS cc_start: 0.8925 (p90) cc_final: 0.8633 (p-80) REVERT: U 441 LYS cc_start: 0.8094 (mttt) cc_final: 0.7739 (mmtt) REVERT: U 515 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7443 (mm-30) REVERT: U 574 ASP cc_start: 0.8280 (p0) cc_final: 0.8006 (p0) REVERT: U 585 MET cc_start: 0.8662 (mtp) cc_final: 0.8314 (mtm) REVERT: U 591 GLN cc_start: 0.8052 (mt0) cc_final: 0.7787 (mp10) REVERT: U 602 ASP cc_start: 0.7320 (m-30) cc_final: 0.6696 (p0) REVERT: U 618 LYS cc_start: 0.8504 (tttt) cc_final: 0.8253 (tttt) REVERT: U 644 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6982 (mm-30) REVERT: U 655 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7435 (mm-30) REVERT: U 658 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7696 (mm-30) REVERT: U 688 LYS cc_start: 0.7491 (mttt) cc_final: 0.7088 (pttm) REVERT: U 733 VAL cc_start: 0.8054 (t) cc_final: 0.7823 (m) REVERT: U 765 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7590 (mp10) REVERT: U 773 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7460 (mt-10) REVERT: U 809 GLU cc_start: 0.8185 (tt0) cc_final: 0.7916 (tp30) REVERT: U 835 ASP cc_start: 0.8747 (m-30) cc_final: 0.8462 (t70) REVERT: U 853 LYS cc_start: 0.8671 (mttt) cc_final: 0.8346 (mmmt) REVERT: U 856 GLU cc_start: 0.7772 (tt0) cc_final: 0.7377 (tm-30) REVERT: V 25 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7639 (p0) REVERT: V 53 TYR cc_start: 0.8807 (m-80) cc_final: 0.8499 (m-80) REVERT: V 68 ARG cc_start: 0.7950 (mtp180) cc_final: 0.7172 (tpt170) REVERT: V 69 TYR cc_start: 0.8744 (m-80) cc_final: 0.8111 (m-80) REVERT: V 78 ASN cc_start: 0.7921 (t0) cc_final: 0.7713 (t0) REVERT: V 80 ASP cc_start: 0.8545 (m-30) cc_final: 0.8327 (m-30) REVERT: V 99 GLU cc_start: 0.8501 (pt0) cc_final: 0.8250 (pm20) REVERT: V 128 ASN cc_start: 0.8127 (m110) cc_final: 0.7553 (t0) REVERT: V 160 THR cc_start: 0.9228 (m) cc_final: 0.9028 (m) REVERT: V 178 ILE cc_start: 0.8241 (mm) cc_final: 0.7892 (mp) REVERT: V 190 MET cc_start: 0.7813 (mtm) cc_final: 0.7582 (mtm) REVERT: V 222 ASP cc_start: 0.7503 (m-30) cc_final: 0.7221 (t0) REVERT: V 225 GLN cc_start: 0.7525 (mt0) cc_final: 0.6764 (tp-100) REVERT: V 232 GLN cc_start: 0.7569 (mt0) cc_final: 0.7186 (pt0) REVERT: V 246 GLN cc_start: 0.6655 (tt0) cc_final: 0.5828 (mm-40) REVERT: V 270 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8436 (mt-10) REVERT: V 291 LYS cc_start: 0.8185 (mttt) cc_final: 0.7983 (mtpp) REVERT: V 292 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7843 (mp0) REVERT: V 305 MET cc_start: 0.8921 (mmm) cc_final: 0.8581 (mmm) REVERT: V 326 LYS cc_start: 0.8338 (tttt) cc_final: 0.7916 (tptp) REVERT: V 360 GLN cc_start: 0.8331 (tt0) cc_final: 0.7856 (mp10) REVERT: W 91 GLN cc_start: 0.8064 (tt0) cc_final: 0.7654 (tp40) REVERT: W 101 ASN cc_start: 0.8570 (t0) cc_final: 0.8121 (p0) REVERT: W 132 MET cc_start: 0.8062 (mtm) cc_final: 0.7708 (mtp) REVERT: W 152 ARG cc_start: 0.8478 (mmm160) cc_final: 0.8220 (mmm160) REVERT: W 172 ASP cc_start: 0.8366 (m-30) cc_final: 0.8155 (m-30) REVERT: W 196 LYS cc_start: 0.7869 (tttt) cc_final: 0.7283 (pttm) REVERT: W 215 GLU cc_start: 0.6634 (mt-10) cc_final: 0.5988 (mp0) REVERT: W 224 GLU cc_start: 0.8210 (tt0) cc_final: 0.7937 (tp30) REVERT: W 256 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7699 (tm-30) REVERT: W 277 GLU cc_start: 0.8873 (tt0) cc_final: 0.8317 (mp0) REVERT: W 394 MET cc_start: 0.7822 (mmt) cc_final: 0.7602 (mmm) REVERT: W 399 ASP cc_start: 0.8403 (m-30) cc_final: 0.8073 (p0) REVERT: W 473 LYS cc_start: 0.7599 (mmtt) cc_final: 0.7272 (ttmt) REVERT: X 51 LYS cc_start: 0.8457 (tttt) cc_final: 0.8181 (ttmm) outliers start: 10 outliers final: 5 residues processed: 297 average time/residue: 0.1310 time to fit residues: 53.9160 Evaluate side-chains 214 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 208 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 495 SER Chi-restraints excluded: chain V residue 25 ASP Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 