Starting phenix.real_space_refine on Wed Jul 30 20:06:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a5o_15179/07_2025/8a5o_15179_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a5o_15179/07_2025/8a5o_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8a5o_15179/07_2025/8a5o_15179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a5o_15179/07_2025/8a5o_15179.map" model { file = "/net/cci-nas-00/data/ceres_data/8a5o_15179/07_2025/8a5o_15179_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a5o_15179/07_2025/8a5o_15179_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.45, per 1000 atoms: 0.59 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: 3.53 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.79 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: 5.14 Time building geometry restraints manager: 3.80 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: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 33.730 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.030 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (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 TRP 0.079 0.014 TRP W 469 HIS 0.039 0.006 HIS W 162 PHE 0.070 0.013 PHE U 572 TYR 0.098 0.013 TYR W 450 ARG 0.023 0.002 ARG V 116 Details of bonding type rmsd hydrogen bonds : bond 0.17728 ( 630) hydrogen bonds : angle 6.96085 ( 1698) covalent geometry : bond 0.01613 (12846) covalent geometry : angle 1.87455 (17413) *********************** 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 : 1.264 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: 0.7340 (p0) REVERT: U 287 HIS cc_start: 0.8925 (p90) cc_final: 0.8632 (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: 0.6699 (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: 0.8112 (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: 0.7504 (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: 0.3038 time to fit residues: 124.0308 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 : 1.629 ------------------------------------------------------------------------------- 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 130 optimal weight: 0.8980 chunk 116 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 V 372 HIS W 95 GLN X 45 ASN X 59 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.144641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116256 restraints weight = 15291.717| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.84 r_work: 0.3106 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12846 Z= 0.143 Angle : 0.611 8.407 17413 Z= 0.327 Chirality : 0.045 0.145 1926 Planarity : 0.005 0.040 2229 Dihedral : 9.035 131.837 1742 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.88 % Favored : 98.05 % Rotamer: Outliers : 1.08 % Allowed : 7.34 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.21), residues: 1541 helix: 0.54 (0.19), residues: 708 sheet: 1.00 (0.35), residues: 211 loop : 0.12 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP V 356 HIS 0.008 0.001 HIS U 823 PHE 0.024 0.002 PHE U 598 TYR 0.015 0.002 TYR W 69 ARG 0.004 0.000 ARG V 177 Details of bonding type rmsd hydrogen bonds : bond 0.04503 ( 630) hydrogen bonds : angle 4.80253 ( 1698) covalent geometry : bond 0.00314 (12846) covalent geometry : angle 0.61072 (17413) *********************** 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 234 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 219 time to evaluate : 1.348 Fit side-chains REVERT: G 490 ARG cc_start: 0.7051 (mtt180) cc_final: 0.6173 (ptt-90) REVERT: G 544 LYS cc_start: 0.8788 (mttt) cc_final: 0.8546 (mtmt) REVERT: G 545 LYS cc_start: 0.8635 (mttt) cc_final: 0.8242 (tppt) REVERT: U 596 TYR cc_start: 0.7307 (m-80) cc_final: 0.7080 (m-80) REVERT: U 688 LYS cc_start: 0.7803 (mttt) cc_final: 0.7353 (pttm) REVERT: V 68 ARG cc_start: 0.7796 (mtp180) cc_final: 0.7510 (ttt90) REVERT: V 69 TYR cc_start: 0.8957 (m-80) cc_final: 0.8648 (m-80) REVERT: V 160 THR cc_start: 0.9273 (m) cc_final: 0.8951 (m) REVERT: V 178 ILE cc_start: 0.8802 (mm) cc_final: 0.8490 (mp) REVERT: V 246 GLN cc_start: 0.7299 (tt0) cc_final: 0.6871 (mm-40) REVERT: V 305 MET cc_start: 0.8931 (mmm) cc_final: 0.8658 (mmm) REVERT: V 311 