Starting phenix.real_space_refine on Wed Mar 4 09:59:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a5o_15179/03_2026/8a5o_15179_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a5o_15179/03_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_15179/03_2026/8a5o_15179_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a5o_15179/03_2026/8a5o_15179_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8a5o_15179/03_2026/8a5o_15179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a5o_15179/03_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-5986/lib/python3.9/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: 2.55, per 1000 atoms: 0.20 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: 0.72 Conformation dependent library (CDL) restraints added in 401.9 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: 0.37 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: 2.08 Time building geometry restraints manager: 0.99 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=" C4 AGS U 900 " pdb=" C5 AGS U 900 " ideal model delta sigma weight residual 1.386 1.470 -0.084 1.00e-02 1.00e+04 7.11e+01 bond pdb=" O2B AGS W 500 " pdb=" PB AGS W 500 " ideal model delta sigma weight residual 1.531 1.401 0.130 1.60e-02 3.91e+03 6.60e+01 bond pdb=" C5 AGS U 900 " pdb=" C6 AGS U 900 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.37e+01 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 V 500 " pdb=" S1G AGS V 500 " ideal model delta sigma weight residual 1.949 1.815 0.134 2.00e-02 2.50e+03 4.52e+01 ... (remaining 12841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 15602 3.01 - 6.02: 1713 6.02 - 9.04: 88 9.04 - 12.05: 6 12.05 - 15.06: 4 Bond angle restraints: 17413 Sorted by residual: angle pdb=" C5 AGS U 900 " pdb=" C4 AGS U 900 " pdb=" N3 AGS U 900 " ideal model delta sigma weight residual 126.80 118.66 8.14 7.41e-01 1.82e+00 1.21e+02 angle pdb=" C4 AGS U 900 " pdb=" C5 AGS U 900 " pdb=" N7 AGS U 900 " ideal model delta sigma weight residual 110.73 106.58 4.15 4.52e-01 4.89e+00 8.42e+01 angle pdb=" C5 AGS U 900 " pdb=" N7 AGS U 900 " pdb=" C8 AGS U 900 " ideal model delta sigma weight residual 103.67 107.45 -3.78 4.26e-01 5.51e+00 7.86e+01 angle pdb=" N3 AGS U 900 " pdb=" C4 AGS U 900 " pdb=" N9 AGS U 900 " ideal model delta sigma weight residual 127.16 135.02 -7.86 1.06e+00 8.92e-01 5.51e+01 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 ... (remaining 17408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.03: 7484 27.03 - 54.07: 265 54.07 - 81.10: 40 81.10 - 108.13: 3 108.13 - 135.17: 1 Dihedral angle restraints: 7793 sinusoidal: 3239 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 7790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1171 0.080 - 0.161: 594 0.161 - 0.241: 122 0.241 - 0.322: 35 0.322 - 0.402: 4 Chirality restraints: 1926 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=" 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 chirality pdb=" CA SER W 143 " pdb=" N SER W 143 " pdb=" C SER W 143 " pdb=" CB SER W 143 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 1923 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: 1.000 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.720 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 0.134 12846 Z= 1.176 Angle : 1.875 15.060 17413 Z= 1.320 Chirality : 0.097 0.402 1926 Planarity : 0.010 0.052 2229 Dihedral : 14.338 135.168 4839 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 covalent geometry : bond 0.01613 (12846) covalent geometry : angle 1.87455 (17413) hydrogen bonds : bond 0.17728 ( 630) hydrogen bonds : angle 6.96085 ( 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 : 0.495 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: 0.1306 time to fit residues: 53.7844 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 : 0.408 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 W 95 GLN X 45 ASN X 59 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.144340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.116044 restraints weight = 15531.329| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.83 r_work: 0.3094 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2044 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= 0.146 Angle : 0.625 11.651 17413 Z= 0.332 Chirality : 0.045 0.141 1926 Planarity : 0.005 0.039 