464 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 468 HIS G 518 GLN U 272 HIS U 324 ASN U 369 ASN U 502 ASN U 799 GLN V 115 ASN V 232 GLN V 372 HIS W 95 GLN W 162 HIS X 45 ASN X 59 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.145069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116983 restraints weight = 15550.372| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.66 r_work: 0.3107 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12846 Z= 0.137 Angle : 0.604 11.849 17413 Z= 0.316 Chirality : 0.045 0.143 1920 Planarity : 0.004 0.040 2229 Dihedral : 14.124 178.710 1796 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.95 % Favored : 97.99 % Rotamer: Outliers : 1.01 % Allowed : 7.49 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.21), residues: 1541 helix: 0.59 (0.19), residues: 709 sheet: 0.97 (0.35), residues: 213 loop : 0.21 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG V 183 TYR 0.015 0.001 TYR U 596 PHE 0.021 0.002 PHE U 598 TRP 0.014 0.002 TRP V 356 HIS 0.007 0.001 HIS U 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (12846) covalent geometry : angle 0.60390 / 0.32 (17413) hydrogen bonds : bond 0.04258 / 2.96 ( 630) hydrogen bonds : angle 4.74592 / 3.58 ( 1698) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 217 time to evaluate : 0.512 Fit side-chains REVERT: G 490 ARG cc_start: 0.7064 (mtt180) cc_final: 0.6159 (ptt180) REVERT: G 544 LYS cc_start: 0.8775 (mttt) cc_final: 0.8552 (mtmt) REVERT: G 545 LYS cc_start: 0.8665 (mttt) cc_final: 0.8233 (tppt) REVERT: U 596 TYR cc_start: 0.7421 (m-80) cc_final: 0.7130 (m-80) REVERT: U 632 PHE cc_start: 0.8395 (m-80) cc_final: 0.8133 (m-80) REVERT: U 688 LYS cc_start: 0.7766 (mttt) cc_final: 0.7347 (pttm) REVERT: V 68 ARG cc_start: 0.7810 (mtp180) cc_final: 0.7556 (ttt90) REVERT: V 69 TYR cc_start: 0.8983 (m-80) cc_final: 0.8662 (m-80) REVERT: V 246 GLN cc_start: 0.7403 (tt0) cc_final: 0.6948 (mm-40) REVERT: V 305 MET cc_start: 0.8919 (mmm) cc_final: 0.8641 (mmm) REVERT: V 311 GLU cc_start: 0.8542 (mp0) cc_final: 0.8330 (mp0) REVERT: W 59 GLU cc_start: 0.7597 (tt0) cc_final: 0.7344 (tt0) REVERT: W 152 ARG cc_start: 0.8416 (mmm160) cc_final: 0.8069 (mmm160) REVERT: W 196 LYS cc_start: 0.8232 (tttt) cc_final: 0.7773 (pttm) REVERT: W 215 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6687 (mp0) REVERT: W 394 MET cc_start: 0.8327 (mmt) cc_final: 0.8121 (mmm) REVERT: X 44 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8448 (mtmt) outliers start: 14 outliers final: 6 residues processed: 228 average time/residue: 0.1135 time to fit residues: 37.0658 Evaluate side-chains 177 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 170 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain V residue 199 SER Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 100 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 130 optimal weight: 0.1980 chunk 97 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.139065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111690 restraints weight = 15886.996| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.57 r_work: 0.3054 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 12846 Z= 0.227 Angle : 0.629 7.077 17413 Z= 0.325 Chirality : 0.047 0.148 1920 Planarity : 0.005 0.044 2229 Dihedral : 14.478 177.652 1790 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.66 % Favored : 97.27 % Rotamer: Outliers : 2.02 % Allowed : 9.14 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.21), residues: 1541 helix: 0.70 (0.19), residues: 701 sheet: 0.75 (0.36), residues: 213 loop : 0.19 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 448 TYR 0.022 0.002 TYR W 450 PHE 0.023 0.002 PHE U 546 TRP 0.017 0.002 TRP V 356 HIS 0.007 0.001 HIS U 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.23 (12846) covalent geometry : angle 0.62868 / 0.32 (17413) hydrogen bonds : bond 0.04650 / 3.21 ( 630) hydrogen bonds : angle 4.63263 / 3.51 ( 