GLU cc_start: 0.8538 (mp0) cc_final: 0.8317 (mp0) REVERT: W 196 LYS cc_start: 0.8171 (tttt) cc_final: 0.7709 (pttm) REVERT: X 51 LYS cc_start: 0.8960 (tttt) cc_final: 0.8757 (ttmm) outliers start: 15 outliers final: 6 residues processed: 229 average time/residue: 0.2610 time to fit residues: 84.2373 Evaluate side-chains 174 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 168 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 46 optimal weight: 0.0270 chunk 119 optimal weight: 0.6980 chunk 118 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 85 optimal weight: 0.0980 overall best weight: 0.3638 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.145987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.118413 restraints weight = 15698.738| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.60 r_work: 0.3125 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12846 Z= 0.107 Angle : 0.523 8.310 17413 Z= 0.275 Chirality : 0.043 0.147 1926 Planarity : 0.004 0.043 2229 Dihedral : 8.241 117.501 1736 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.08 % Favored : 97.86 % Rotamer: Outliers : 1.58 % Allowed : 8.78 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.21), residues: 1541 helix: 1.16 (0.19), residues: 708 sheet: 0.92 (0.34), residues: 217 loop : 0.34 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 356 HIS 0.007 0.001 HIS U 823 PHE 0.014 0.001 PHE W 207 TYR 0.014 0.001 TYR U 596 ARG 0.003 0.000 ARG U 834 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 630) hydrogen bonds : angle 4.39990 ( 1698) covalent geometry : bond 0.00225 (12846) covalent geometry : angle 0.52332 (17413) *********************** 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 209 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 1.478 Fit side-chains revert: symmetry clash REVERT: G 490 ARG cc_start: 0.7025 (mtt180) cc_final: 0.5983 (ptt180) REVERT: G 545 LYS cc_start: 0.8611 (mttt) cc_final: 0.8359 (tptt) REVERT: U 585 MET cc_start: 0.8539 (ttm) cc_final: 0.8174 (ttp) REVERT: U 596 TYR cc_start: 0.7387 (m-80) cc_final: 0.7055 (m-80) REVERT: U 632 PHE cc_start: 0.8439 (m-80) cc_final: 0.8218 (m-80) REVERT: U 688 LYS cc_start: 0.7641 (mttt) cc_final: 0.7239 (pttm) REVERT: V 69 TYR cc_start: 0.8955 (m-80) cc_final: 0.8651 (m-80) REVERT: V 246 GLN cc_start: 0.7473 (tt0) cc_final: 0.7008 (mm-40) REVERT: V 305 MET cc_start: 0.8871 (mmm) cc_final: 0.8613 (mmm) REVERT: W 196 LYS cc_start: 0.8292 (tttt) cc_final: 0.7715 (pttm) REVERT: W 284 THR cc_start: 0.8647 (m) cc_final: 0.8284 (p) REVERT: W 430 LYS cc_start: 0.7673 (mttt) cc_final: 0.7332 (mptt) REVERT: X 44 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8420 (mtmt) REVERT: X 51 LYS cc_start: 0.8967 (tttt) cc_final: 0.8747 (ttmm) outliers start: 22 outliers final: 16 residues processed: 203 average time/residue: 0.2688 time to fit residues: 77.5276 Evaluate side-chains 176 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 581 LEU Chi-restraints excluded: chain U residue 618 LYS Chi-restraints excluded: chain U residue 622 THR 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 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 108 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 0.4980 chunk 13 optimal weight: 0.0770 chunk 16 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.2540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 541 ASN W 162 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.141675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.114419 restraints weight = 15563.260| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.57 r_work: 0.3078 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12846 Z= 0.160 Angle : 0.547 6.450 17413 Z= 0.285 Chirality : 0.045 0.146 1926 Planarity : 0.005 0.042 2229 Dihedral : 8.200 116.950 1736 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.92 % Rotamer: Outliers : 1.80 % Allowed : 9.50 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.21), residues: 1541 helix: 1.07 (0.19), residues: 715 sheet: 0.84 (0.35), residues: 211 loop : 0.24 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 356 HIS 0.007 0.001 HIS U 823 PHE 0.018 0.002 PHE U 546 TYR 0.019 0.002 TYR W 450 ARG 