2229 Dihedral : 9.070 132.662 1742 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.95 % Favored : 97.99 % Rotamer: Outliers : 1.01 % Allowed : 7.27 % Favored : 91.72 % 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: 0.51 (0.21), residues: 1541 helix: 0.49 (0.19), residues: 708 sheet: 1.01 (0.35), residues: 211 loop : 0.11 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG V 177 TYR 0.015 0.002 TYR W 69 PHE 0.024 0.002 PHE U 598 TRP 0.017 0.002 TRP V 356 HIS 0.008 0.001 HIS U 823 Details of bonding type rmsd covalent geometry : bond 0.00321 (12846) covalent geometry : angle 0.62534 (17413) hydrogen bonds : bond 0.04584 ( 630) hydrogen bonds : angle 4.82985 ( 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 : 0.389 Fit side-chains REVERT: G 490 ARG cc_start: 0.7063 (mtt180) cc_final: 0.6210 (ptt-90) REVERT: G 544 LYS cc_start: 0.8807 (mttt) cc_final: 0.8573 (mtmt) REVERT: G 545 LYS cc_start: 0.8662 (mttt) cc_final: 0.8297 (tppt) REVERT: U 596 TYR cc_start: 0.7389 (m-80) cc_final: 0.7164 (m-80) REVERT: U 688 LYS cc_start: 0.7802 (mttt) cc_final: 0.7386 (pttm) REVERT: V 68 ARG cc_start: 0.7815 (mtp180) cc_final: 0.7511 (ttt90) REVERT: V 69 TYR cc_start: 0.8947 (m-80) cc_final: 0.8637 (m-80) REVERT: V 160 THR cc_start: 0.9277 (m) cc_final: 0.8956 (m) REVERT: V 178 ILE cc_start: 0.8810 (mm) cc_final: 0.8501 (mp) REVERT: V 246 GLN cc_start: 0.7316 (tt0) cc_final: 0.6899 (mm-40) REVERT: V 305 MET cc_start: 0.8935 (mmm) cc_final: 0.8658 (mmm) REVERT: V 311 GLU cc_start: 0.8505 (mp0) cc_final: 0.8281 (mp0) REVERT: W 196 LYS cc_start: 0.8169 (tttt) cc_final: 0.7712 (pttm) REVERT: W 394 MET cc_start: 0.8324 (mmt) cc_final: 0.8122 (mmm) outliers start: 14 outliers final: 6 residues processed: 227 average time/residue: 0.1221 time to fit residues: 39.4045 Evaluate side-chains 175 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 169 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 271 SER Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 294 LEU 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: 1.9990 chunk 122 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 130 optimal weight: 0.2980 chunk 97 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 287 HIS W 91 GLN W 162 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.142962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.115252 restraints weight = 15785.932| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.60 r_work: 0.3085 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12846 Z= 0.141 Angle : 0.561 8.350 17413 Z= 0.294 Chirality : 0.045 0.158 1926 Planarity : 0.004 0.045 2229 Dihedral : 8.476 123.852 1736 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.27 % Favored : 97.66 % Rotamer: Outliers : 1.73 % Allowed : 9.36 % Favored : 88.91 % 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: 0.86 (0.21), residues: 1541 helix: 0.95 (0.19), residues: 708 sheet: 0.81 (0.35), residues: 211 loop : 0.21 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG W 448 TYR 0.016 0.001 TYR U 596 PHE 0.019 0.002 PHE U 546 TRP 0.015 0.001 TRP V 356 HIS 0.007 0.001 HIS U 823 Details of bonding type rmsd covalent geometry : bond 0.00329 (12846) covalent geometry : angle 0.56061 (17413) hydrogen bonds : bond 0.04162 ( 630) hydrogen bonds : angle 4.49414 ( 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: 24 poor density : 182 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: G 490 ARG cc_start: 0.7093 (mtt180) cc_final: 0.6168 (ptt180) REVERT: G 545 LYS cc_start: 0.8616 (mttt) cc_final: 0.8361 (tptt) REVERT: U 596 TYR cc_start: 0.7373 (m-80) cc_final: 0.7028 (m-80) REVERT: U 688 LYS cc_start: 0.7607 (mttt) cc_final: 0.7227 (pttm) REVERT: V 69 TYR cc_start: 0.8964 (m-80) cc_final: 0.8664 (m-80) REVERT: V 160 THR cc_start: 0.9341 (m) cc_final: 0.9060 (m) REVERT: V 179 ASP cc_start: 0.7667 (m-30) cc_final: 0.7414 (m-30) REVERT: V 246 GLN cc_start: 0.7433 (tt0) cc_final: 0.6974 (mm-40) REVERT: V 305 MET cc_start: 0.8922 (mmm) cc_final: 0.8614 (mmm) REVERT: W 196 LYS cc_start: 0.8263 (tttt) cc_final: 0.7691 (pttm) REVERT: W 215 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6749 (mp0) REVERT: W 284 THR cc_start: 0.8663 (m) cc_final: 0.8290 (p) REVERT: W 425 MET cc_start: 0.7890 (tpt) cc_final: 0.7363 (tpt) REVERT: W 430 LYS cc_start: 0.7694 (mttt) cc_final: 0.7267 (mmtt) REVERT: X 44 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8517 (mtmt) outliers start: 24 outliers final: 18 residues processed: 198 average time/residue: 0.1239 time to fit residues: 35.0340 Evaluate side-chains 178 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 287 HIS Chi-restraints excluded: chain U residue 495 SER 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 836 MET Chi-restraints excluded: chain V residue 252 ASN Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 95 GLN Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 428 LEU Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 64 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 21 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 0.0870 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 0.0270 chunk 85 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 541 ASN U 792 ASN V 78 ASN V 228 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.143437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.116456 restraints weight = 15618.317| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.57 r_work: 0.3075 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12846 Z= 0.109 Angle : 0.507 6.826 17413 Z= 0.265 Chirality : 0.043 0.139 1926 Planarity : 0.004 0.042 2229 Dihedral : 8.064 116.012 1736 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.82 % Favored : 98.12 % Rotamer: Outliers : 1.58 % Allowed : 9.86 % Favored : 88.55 % 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: 1.06 (0.21), residues: 1541 helix: 1.15 (0.19), residues: 716 sheet: 0.86 (0.35), residues: 209 loop : 0.27 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 68 TYR 0.014 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 covalent geometry : bond 0.00240 (12846) covalent geometry : angle 0.50682 (17413) hydrogen bonds : bond 0.03609 ( 630) hydrogen bonds : angle 4.32584 ( 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 193 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.483 Fit side-chains REVERT: G 490 ARG cc_start: 0.6942 (mtt180) cc_final: 0.5922 (ptt180) REVERT: G 524 GLN cc_start: 0.7861 (mt0) cc_final: 0.7644 (mt0) REVERT: G 526 LYS cc_start: 0.8289 (mttt) cc_final: 0.7853 (ttpp) REVERT: G 545 LYS cc_start: 0.8582 (mttt) cc_final: 0.8255 (tppt) REVERT: U 596 TYR cc_start: 0.7364 (m-80) cc_final: 0.7034 (m-80) REVERT: U 688 LYS cc_start: 0.7550 (mttt) cc_final: 0.7140 (pttm) REVERT: V 69 TYR cc_start: 0.8946 (m-80) cc_final: 0.8548 (m-80) REVERT: V 160 THR cc_start: 0.9343 (m) cc_final: 0.9052 (m) REVERT: V 246 GLN cc_start: 0.7259 (tt0) cc_final: 0.6913 (mm-40) REVERT: W 196 LYS cc_start: 0.8253 (tttt) cc_final: 0.7673 (ttpt) REVERT: W 215 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6578 (mp0) REVERT: W 425 MET cc_start: 0.7899 (tpt) cc_final: 0.7327 (tpt) REVERT: W 430 LYS cc_start: 0.7764 (mttt) cc_final: 0.7283 (mmtt) REVERT: X 44 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8434 (mtmt) outliers start: 22 outliers final: 16 residues processed: 187 average time/residue: 0.1148 time to fit residues: 30.8825 Evaluate side-chains 167 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 287 HIS Chi-restraints excluded: chain U residue 495 SER Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 622 THR 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 95 GLN Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 428 LEU Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain X residue 44 LYS 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: 0.8980 chunk 64 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 31 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 287 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.144083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.116655 restraints weight = 15678.068| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.61 r_work: 0.3075 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12846 Z= 0.111 Angle : 0.494 6.169 17413 Z= 0.258 Chirality : 0.043 0.166 1926 Planarity : 0.004 0.039 2229 Dihedral : 7.762 107.661 1736 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.92 % Rotamer: Outliers : 1.73 % Allowed : 10.37 % Favored : 87.90 % 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: 1.21 (0.21), residues: 1541 helix: 1.31 (0.20), residues: 711 sheet: 0.87 (0.35), residues: 