1698) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: G 490 ARG cc_start: 0.7026 (mtt180) cc_final: 0.6182 (ptt-90) REVERT: G 544 LYS cc_start: 0.8793 (mttt) cc_final: 0.8571 (mtmt) REVERT: G 545 LYS cc_start: 0.8642 (mttt) cc_final: 0.8346 (tppt) REVERT: U 688 LYS cc_start: 0.7629 (mttt) cc_final: 0.7235 (pttm) REVERT: V 69 TYR cc_start: 0.8979 (m-80) cc_final: 0.8653 (m-80) REVERT: V 160 THR cc_start: 0.9339 (m) cc_final: 0.9034 (m) REVERT: V 246 GLN cc_start: 0.7279 (tt0) cc_final: 0.6898 (mm-40) REVERT: W 59 GLU cc_start: 0.7814 (tt0) cc_final: 0.7585 (tt0) REVERT: W 196 LYS cc_start: 0.8199 (tttt) cc_final: 0.7859 (ttpt) REVERT: W 215 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6810 (mp0) REVERT: W 284 THR cc_start: 0.8685 (m) cc_final: 0.8340 (p) REVERT: W 425 MET cc_start: 0.7898 (tpt) cc_final: 0.7328 (tpt) REVERT: W 430 LYS cc_start: 0.7732 (mttt) cc_final: 0.7242 (mmtt) outliers start: 28 outliers final: 19 residues processed: 195 average time/residue: 0.1275 time to fit residues: 35.4877 Evaluate side-chains 179 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain U residue 683 ASP Chi-restraints excluded: chain U residue 836 MET Chi-restraints excluded: chain V residue 199 SER Chi-restraints excluded: chain V residue 252 ASN Chi-restraints excluded: chain V residue 364 GLU Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 95 GLN Chi-restraints excluded: chain W residue 166 SER Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 428 LEU Chi-restraints excluded: chain W residue 462 LEU Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 21 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.146538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121472 restraints weight = 15662.430| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.55 r_work: 0.3088 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12846 Z= 0.121 Angle : 0.518 6.691 17413 Z= 0.269 Chirality : 0.043 0.139 1920 Planarity : 0.004 0.043 2229 Dihedral : 13.236 177.526 1790 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.88 % Favored : 98.05 % Rotamer: Outliers : 1.66 % Allowed : 10.58 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.21), residues: 1541 helix: 1.04 (0.19), residues: 711 sheet: 0.87 (0.35), residues: 215 loop : 0.28 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 68 TYR 0.014 0.001 TYR U 596 PHE 0.013 0.001 PHE W 207 TRP 0.015 0.001 TRP V 356 HIS 0.007 0.001 HIS U 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (12846) covalent geometry : angle 0.51846 / 0.27 (17413) hydrogen bonds : bond 0.03617 / 2.51 ( 630) hydrogen bonds : angle 4.34147 / 3.30 ( 1698) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: G 490 ARG cc_start: 0.7096 (mtt180) cc_final: 0.6169 (ptt180) REVERT: G 544 LYS cc_start: 0.8825 (mttt) cc_final: 0.8572 (mtmt) REVERT: G 545 LYS cc_start: 0.8693 (mttt) cc_final: 0.8467 (tppt) REVERT: U 596 TYR cc_start: 0.7463 (m-80) cc_final: 0.7119 (m-80) REVERT: U 688 LYS cc_start: 0.7627 (mttt) cc_final: 0.7259 (pttm) REVERT: U 801 LYS cc_start: 0.8715 (tttt) cc_final: 0.8263 (mttp) REVERT: U 802 GLU cc_start: 0.7655 (tt0) cc_final: 0.7376 (mt-10) REVERT: V 69 TYR cc_start: 0.8979 (m-80) cc_final: 0.8594 (m-80) REVERT: V 160 THR cc_start: 0.9330 (m) cc_final: 0.9046 (m) REVERT: V 246 GLN cc_start: 0.7350 (tt0) cc_final: 0.7010 (mm-40) REVERT: V 305 MET cc_start: 0.8775 (mmm) cc_final: 0.8568 (mmm) REVERT: W 196 LYS cc_start: 0.8164 (tttt) cc_final: 0.7713 (ttpt) REVERT: W 215 GLU cc_start: 0.7259 (mt-10) cc_final: 0.7036 (mp0) REVERT: W 425 MET cc_start: 0.7815 (tpt) cc_final: 0.7278 (tpt) REVERT: W 430 LYS cc_start: 0.7601 (mttt) cc_final: 0.7295 (mmtt) outliers start: 23 outliers final: 14 residues processed: 192 average time/residue: 0.1045 time to fit residues: 29.0483 Evaluate side-chains 165 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 581 LEU Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain U residue 683 ASP Chi-restraints excluded: chain U residue 836 MET