0.005 0.000 ARG V 68 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 630) hydrogen bonds : angle 4.39090 ( 1698) covalent geometry : bond 0.00388 (12846) covalent geometry : angle 0.54716 (17413) *********************** 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 190 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 1.463 Fit side-chains revert: symmetry clash REVERT: G 490 ARG cc_start: 0.7020 (mtt180) cc_final: 0.6185 (ptt180) REVERT: G 545 LYS cc_start: 0.8602 (mttt) cc_final: 0.8391 (tppt) REVERT: U 596 TYR cc_start: 0.7417 (m-80) cc_final: 0.7078 (m-80) REVERT: U 688 LYS cc_start: 0.7560 (mttt) cc_final: 0.7139 (pttm) REVERT: V 69 TYR cc_start: 0.8951 (m-80) cc_final: 0.8563 (m-80) REVERT: V 160 THR cc_start: 0.9323 (m) cc_final: 0.8986 (m) REVERT: V 246 GLN cc_start: 0.7310 (tt0) cc_final: 0.6929 (mm-40) REVERT: W 196 LYS cc_start: 0.8282 (tttt) cc_final: 0.7982 (ttpt) REVERT: W 215 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6821 (mp0) REVERT: W 284 THR cc_start: 0.8717 (m) cc_final: 0.8375 (p) REVERT: W 319 TYR cc_start: 0.7916 (t80) cc_final: 0.7360 (t80) REVERT: W 425 MET cc_start: 0.7930 (tpt) cc_final: 0.7367 (tpt) REVERT: W 430 LYS cc_start: 0.7716 (mttt) cc_final: 0.7278 (mmtt) REVERT: X 44 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8503 (mtmt) REVERT: X 51 LYS cc_start: 0.8962 (tttt) cc_final: 0.8698 (ttmm) outliers start: 25 outliers final: 14 residues processed: 181 average time/residue: 0.2661 time to fit residues: 69.5005 Evaluate side-chains 162 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 260 ILE 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 V residue 300 SER Chi-restraints excluded: chain W residue 17 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 42 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 792 ASN W 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.143173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.118016 restraints weight = 15705.086| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.47 r_work: 0.3070 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12846 Z= 0.163 Angle : 0.533 6.337 17413 Z= 0.279 Chirality : 0.044 0.140 1926 Planarity : 0.004 0.042 2229 Dihedral : 8.142 113.864 1736 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.92 % Rotamer: Outliers : 2.30 % Allowed : 10.08 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.21), residues: 1541 helix: 1.06 (0.19), residues: 715 sheet: 0.80 (0.35), residues: 211 loop : 0.17 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 356 HIS 0.007 0.001 HIS U 823 PHE 0.013 0.001 PHE U 546 TYR 0.017 0.002 TYR W 450 ARG 0.003 0.000 ARG W 448 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 630) hydrogen bonds : angle 4.37592 ( 1698) covalent geometry : bond 0.00393 (12846) covalent geometry : angle 0.53345 (17413) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 1.591 Fit side-chains revert: symmetry clash REVERT: G 490 ARG cc_start: 0.7137 (mtt180) cc_final: 0.6238 (ptt180) REVERT: G 526 LYS cc_start: 0.8340 (mttt) cc_final: 0.7946 (ttpp) REVERT: U 596 TYR cc_start: 0.7465 (m-80) cc_final: 0.7111 (m-80) REVERT: U 688 LYS cc_start: 0.7577 (mttt) cc_final: 0.7237 (pttm) REVERT: V 69 TYR cc_start: 0.8950 (m-80) cc_final: 0.8528 (m-80) REVERT: V 160 THR cc_start: 0.9319 (m) cc_final: 0.9010 (m) REVERT: V 246 GLN cc_start: 0.7389 (tt0) cc_final: 0.7014 (mm-40) REVERT: V 305 MET cc_start: 0.8814 (mmm) cc_final: 0.8570 (mmm) REVERT: W 196 LYS cc_start: 0.8190 (tttt) cc_final: 0.7909 (ttpt) REVERT: W 215 GLU cc_start: 0.7271 (mt-10) cc_final: 0.7019 (mp0) REVERT: W 425 MET cc_start: 0.7828 (tpt) cc_final: 0.7303 (tpt) REVERT: W 430 LYS cc_start: 0.7663 (mttt) cc_final: 0.7163 (mmtt) REVERT: X 44 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8510 (mtmt) REVERT: X 51 LYS cc_start: 0.8951 (tttt) cc_final: 0.8717 (ttmm) outliers start: 32 outliers final: 20 residues processed: 181 average time/residue: 0.3291 time to fit residues: 85.8338 Evaluate side-chains 166 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 260 ILE 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 800 ILE Chi-restraints excluded: chain U residue 836 MET Chi-restraints excluded: chain V residue 252 ASN Chi-restraints excluded: chain V residue 300 SER Chi-restraints excluded: chain V residue 364 GLU Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 137 CYS Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 279 VAL Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 462 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 64 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 123 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 372 HIS W 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.144930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.118912 restraints weight = 15853.217| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.59 r_work: 0.3076 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12846 Z= 0.129 Angle : 0.503 6.136 17413 Z= 0.264 Chirality : 0.043 0.138 1926 Planarity : 0.004 0.043 2229 Dihedral : 7.932 108.613 1736 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.95 % Favored : 97.99 % Rotamer: Outliers : 2.02 % Allowed : 11.23 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.21), residues: 1541 helix: 1.24 (0.19), residues: 710 sheet: 0.83 (0.35), residues: 214 loop : 0.20 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 356 HIS 0.007 0.001 HIS U 823 PHE 0.013 0.001 PHE W 207 TYR 0.014 0.001 TYR W 450 ARG 0.007 0.000 ARG V 68 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 630) hydrogen bonds : angle 4.27271 ( 1698) covalent geometry : bond 0.00304 (12846) covalent geometry : angle 0.50296 (17413) *********************** 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 182 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 1.472 Fit side-chains revert: symmetry clash REVERT: G 490 ARG cc_start: 0.7123 (mtt180) cc_final: 0.6059 (ptt180) REVERT: U 596 TYR cc_start: 0.7449 (m-80) cc_final: 0.7112 (m-80) REVERT: U 688 LYS cc_start: 0.7601 (mttt) cc_final: 0.7218 (pttm) REVERT: V 69 TYR cc_start: 0.8942 (m-80) cc_final: 0.8499 (m-80) REVERT: V 160 THR cc_start: 0.9353 (m) cc_final: 0.9049 (m) REVERT: V 246 GLN cc_start: 0.7397 (tt0) cc_final: 0.7014 (mm-40) REVERT: W 196 LYS cc_start: 0.8187 (tttt) cc_final: 0.7894 (ttpt) REVERT: W 215 GLU cc_start: 0.7287 (mt-10) cc_final: 0.7051 (mp0) REVERT: W 319 TYR cc_start: 0.7789 (t80) cc_final: 0.7272 (t80) REVERT: W 425 MET cc_start: 0.7795 (tpt) cc_final: 0.7296 (tpt) REVERT: W 430 LYS cc_start: 0.7787 (mttt) cc_final: 0.7306 (mmtt) REVERT: X 44 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8563 (mtmt) REVERT: X 51 LYS cc_start: 0.8953 (tttt) cc_final: 0.8710 (ttmm) outliers start: 28 outliers final: 20 residues processed: 175 average time/residue: 0.2619 time to fit residues: 65.7086 Evaluate side-chains 166 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 260 ILE 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 685 LEU Chi-restraints excluded: chain U residue 800 ILE 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 300 SER Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 166 SER Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 279 VAL Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 462 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 82 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 103 optimal weight: 0.0270 chunk 25 optimal weight: 0.0770 chunk 97 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 821 ASN W 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.145997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120683 restraints weight = 15705.412| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.51 r_work: 0.3177 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3377 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= 0.099 Angle : 0.474 5.836 17413 Z= 0.249 Chirality : 0.042 0.141 1926 Planarity : 0.004 0.040 2229 Dihedral : 7.520 100.858 1736 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.21 % Favored : 97.73 % Rotamer: Outliers : 1.73 % Allowed : 12.10 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.22), residues: 1541 helix: 1.45 (0.20), residues: 704 sheet: 0.75 (0.35), residues: 226 loop : 0.30 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 356 HIS 0.007 0.001 HIS U 823 PHE 0.013 0.001 PHE W 207 TYR 0.012 