214 loop : 0.33 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 68 TYR 0.013 0.001 TYR U 596 PHE 0.012 0.001 PHE W 207 TRP 0.013 0.001 TRP V 356 HIS 0.007 0.001 HIS U 823 Details of bonding type rmsd covalent geometry : bond 0.00252 (12846) covalent geometry : angle 0.49438 (17413) hydrogen bonds : bond 0.03454 ( 630) hydrogen bonds : angle 4.22646 ( 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 193 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.461 Fit side-chains REVERT: G 490 ARG cc_start: 0.6890 (mtt180) cc_final: 0.5908 (ptt180) REVERT: G 524 GLN cc_start: 0.7806 (mt0) cc_final: 0.7483 (mt0) REVERT: G 526 LYS cc_start: 0.8289 (mttt) cc_final: 0.7861 (ttpp) REVERT: U 596 TYR cc_start: 0.7418 (m-80) cc_final: 0.7102 (m-80) REVERT: U 688 LYS cc_start: 0.7501 (mttt) cc_final: 0.7148 (pttm) REVERT: V 69 TYR cc_start: 0.8945 (m-80) cc_final: 0.8462 (m-80) REVERT: V 160 THR cc_start: 0.9363 (m) cc_final: 0.9074 (m) REVERT: V 180 LEU cc_start: 0.9041 (tp) cc_final: 0.8826 (tp) REVERT: V 246 GLN cc_start: 0.7396 (tt0) cc_final: 0.6932 (mm-40) REVERT: V 305 MET cc_start: 0.8814 (mmm) cc_final: 0.8614 (mmm) REVERT: W 196 LYS cc_start: 0.8160 (tttt) cc_final: 0.7846 (ttpt) REVERT: W 215 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6734 (mp0) REVERT: W 319 TYR cc_start: 0.7827 (t80) cc_final: 0.7473 (t80) REVERT: W 425 MET cc_start: 0.7920 (tpt) cc_final: 0.7345 (tpt) REVERT: W 430 LYS cc_start: 0.7611 (mttt) cc_final: 0.7252 (mmtt) REVERT: X 44 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8453 (mtmt) outliers start: 24 outliers final: 18 residues processed: 185 average time/residue: 0.1175 time to fit residues: 31.1652 Evaluate side-chains 170 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 287 HIS Chi-restraints excluded: chain U residue 410 VAL Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain U residue 495 SER 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 836 MET Chi-restraints excluded: chain V residue 252 ASN Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain X residue 44 LYS 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: 0.3980 chunk 122 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 287 HIS V 372 HIS W 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.143668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.116183 restraints weight = 15669.217| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.61 r_work: 0.3106 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12846 Z= 0.114 Angle : 0.492 6.395 17413 Z= 0.256 Chirality : 0.043 0.149 1926 Planarity : 0.004 0.039 2229 Dihedral : 7.629 103.556 1736 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.88 % Favored : 98.05 % Rotamer: Outliers : 1.94 % Allowed : 10.73 % Favored : 87.33 % 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: 1.24 (0.22), residues: 1541 helix: 1.36 (0.20), residues: 711 sheet: 0.89 (0.35), residues: 214 loop : 0.31 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG V 68 TYR 0.013 0.001 TYR W 450 PHE 0.012 0.001 PHE W 207 TRP 0.013 0.001 TRP V 356 HIS 0.007 0.001 HIS U 823 Details of bonding type rmsd covalent geometry : bond 0.00264 (12846) covalent geometry : angle 0.49178 (17413) hydrogen bonds : bond 0.03393 ( 630) hydrogen bonds : angle 4.19707 ( 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 186 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.482 Fit side-chains REVERT: G 490 ARG cc_start: 0.6885 (mtt180) cc_final: 0.5923 (ptt180) REVERT: G 524 GLN cc_start: 0.7871 (mt0) cc_final: 0.7533 (mt0) REVERT: U 596 TYR cc_start: 0.7452 (m-80) cc_final: 0.7138 (m-80) REVERT: U 688 LYS cc_start: 0.7525 (mttt) cc_final: 0.7150 (pttm) REVERT: V 69 TYR cc_start: 0.8943 (m-80) cc_final: 0.8457 (m-80) REVERT: V 160 THR cc_start: 0.9371 (m) cc_final: 0.9078 (m) REVERT: V 246 GLN cc_start: 0.7403 (tt0) cc_final: 0.6932 (mm-40) REVERT: W 196 LYS cc_start: 0.8157 (tttt) cc_final: 0.7791 (ttpt) REVERT: W 215 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6771 (mp0) REVERT: W 319 TYR cc_start: 0.7696 (t80) cc_final: 0.7308 (t80) REVERT: W 425 MET cc_start: 0.7906 (tpt) cc_final: 0.7344 (tpt) REVERT: W 430 LYS cc_start: 0.7753 (mttt) cc_final: 0.7262 (mmtt) REVERT: X 44 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8469 (mtmt) outliers start: 27 outliers final: 17 residues processed: 179 