Chi-restraints excluded: chain V residue 252 ASN Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 166 SER Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 792 ASN V 372 HIS W 95 GLN W 449 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.144612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.119337 restraints weight = 15783.180| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.52 r_work: 0.3071 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12846 Z= 0.164 Angle : 0.545 6.870 17413 Z= 0.281 Chirality : 0.045 0.165 1920 Planarity : 0.004 0.044 2229 Dihedral : 13.226 177.097 1790 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.47 % Favored : 97.47 % Rotamer: Outliers : 2.16 % Allowed : 11.81 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.21), residues: 1541 helix: 1.03 (0.19), residues: 711 sheet: 0.88 (0.36), residues: 209 loop : 0.18 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG V 68 TYR 0.017 0.001 TYR W 450 PHE 0.013 0.001 PHE U 546 TRP 0.015 0.001 TRP V 356 HIS 0.007 0.001 HIS U 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 (12846) covalent geometry : angle 0.54503 / 0.28 (17413) hydrogen bonds : bond 0.03893 / 2.68 ( 630) hydrogen bonds : angle 4.34528 / 3.30 ( 1698) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.506 Fit side-chains REVERT: G 490 ARG cc_start: 0.7126 (mtt180) cc_final: 0.6217 (ptt180) REVERT: G 526 LYS cc_start: 0.8339 (mttt) cc_final: 0.7929 (ttpp) REVERT: G 545 LYS cc_start: 0.8674 (mttt) cc_final: 0.8453 (tppt) REVERT: U 596 TYR cc_start: 0.7492 (m-80) cc_final: 0.7137 (m-80) REVERT: U 688 LYS cc_start: 0.7547 (mttt) cc_final: 0.7212 (pttm) REVERT: U 801 LYS cc_start: 0.8719 (tttt) cc_final: 0.8269 (mttp) REVERT: U 802 GLU cc_start: 0.7578 (tt0) cc_final: 0.7286 (mt-10) REVERT: V 69 TYR cc_start: 0.8952 (m-80) cc_final: 0.8574 (m-80) REVERT: V 160 THR cc_start: 0.9354 (m) cc_final: 0.9074 (m) REVERT: V 246 GLN cc_start: 0.7439 (tt0) cc_final: 0.6984 (mm-40) REVERT: W 196 LYS cc_start: 0.8049 (tttt) cc_final: 0.7815 (ttpt) REVERT: W 215 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6994 (mp0) REVERT: W 425 MET cc_start: 0.7807 (tpt) cc_final: 0.7294 (tpt) REVERT: W 430 LYS cc_start: 0.7802 (mttt) cc_final: 0.7328 (mmtt) outliers start: 30 outliers final: 20 residues processed: 180 average time/residue: 0.1210 time to fit residues: 30.8953 Evaluate side-chains 172 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain U residue 685 LEU Chi-restraints excluded: chain U residue 716 ILE Chi-restraints excluded: chain U residue 800 ILE Chi-restraints excluded: chain U residue 836 MET Chi-restraints excluded: chain V residue 199 SER Chi-restraints excluded: chain V residue 252 ASN Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 137 CYS Chi-restraints excluded: chain W residue 166 SER Chi-restraints excluded: chain W residue 279 VAL Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 441 THR Chi-restraints excluded: chain W residue 462 LEU Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 47 optimal weight: 0.4980 chunk 122 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 146 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 541 ASN U 821 ASN W 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.145536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120610 restraints weight = 15681.816| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.62 r_work: 0.3089 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12846 Z= 0.111 Angle : 0.497 6.879 17413 Z= 0.257 Chirality : 0.043 0.150 1920 Planarity : 0.004 0.042 2229 Dihedral : 12.533 173.263 1790 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.92 % Rotamer: Outliers : 2.09 % Allowed : 11.59 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.22), residues: 1541 helix: 1.29 (0.20), residues: 704 sheet: 0.86 (0.35), residues: 218 loop : 0.23 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 68 TYR 0.012 0.001 TYR U 596 PHE 0.012 0.001 PHE W 