0.001 TYR U 596 ARG 0.007 0.000 ARG V 68 Details of bonding type rmsd hydrogen bonds : bond 0.03211 ( 630) hydrogen bonds : angle 4.16484 ( 1698) covalent geometry : bond 0.00219 (12846) covalent geometry : angle 0.47432 (17413) *********************** 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: 24 poor density : 162 time to evaluate : 1.418 Fit side-chains revert: symmetry clash REVERT: G 490 ARG cc_start: 0.7025 (mtt180) cc_final: 0.5992 (ptt180) REVERT: G 526 LYS cc_start: 0.8338 (mttt) cc_final: 0.7944 (ttpp) REVERT: U 596 TYR cc_start: 0.7461 (m-80) cc_final: 0.7150 (m-80) REVERT: U 688 LYS cc_start: 0.7526 (mttt) cc_final: 0.7161 (pttm) REVERT: U 801 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8309 (mttp) REVERT: V 69 TYR cc_start: 0.8925 (m-80) cc_final: 0.8531 (m-80) REVERT: V 160 THR cc_start: 0.9328 (m) cc_final: 0.9040 (m) REVERT: V 246 GLN cc_start: 0.7545 (tt0) cc_final: 0.7130 (mm-40) REVERT: V 269 LEU cc_start: 0.8774 (mp) cc_final: 0.8335 (mt) REVERT: W 196 LYS cc_start: 0.8190 (tttt) cc_final: 0.7983 (ttpt) REVERT: W 215 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6898 (mp0) REVERT: W 425 MET cc_start: 0.7825 (tpt) cc_final: 0.7349 (tpt) REVERT: W 430 LYS cc_start: 0.7707 (mttt) cc_final: 0.7261 (mmtt) REVERT: X 44 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8517 (mtmt) REVERT: X 51 LYS cc_start: 0.8946 (tttt) cc_final: 0.8671 (ttmm) outliers start: 24 outliers final: 18 residues processed: 179 average time/residue: 0.2637 time to fit residues: 68.4044 Evaluate side-chains 170 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain U residue 473 GLU 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 626 LYS 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 300 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.148048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.122464 restraints weight = 15751.681| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.61 r_work: 0.3194 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12846 Z= 0.110 Angle : 0.482 5.976 17413 Z= 0.252 Chirality : 0.042 0.139 1926 Planarity : 0.004 0.040 2229 Dihedral : 7.450 99.155 1736 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.92 % Rotamer: Outliers : 1.66 % Allowed : 12.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.22), residues: 1541 helix: 1.49 (0.20), residues: 704 sheet: 0.82 (0.35), residues: 226 loop : 0.34 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 356 HIS 0.007 0.001 HIS U 823 PHE 0.012 0.001 PHE W 207 TYR 0.012 0.001 TYR W 450 ARG 0.008 0.000 ARG V 68 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 630) hydrogen bonds : angle 4.15144 ( 1698) covalent geometry : bond 0.00256 (12846) covalent geometry : angle 0.48163 (17413) *********************** 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 179 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 1.485 Fit side-chains revert: symmetry clash REVERT: G 490 ARG cc_start: 0.7044 (mtt180) cc_final: 0.6038 (ptt180) REVERT: G 526 LYS cc_start: 0.8318 (mttt) cc_final: 0.7971 (ttpp) REVERT: U 339 ARG cc_start: 0.7450 (ttp-110) cc_final: 0.7152 (ttp80) REVERT: U 596 TYR cc_start: 0.7467 (m-80) cc_final: 0.7153 (m-80) REVERT: U 688 LYS cc_start: 0.7520 (mttt) cc_final: 0.7192 (pttm) REVERT: U 801 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8314 (mttp) REVERT: V 68 ARG cc_start: 0.7634 (mtp-110) cc_final: 0.7314 (mtp85) REVERT: V 69 TYR cc_start: 0.8916 (m-80) cc_final: 0.8500 (m-80) REVERT: V 160 THR cc_start: 0.9337 (m) cc_final: 0.9047 (m) REVERT: V 246 GLN cc_start: 0.7576 (tt0) cc_final: 0.7176 (mm-40) REVERT: V 269 LEU cc_start: 0.8768 (mp) cc_final: 0.8376 (mt) REVERT: W 215 GLU cc_start: 0.7289 (mt-10) cc_final: 0.7066 (mp0) REVERT: W 319 TYR cc_start: 0.7803 (t80) cc_final: 0.7352 (t80) REVERT: W 425 MET cc_start: 0.7824 (tpt) cc_final: 0.7361 (tpt) REVERT: W 430 LYS cc_start: 0.7721 (mttt) cc_final: 0.7270 (mmtt) REVERT: X 44 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8532 (mtmt) REVERT: X 51 LYS cc_start: 0.8941 (tttt) cc_final: 0.8679 (ttmm) outliers start: 23 outliers final: 17 residues processed: 173 average time/residue: 0.2827 time to fit residues: 71.2714 Evaluate