average time/residue: 0.1124 time to fit residues: 29.1754 Evaluate side-chains 169 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 287 HIS Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain U residue 495 SER Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain U residue 801 LYS 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 165 CYS Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain W residue 473 LYS Chi-restraints excluded: chain X residue 44 LYS 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: 0.4980 chunk 101 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 107 optimal weight: 0.0470 chunk 129 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 116 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 287 HIS 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 = 0.3649 r_free = 0.3649 target = 0.144533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.117106 restraints weight = 15554.306| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.59 r_work: 0.3111 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3335 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= 0.101 Angle : 0.481 6.343 17413 Z= 0.249 Chirality : 0.042 0.146 1926 Planarity : 0.004 0.037 2229 Dihedral : 7.453 99.665 1736 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.95 % Favored : 97.99 % Rotamer: Outliers : 1.66 % Allowed : 11.30 % Favored : 87.04 % 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: 1.34 (0.22), residues: 1541 helix: 1.44 (0.20), residues: 711 sheet: 0.93 (0.35), residues: 214 loop : 0.37 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 68 TYR 0.012 0.001 TYR U 596 PHE 0.012 0.001 PHE W 207 TRP 0.012 0.001 TRP V 356 HIS 0.007 0.001 HIS U 823 Details of bonding type rmsd covalent geometry : bond 0.00227 (12846) covalent geometry : angle 0.48084 (17413) hydrogen bonds : bond 0.03236 ( 630) hydrogen bonds : angle 4.15310 ( 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: 23 poor density : 163 time to evaluate : 0.562 Fit side-chains REVERT: G 490 ARG cc_start: 0.6887 (mtt180) cc_final: 0.5909 (ptt180) REVERT: G 524 GLN cc_start: 0.7919 (mt0) cc_final: 0.7463 (mt0) REVERT: U 596 TYR cc_start: 0.7433 (m-80) cc_final: 0.7126 (m-80) REVERT: U 688 LYS cc_start: 0.7511 (mttt) cc_final: 0.7135 (pttm) REVERT: V 69 TYR cc_start: 0.8949 (m-80) cc_final: 0.8507 (m-80) REVERT: V 160 THR cc_start: 0.9376 (m) cc_final: 0.9077 (m) REVERT: V 246 GLN cc_start: 0.7459 (tt0) cc_final: 0.6930 (mm-40) REVERT: W 196 LYS cc_start: 0.8174 (tttt) cc_final: 0.7878 (ttpt) REVERT: W 215 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6701 (mp0) REVERT: W 425 MET cc_start: 0.7906 (tpt) cc_final: 0.7346 (tpt) REVERT: W 430 LYS cc_start: 0.7657 (mttt) cc_final: 0.7195 (mmtt) REVERT: X 44 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8468 (mtmt) outliers start: 23 outliers final: 19 residues processed: 179 average time/residue: 0.1186 time to fit residues: 31.0005 Evaluate side-chains 173 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 495 SER Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 609 LEU Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain U residue 801 LYS 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 206 LEU Chi-restraints excluded: chain W residue 279 VAL Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain W residue 473 LYS Chi-restraints excluded: chain X residue 44 LYS 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: 1.9990 chunk 119 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 chunk 140 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3640 r_free = 0.3640 target = 0.143671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116660 restraints weight = 15511.561| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.56 r_work: 0.3110 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12846 Z= 0.116 Angle : 0.494 6.594 17413 Z= 0.257 Chirality : 0.043 0.147 1926 Planarity : 0.004 0.040 2229 Dihedral : 7.418 97.717 1736 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.82 % Favored : 98.12 % Rotamer: Outliers : 1.87 % Allowed : 11.45 % Favored : 86.68 % 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: 1.33 (0.22), residues: 1541 helix: 1.41 (0.20), residues: 711 sheet: 0.96 (0.36), residues: 214 loop : 0.38 (0.26), residues: 616 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 