207 TRP 0.014 0.001 TRP V 356 HIS 0.007 0.001 HIS U 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (12846) covalent geometry : angle 0.49724 / 0.26 (17413) hydrogen bonds : bond 0.03385 / 2.34 ( 630) hydrogen bonds : angle 4.21444 / 3.20 ( 1698) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.496 Fit side-chains REVERT: G 490 ARG cc_start: 0.7049 (mtt180) cc_final: 0.5975 (ptt180) REVERT: G 526 LYS cc_start: 0.8351 (mttt) cc_final: 0.7913 (ttpp) REVERT: G 545 LYS cc_start: 0.8689 (mttt) cc_final: 0.8440 (tppt) REVERT: U 596 TYR cc_start: 0.7475 (m-80) cc_final: 0.7138 (m-80) REVERT: U 688 LYS cc_start: 0.7514 (mttt) cc_final: 0.7152 (pttm) REVERT: U 801 LYS cc_start: 0.8753 (tttt) cc_final: 0.8325 (mttp) REVERT: U 802 GLU cc_start: 0.7602 (tt0) cc_final: 0.7309 (mt-10) REVERT: V 69 TYR cc_start: 0.9005 (m-80) cc_final: 0.8616 (m-80) REVERT: V 160 THR cc_start: 0.9346 (m) cc_final: 0.9080 (m) REVERT: V 180 LEU cc_start: 0.9016 (tp) cc_final: 0.8768 (tp) REVERT: V 246 GLN cc_start: 0.7511 (tt0) cc_final: 0.7065 (mm-40) REVERT: W 196 LYS cc_start: 0.8024 (tttt) cc_final: 0.7791 (ttpt) REVERT: W 215 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6978 (mp0) REVERT: W 425 MET cc_start: 0.7793 (tpt) cc_final: 0.7277 (tpt) REVERT: W 430 LYS cc_start: 0.7672 (mttt) cc_final: 0.7218 (mmtt) outliers start: 29 outliers final: 21 residues processed: 186 average time/residue: 0.1114 time to fit residues: 29.9914 Evaluate side-chains 173 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain U residue 683 ASP Chi-restraints excluded: chain U residue 685 LEU Chi-restraints excluded: chain U residue 800 ILE Chi-restraints excluded: chain U residue 836 MET Chi-restraints excluded: chain V residue 85 ILE Chi-restraints excluded: chain V residue 199 SER Chi-restraints excluded: chain V residue 252 ASN Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 166 SER Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 279 VAL Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 382 LEU Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 10 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 107 optimal weight: 0.2980 chunk 129 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... W 95 GLN W 211 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.145560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.121094 restraints weight = 15606.390| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.57 r_work: 0.3180 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12846 Z= 0.112 Angle : 0.496 6.710 17413 Z= 0.255 Chirality : 0.043 0.148 1920 Planarity : 0.004 0.041 2229 Dihedral : 12.260 171.655 1790 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.08 % Favored : 97.86 % Rotamer: Outliers : 1.94 % Allowed : 12.31 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.22), residues: 1541 helix: 1.37 (0.20), residues: 704 sheet: 0.90 (0.36), residues: 218 loop : 0.27 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 68 TYR 0.012 0.001 TYR W 450 PHE 0.012 0.001 PHE W 207 TRP 0.014 0.001 TRP V 356 HIS 0.007 0.001 HIS U 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (12846) covalent geometry : angle 0.49605 / 0.25 (17413) hydrogen bonds : bond 0.03337 / 2.30 ( 630) hydrogen bonds : angle 4.17567 / 3.18 ( 1698) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.488 Fit side-chains REVERT: G 457 MET cc_start: 0.5488 (tpt) cc_final: 0.5164 (tpt) REVERT: G 490 ARG cc_start: 0.7119 (mtt180) cc_final: 0.6098 (ptt180) REVERT: G 526 LYS cc_start: 0.8351 (mttt) cc_final: 0.7933 (ttpp) REVERT: G 545 LYS cc_start: 0.8678 (mttt) cc_final: 0.8395 (tppt) REVERT: U 596 TYR cc_start: 0.7490 (m-80) cc_final: 0.7156 (m-80) REVERT: U 688 LYS cc_start: 0.7498 (mttt) cc_final: 0.7159 (pttm) REVERT: U 801 LYS cc_start: 0.8748 (tttt) cc_final: 0.8348 (mttp) REVERT: U 802 GLU cc_start: 0.7573 (tt0) cc_final: 0.7292 (mt-10) REVERT: V 69 TYR cc_start: 0.8991 (m-80) cc_final: 0.8602 (m-80) REVERT: V 160 THR cc_start: 0.9357 (m) cc_final: 0.9079 (m) REVERT: V 180 LEU cc_start: 0.9020 (tp) cc_final: 0.8788 (tp) REVERT: V 246 GLN cc_start: 0.7594 (tt0) cc_final: 0.7119 (mm-40) REVERT: V 269 LEU cc_start: 0.8765 (mp) cc_final: 0.8364 (mt) REVERT: W 196 LYS cc_start: 0.8025 (tttt) cc_final: 0.7801 (ttpt) REVERT: W 215 GLU cc_start: 0.7301 (mt-10) cc_final: 0.7044 (mp0) REVERT: W 425 MET cc_start: 0.7745 (tpt) cc_final: 0.7259 (tpt) REVERT: W 428 LEU cc_start: 0.8446 (mm) cc_final: 0.8201 (mm) REVERT: W 430 LYS cc_start: 0.7707 (mttt) cc_final: 0.7248 (mmtt) outliers start: 27 outliers final: 23 residues processed: 181 average time/residue: 0.0988 time to fit residues: 26.2235 Evaluate side-chains 179 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain U residue 683 ASP Chi-restraints excluded: chain U residue 685 LEU Chi-restraints excluded: chain U residue 716 ILE Chi-restraints excluded: chain U residue 800 ILE Chi-restraints excluded: chain U residue 836 MET Chi-restraints excluded: chain V residue 85 ILE Chi-restraints excluded: chain V residue 199 SER Chi-restraints excluded: chain V residue 252 ASN Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 279 VAL Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 382 LEU Chi-restraints excluded: chain W residue 442 THR Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 40 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.147118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120139 restraints weight = 15646.354| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.52 r_work: 0.3222 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12846 Z= 0.120 Angle : 0.496 6.743 17413 Z= 0.255 Chirality : 0.043 0.146 1920 Planarity : 0.004 0.040 2229 Dihedral : 12.181 169.298 1790 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.14 % Favored : 97.79 % Rotamer: Outliers : 2.16 % Allowed : 12.31 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.22), residues: 1541 helix: 1.37 (0.20), residues: 704 sheet: 0.95 (0.36), residues: 218 loop : 0.25 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG V 68 TYR 0.013 0.001 TYR W 450 PHE 0.012 0.001 PHE U 584 TRP 0.013 0.001 TRP V 356 HIS 0.008 0.001 HIS U 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (12846) covalent geometry : angle 0.49600 / 0.26 (17413) hydrogen bonds : bond 0.03362 / 2.32 ( 630) hydrogen bonds : angle 4.17242 / 3.18 ( 1698) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.466 Fit side-chains REVERT: G 490 ARG cc_start: 0.7078 (mtt180) cc_final: 0.6057 (ptt180) REVERT: G 526 LYS cc_start: 0.8292 (mttt) cc_final: 0.7881 (ttpp) REVERT: U 596 TYR cc_start: 0.7416 (m-80) cc_final: 0.7089 (m-80) REVERT: U 688 LYS cc_start: 0.7519 (mttt) cc_final: 0.7177 (pttm) REVERT: U 801 LYS cc_start: 0.8725 (tttt) cc_final: 0.8312 (mttp) REVERT: U 802 GLU cc_start: 0.7541 (tt0) cc_final: 0.7238 (mt-10) REVERT: V 69 TYR cc_start: 0.8945 (m-80) cc_final: 0.8552 (m-80) REVERT: V 160 THR cc_start: 0.9374 (m) cc_final: 0.9092 (m) REVERT: V 180 LEU cc_start: 0.9014 (tp) cc_final: 0.8792 (tp) REVERT: V 246 GLN cc_start: 0.7540 (tt0) cc_final: 0.7046 (mm-40) REVERT: V 269 LEU cc_start: 0.8762 (mp) cc_final: 0.8352 (mt) REVERT: W 163 ASP cc_start: 0.8407 (m-30) cc_final: 0.8184 (m-30) REVERT: W 196 LYS cc_start: 0.7960 (tttt) cc_final: 0.7709 (ttpt) REVERT: W 215 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6967 (mp0) REVERT: W 425 MET cc_start: 0.7713 (tpt) cc_final: 0.7195 (tpt) REVERT: W 428 LEU cc_start: 0.8449 (mm) cc_final: 0.8199 (mm) REVERT: W 430 LYS cc_start: 0.7693 (mttt) cc_final: 0.7243 (mmtt) outliers start: 30 outliers final: 26 residues processed: 186 average time/residue: 0.1041 time to fit residues: 28.1311 Evaluate side-chains 182 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain U residue 683 ASP Chi-restraints excluded: chain U residue 685 LEU Chi-restraints excluded: chain U residue 716 ILE Chi-restraints excluded: chain U residue 800 ILE Chi-restraints excluded: chain U residue 836 MET