side-chains 166 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 260 ILE 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 626 LYS 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 300 SER 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 279 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 115 optimal weight: 0.1980 chunk 153 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 134 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.147848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.122441 restraints weight = 15604.180| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.48 r_work: 0.3149 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12846 Z= 0.103 Angle : 0.479 7.856 17413 Z= 0.249 Chirality : 0.042 0.140 1926 Planarity : 0.004 0.039 2229 Dihedral : 7.314 96.873 1736 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.08 % Favored : 97.86 % Rotamer: Outliers : 1.66 % Allowed : 12.46 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.22), residues: 1541 helix: 1.52 (0.20), residues: 710 sheet: 0.84 (0.35), residues: 226 loop : 0.32 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 356 HIS 0.007 0.001 HIS U 823 PHE 0.012 0.001 PHE W 207 TYR 0.012 0.001 TYR U 596 ARG 0.007 0.000 ARG V 68 Details of bonding type rmsd hydrogen bonds : bond 0.03194 ( 630) hydrogen bonds : angle 4.12333 ( 1698) covalent geometry : bond 0.00233 (12846) covalent geometry : angle 0.47925 (17413) *********************** 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 178 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 1.430 Fit side-chains revert: symmetry clash REVERT: G 457 MET cc_start: 0.5569 (tpt) cc_final: 0.2315 (ttt) REVERT: G 490 ARG cc_start: 0.7014 (mtt180) cc_final: 0.5982 (ptt180) REVERT: G 526 LYS cc_start: 0.8304 (mttt) cc_final: 0.7924 (ttpp) REVERT: U 339 ARG cc_start: 0.7478 (ttp-110) cc_final: 0.7252 (ttp80) REVERT: U 596 TYR cc_start: 0.7434 (m-80) cc_final: 0.7134 (m-80) REVERT: U 688 LYS cc_start: 0.7513 (mttt) cc_final: 0.7152 (pttm) REVERT: U 801 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8299 (mttp) REVERT: V 68 ARG cc_start: 0.7622 (mtp-110) cc_final: 0.7309 (mtp85) REVERT: V 69 TYR cc_start: 0.8971 (m-80) cc_final: 0.8570 (m-80) REVERT: V 160 THR cc_start: 0.9333 (m) cc_final: 0.9045 (m) REVERT: V 246 GLN cc_start: 0.7573 (tt0) cc_final: 0.7142 (mm-40) REVERT: V 269 LEU cc_start: 0.8741 (mp) cc_final: 0.8332 (mt) REVERT: W 215 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6938 (mp0) REVERT: W 319 TYR cc_start: 0.7770 (t80) cc_final: 0.7302 (t80) REVERT: W 425 MET cc_start: 0.7833 (tpt) cc_final: 0.7349 (tpt) REVERT: W 430 LYS cc_start: 0.7700 (mttt) cc_final: 0.7262 (mmtt) REVERT: X 44 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8530 (mtmt) REVERT: X 51 LYS cc_start: 0.8929 (tttt) cc_final: 0.8658 (ttmm) outliers start: 23 outliers final: 19 residues processed: 170 average time/residue: 0.4354 time to fit residues: 110.2721 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 : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain U residue 495 SER Chi-restraints excluded: chain U residue 609 LEU Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain U residue 685 LEU Chi-restraints excluded: chain U residue 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 V residue 300 SER Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 166 SER Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 279 VAL Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 382 LEU Chi-restraints excluded: chain 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 100 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 109 optimal weight: 0.0670 chunk 73 optimal weight: 3.9990 chunk 85 optimal weight: 0.0770 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 116 optimal weight: 0.9980 overall best weight: 0.4876 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.149650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.125189 restraints weight = 15521.941| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.41 r_work: 0.3231 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12846 Z= 0.096 Angle : 0.470 7.748 17413 Z= 0.244 Chirality : 0.042 0.141 