0.012 0.001 TRP V 356 HIS 0.007 0.001 HIS U 823 Details of bonding type rmsd covalent geometry : bond 0.00268 (12846) covalent geometry : angle 0.49432 (17413) hydrogen bonds : bond 0.03324 ( 630) hydrogen bonds : angle 4.14855 ( 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 186 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.481 Fit side-chains REVERT: G 490 ARG cc_start: 0.7003 (mtt180) cc_final: 0.6016 (ptt180) REVERT: G 524 GLN cc_start: 0.7896 (mt0) cc_final: 0.7536 (mt0) REVERT: U 596 TYR cc_start: 0.7438 (m-80) cc_final: 0.7130 (m-80) REVERT: U 688 LYS cc_start: 0.7438 (mttt) cc_final: 0.7073 (pttm) REVERT: V 69 TYR cc_start: 0.8919 (m-80) cc_final: 0.8429 (m-80) REVERT: V 160 THR cc_start: 0.9372 (m) cc_final: 0.9078 (m) REVERT: V 246 GLN cc_start: 0.7465 (tt0) cc_final: 0.6975 (mm-40) REVERT: V 269 LEU cc_start: 0.8703 (mp) cc_final: 0.8243 (mt) REVERT: W 196 LYS cc_start: 0.8104 (tttt) cc_final: 0.7815 (ttpt) REVERT: W 215 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6791 (mp0) REVERT: W 319 TYR cc_start: 0.7744 (t80) cc_final: 0.7407 (t80) REVERT: W 425 MET cc_start: 0.7863 (tpt) cc_final: 0.7324 (tpt) REVERT: W 430 LYS cc_start: 0.7628 (mttt) cc_final: 0.7186 (mmtt) REVERT: X 44 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8480 (mtmt) outliers start: 26 outliers final: 20 residues processed: 178 average time/residue: 0.1154 time to fit residues: 30.0752 Evaluate side-chains 174 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 495 SER 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 801 LYS 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 206 LEU 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 464 THR Chi-restraints excluded: chain W residue 473 LYS Chi-restraints excluded: chain X residue 44 LYS 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: 1.9990 chunk 44 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.145051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.119339 restraints weight = 15717.663| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.49 r_work: 0.3164 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12846 Z= 0.166 Angle : 0.538 6.720 17413 Z= 0.279 Chirality : 0.044 0.151 1926 Planarity : 0.004 0.046 2229 Dihedral : 7.713 99.215 1736 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.34 % Favored : 97.60 % Rotamer: Outliers : 2.09 % Allowed : 11.81 % Favored : 86.11 % 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: 1.09 (0.22), residues: 1541 helix: 1.20 (0.20), residues: 716 sheet: 0.90 (0.36), residues: 213 loop : 0.24 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG V 68 TYR 0.019 0.001 TYR W 450 PHE 0.013 0.001 PHE U 584 TRP 0.011 0.001 TRP V 356 HIS 0.007 0.001 HIS U 823 Details of bonding type rmsd covalent geometry : bond 0.00402 (12846) covalent geometry : angle 0.53841 (17413) hydrogen bonds : bond 0.03748 ( 630) hydrogen bonds : angle 4.27825 ( 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 183 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.339 Fit side-chains REVERT: G 490 ARG cc_start: 0.7114 (mtt180) cc_final: 0.6073 (ptt180) REVERT: G 524 GLN cc_start: 0.7957 (mt0) cc_final: 0.7638 (mt0) REVERT: U 596 TYR cc_start: 0.7479 (m-80) cc_final: 0.7126 (m-80) REVERT: U 688 LYS cc_start: 0.7547 (mttt) cc_final: 0.7202 (pttm) REVERT: V 160 THR cc_start: 0.9363 (m) cc_final: 0.9081 (m) REVERT: V 246 GLN cc_start: 0.7528 (tt0) cc_final: 0.7120 (mm-40) REVERT: W 196 LYS cc_start: 0.8101 (tttt) cc_final: 0.7859 (ttpt) REVERT: W 215 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7030 (mp0) REVERT: W 319 TYR cc_start: 0.7814 (t80) cc_final: 0.7414 (t80) REVERT: W 425 MET cc_start: 0.7797 (tpt) cc_final: 0.7347 (tpt) REVERT: W 430 LYS cc_start: 0.7737 (mttt) cc_final: 0.7296 (mmtt) REVERT: X 44 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8592 (mtmt) outliers start: 29 outliers final: 25 residues processed: 173 average time/residue: 0.1055 time to fit residues: 26.6943 Evaluate side-chains 174 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 495 SER 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 801 LYS Chi-restraints excluded: chain U residue 836 MET 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 159 ASP Chi-restraints excluded: chain W residue 165 CYS 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 