Chi-restraints excluded: chain V residue 85 ILE Chi-restraints excluded: chain V residue 199 SER Chi-restraints excluded: chain V residue 252 ASN Chi-restraints excluded: chain V residue 364 GLU Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 137 CYS Chi-restraints excluded: chain W residue 166 SER Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 279 VAL Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 382 LEU Chi-restraints excluded: chain W residue 441 THR Chi-restraints excluded: chain W residue 442 THR Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 53 optimal weight: 0.0770 chunk 153 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.0270 chunk 134 optimal weight: 9.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.148799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122026 restraints weight = 15659.872| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.52 r_work: 0.3247 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12846 Z= 0.096 Angle : 0.478 6.034 17413 Z= 0.246 Chirality : 0.042 0.142 1920 Planarity : 0.004 0.039 2229 Dihedral : 11.747 168.118 1790 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.92 % Rotamer: Outliers : 1.44 % Allowed : 13.39 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.22), residues: 1541 helix: 1.50 (0.20), residues: 704 sheet: 0.99 (0.36), residues: 218 loop : 0.32 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 482 TYR 0.016 0.001 TYR W 319 PHE 0.011 0.001 PHE W 207 TRP 0.014 0.001 TRP V 356 HIS 0.008 0.001 HIS U 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (12846) covalent geometry : angle 0.47792 / 0.25 (17413) hydrogen bonds : bond 0.03080 / 2.12 ( 630) hydrogen bonds : angle 4.10463 / 3.13 ( 1698) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.317 Fit side-chains REVERT: G 490 ARG cc_start: 0.6988 (mtt180) cc_final: 0.5952 (ptt180) REVERT: G 526 LYS cc_start: 0.8302 (mttt) cc_final: 0.7876 (ttpp) REVERT: U 596 TYR cc_start: 0.7454 (m-80) cc_final: 0.7151 (m-80) REVERT: U 626 LYS cc_start: 0.8073 (mtmm) cc_final: 0.7742 (mtmt) REVERT: U 688 LYS cc_start: 0.7447 (mttt) cc_final: 0.7089 (pttm) REVERT: U 801 LYS cc_start: 0.8712 (tttt) cc_final: 0.8297 (mttp) REVERT: U 802 GLU cc_start: 0.7520 (tt0) cc_final: 0.7214 (mt-10) REVERT: V 69 TYR cc_start: 0.8951 (m-80) cc_final: 0.8549 (m-80) REVERT: V 160 THR cc_start: 0.9363 (m) cc_final: 0.9084 (m) REVERT: V 180 LEU cc_start: 0.9021 (tp) cc_final: 0.8806 (tp) REVERT: V 246 GLN cc_start: 0.7587 (tt0) cc_final: 0.7142 (mm-40) REVERT: V 269 LEU cc_start: 0.8702 (mp) cc_final: 0.8313 (mt) REVERT: W 196 LYS cc_start: 0.7975 (tttt) cc_final: 0.7726 (ttpt) REVERT: W 215 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6796 (mp0) REVERT: W 425 MET cc_start: 0.7703 (tpt) cc_final: 0.7185 (tpt) REVERT: W 428 LEU cc_start: 0.8416 (mm) cc_final: 0.8163 (mm) REVERT: W 430 LYS cc_start: 0.7702 (mttt) cc_final: 0.7244 (mmtt) outliers start: 20 outliers final: 18 residues processed: 177 average time/residue: 0.1032 time to fit residues: 26.7411 Evaluate side-chains 173 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain U residue 685 LEU Chi-restraints excluded: chain U residue 836 MET Chi-restraints excluded: chain V residue 85 ILE Chi-restraints excluded: chain V residue 199 SER Chi-restraints excluded: chain V residue 252 ASN Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 147 SER Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 279 VAL Chi-restraints excluded: chain W residue 382 LEU Chi-restraints excluded: chain W residue 442 THR Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 116 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 25 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 127 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... W 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.148469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.121725 restraints weight = 15733.421| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.52 