1926 Planarity : 0.004 0.038 2229 Dihedral : 7.117 92.739 1736 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.92 % Rotamer: Outliers : 1.58 % Allowed : 12.60 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.22), residues: 1541 helix: 1.60 (0.20), residues: 710 sheet: 0.92 (0.35), residues: 225 loop : 0.36 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 356 HIS 0.008 0.001 HIS U 823 PHE 0.011 0.001 PHE W 207 TYR 0.011 0.001 TYR U 596 ARG 0.007 0.000 ARG V 68 Details of bonding type rmsd hydrogen bonds : bond 0.03056 ( 630) hydrogen bonds : angle 4.08129 ( 1698) covalent geometry : bond 0.00214 (12846) covalent geometry : angle 0.47033 (17413) ********************** 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 185 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 1.942 Fit side-chains revert: symmetry clash REVERT: G 457 MET cc_start: 0.5566 (tpt) cc_final: 0.2538 (ttt) REVERT: G 490 ARG cc_start: 0.7017 (mtt180) cc_final: 0.6002 (ptt180) REVERT: G 526 LYS cc_start: 0.8257 (mttt) cc_final: 0.7910 (ttpp) REVERT: U 339 ARG cc_start: 0.7453 (ttp-110) cc_final: 0.7248 (ttp80) REVERT: U 596 TYR cc_start: 0.7486 (m-80) cc_final: 0.7202 (m-80) REVERT: U 688 LYS cc_start: 0.7430 (mttt) cc_final: 0.7077 (pttm) REVERT: U 801 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8304 (mttp) REVERT: V 69 TYR cc_start: 0.8969 (m-80) cc_final: 0.8580 (m-80) REVERT: V 160 THR cc_start: 0.9324 (m) cc_final: 0.9038 (m) REVERT: V 246 GLN cc_start: 0.7633 (tt0) cc_final: 0.7242 (mm-40) REVERT: W 215 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6885 (mp0) REVERT: W 319 TYR cc_start: 0.7767 (t80) cc_final: 0.7348 (t80) REVERT: W 425 MET cc_start: 0.7794 (tpt) cc_final: 0.7324 (tpt) REVERT: W 430 LYS cc_start: 0.7721 (mttt) cc_final: 0.7275 (mmtt) REVERT: X 51 LYS cc_start: 0.8902 (tttt) cc_final: 0.8647 (ttmm) outliers start: 22 outliers final: 19 residues processed: 178 average time/residue: 0.3578 time to fit residues: 92.6398 Evaluate side-chains 175 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 260 ILE Chi-restraints excluded: chain U residue 450 VAL Chi-restraints excluded: chain U residue 495 SER Chi-restraints excluded: chain U residue 609 LEU Chi-restraints excluded: chain U residue 622 THR Chi-restraints excluded: chain U residue 626 LYS 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 V residue 300 SER Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 165 CYS Chi-restraints excluded: chain W residue 166 SER Chi-restraints excluded: chain W residue 206 LEU Chi-restraints excluded: chain W residue 279 VAL Chi-restraints excluded: chain W residue 294 LEU Chi-restraints excluded: chain W residue 382 LEU Chi-restraints excluded: chain 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 50 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 111 optimal weight: 0.0570 chunk 123 optimal weight: 4.9990 chunk 100 optimal weight: 0.0370 chunk 118 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 12 optimal weight: 0.4980 chunk 143 optimal weight: 1.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.149039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123870 restraints weight = 15655.061| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.48 r_work: 0.3229 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12846 Z= 0.092 Angle : 0.467 7.816 17413 Z= 0.243 Chirality : 0.041 0.140 1926 Planarity : 0.004 0.037 2229 Dihedral : 6.910 89.500 1736 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.21 % Favored : 97.73 % Rotamer: Outliers : 1.51 % Allowed : 12.81 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.22), residues: 1541 helix: 1.62 (0.20), residues: 711 sheet: 0.95 (0.35), residues: 221 loop : 0.41 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 356 HIS 0.008 0.001 HIS U 823 PHE 0.011 0.001 PHE U 584 TYR 0.010 0.001 TYR U 596 ARG 0.009 0.000 ARG V 68 Details of bonding type rmsd hydrogen bonds : bond 0.02989 ( 630) hydrogen bonds : angle 4.04411 ( 1698) covalent geometry : bond 0.00203 (12846) covalent geometry : angle 0.46693 (17413) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7352.46 seconds wall clock time: 134 minutes 29.22 seconds (8069.22 seconds total)