462 LEU Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain W residue 473 LYS Chi-restraints excluded: chain X residue 44 LYS 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: 0.5980 chunk 78 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 43 optimal weight: 0.0030 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.144124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117455 restraints weight = 15626.858| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.51 r_work: 0.3142 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3516 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= 0.105 Angle : 0.492 8.788 17413 Z= 0.256 Chirality : 0.042 0.180 1926 Planarity : 0.004 0.037 2229 Dihedral : 7.381 95.923 1736 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.92 % Rotamer: Outliers : 1.30 % Allowed : 12.67 % 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: 1.33 (0.22), residues: 1541 helix: 1.42 (0.20), residues: 704 sheet: 0.93 (0.36), residues: 219 loop : 0.39 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG V 68 TYR 0.012 0.001 TYR U 596 PHE 0.011 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 covalent geometry : bond 0.00238 (12846) covalent geometry : angle 0.49187 (17413) hydrogen bonds : bond 0.03215 ( 630) hydrogen bonds : angle 4.16965 ( 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: 18 poor density : 163 time to evaluate : 0.341 Fit side-chains REVERT: G 490 ARG cc_start: 0.7024 (mtt180) cc_final: 0.6042 (ptt180) REVERT: G 524 GLN cc_start: 0.7854 (mt0) cc_final: 0.7454 (mt0) REVERT: U 339 ARG cc_start: 0.7460 (ttp-110) cc_final: 0.7228 (ttp80) REVERT: U 596 TYR cc_start: 0.7420 (m-80) cc_final: 0.7100 (m-80) REVERT: U 688 LYS cc_start: 0.7498 (mttt) cc_final: 0.7110 (pttm) REVERT: V 68 ARG cc_start: 0.7525 (mtp-110) cc_final: 0.7182 (mtp85) REVERT: V 160 THR cc_start: 0.9402 (m) cc_final: 0.9128 (m) REVERT: V 246 GLN cc_start: 0.7523 (tt0) cc_final: 0.7066 (mm-40) REVERT: V 269 LEU cc_start: 0.8730 (mp) cc_final: 0.8266 (mt) REVERT: W 196 LYS cc_start: 0.8075 (tttt) cc_final: 0.7787 (ttpt) REVERT: W 215 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6833 (mp0) REVERT: W 319 TYR cc_start: 0.7728 (t80) cc_final: 0.7410 (t80) REVERT: W 425 MET cc_start: 0.7854 (tpt) cc_final: 0.7330 (tpt) REVERT: W 430 LYS cc_start: 0.7635 (mttt) cc_final: 0.7211 (mmtt) REVERT: X 44 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8472 (mtmt) outliers start: 18 outliers final: 15 residues processed: 174 average time/residue: 0.1039 time to fit residues: 26.4650 Evaluate side-chains 170 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 410 VAL Chi-restraints excluded: chain U residue 495 SER Chi-restraints excluded: chain U residue 539 LEU Chi-restraints excluded: chain U residue 801 LYS Chi-restraints excluded: chain U residue 836 MET Chi-restraints excluded: chain V residue 85 ILE 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 382 LEU Chi-restraints excluded: chain W residue 464 THR Chi-restraints excluded: chain X residue 44 LYS 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: 0.8980 chunk 68 optimal weight: 0.0030 chunk 98 optimal weight: 0.0970 chunk 92 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.148757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.123375 restraints weight = 15697.019| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.51 r_work: 0.3209 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12846 Z= 0.098 Angle : 0.488 8.462 17413 Z= 0.252 Chirality : 0.042 0.196 1926 Planarity : 0.004 0.040 2229 Dihedral : 7.125 92.041 1736 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.08 % Favored : 97.86 % Rotamer: Outliers : 1.15 % Allowed : 13.10 % 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: 1.42 (0.22), residues: 1541 helix: 1.51 (0.20), residues: 710 sheet: 0.91 (0.35), residues: 226 loop : 0.42 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG V 68 TYR 0.011 0.001 TYR U 596 PHE 0.012 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 covalent geometry : bond 0.00219 (12846) covalent geometry : angle 0.48814 (17413) hydrogen bonds : bond 0.03063 ( 630) hydrogen bonds : angle 4.10103 ( 1698) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3056.60 seconds wall clock time: 53 minutes 4.07 seconds (3184.07 seconds total)