r_work: 0.3247 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12846 Z= 0.105 Angle : 0.489 6.422 17413 Z= 0.251 Chirality : 0.042 0.145 1920 Planarity : 0.004 0.038 2229 Dihedral : 11.679 167.016 1790 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.92 % Rotamer: Outliers : 1.51 % Allowed : 13.53 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.22), residues: 1541 helix: 1.52 (0.20), residues: 705 sheet: 1.05 (0.36), residues: 214 loop : 0.34 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG V 68 TYR 0.014 0.001 TYR W 319 PHE 0.011 0.001 PHE U 584 TRP 0.014 0.001 TRP V 356 HIS 0.008 0.001 HIS U 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (12846) covalent geometry : angle 0.48892 / 0.25 (17413) hydrogen bonds : bond 0.03133 / 2.15 ( 630) hydrogen bonds : angle 4.08820 / 3.12 ( 1698) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.348 Fit side-chains REVERT: G 490 ARG cc_start: 0.6956 (mtt180) cc_final: 0.5932 (ptt180) REVERT: G 526 LYS cc_start: 0.8289 (mttt) cc_final: 0.7875 (ttpp) REVERT: U 596 TYR cc_start: 0.7386 (m-80) cc_final: 0.7088 (m-80) REVERT: U 626 LYS cc_start: 0.8070 (mtmm) cc_final: 0.7739 (mtmt) REVERT: U 688 LYS cc_start: 0.7444 (mttt) cc_final: 0.7102 (pttm) REVERT: U 801 LYS cc_start: 0.8718 (tttt) cc_final: 0.8335 (mttp) REVERT: U 802 GLU cc_start: 0.7476 (tt0) cc_final: 0.7198 (mt-10) REVERT: V 160 THR cc_start: 0.9367 (m) cc_final: 0.9095 (m) REVERT: V 180 LEU cc_start: 0.9006 (tp) cc_final: 0.8782 (tp) REVERT: V 246 GLN cc_start: 0.7592 (tt0) cc_final: 0.7129 (mm-40) REVERT: W 196 LYS cc_start: 0.7992 (tttt) cc_final: 0.7736 (ttpt) REVERT: W 215 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6925 (mp0) REVERT: W 425 MET cc_start: 0.7698 (tpt) cc_final: 0.7179 (tpt) REVERT: W 428 LEU cc_start: 0.8467 (mm) cc_final: 0.8220 (mm) REVERT: W 430 LYS cc_start: 0.7700 (mttt) cc_final: 0.7247 (mmtt) outliers start: 21 outliers final: 20 residues processed: 176 average time/residue: 0.1089 time to fit residues: 28.0132 Evaluate side-chains 177 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 410 VAL Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain U residue 609 LEU Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain U residue 685 LEU Chi-restraints excluded: chain U residue 836 MET Chi-restraints excluded: chain V residue 85 ILE Chi-restraints excluded: chain V residue 199 SER Chi-restraints excluded: chain V residue 252 ASN Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 147 SER Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 279 VAL Chi-restraints excluded: chain W residue 382 LEU Chi-restraints excluded: chain W residue 442 THR Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 10 optimal weight: 7.9990 chunk 63 optimal weight: 0.1980 chunk 68 optimal weight: 0.2980 chunk 98 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.148644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.124324 restraints weight = 15676.195| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.49 r_work: 0.3239 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12846 Z= 0.097 Angle : 0.485 6.291 17413 Z= 0.251 Chirality : 0.042 0.142 1920 Planarity : 0.004 0.037 2229 Dihedral : 11.424 165.936 1790 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.92 % Rotamer: Outliers : 1.44 % Allowed : 14.11 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.22), residues: 1541 helix: 1.60 (0.20), residues: 705 sheet: 1.02 (0.36), residues: 221 loop : 0.40 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 68 TYR 0.014 0.001 TYR W 319 PHE 0.011 0.001 PHE U 584 TRP 0.014 0.001 TRP V 356 HIS 0.008 0.001 HIS U 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (12846) covalent geometry : angle 0.48506 / 0.25 (17413) hydrogen bonds : bond 0.03008 / 2.07 ( 630) hydrogen bonds : angle 4.05957 / 3.09 ( 1698) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2967.76 seconds wall clock time: 51 minutes 40.27 seconds (3100.27 seconds total)