Starting phenix.real_space_refine on Mon Jul 6 05:33:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xzj_72358/07_2026/9xzj_72358_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xzj_72358/07_2026/9xzj_72358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xzj_72358/07_2026/9xzj_72358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xzj_72358/07_2026/9xzj_72358.map" model { file = "/net/cci-nas-00/data/ceres_data/9xzj_72358/07_2026/9xzj_72358_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xzj_72358/07_2026/9xzj_72358_trim.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 126 5.49 5 Mg 1 5.21 5 S 74 5.16 5 C 10095 2.51 5 N 2864 2.21 5 O 3361 1.98 5 H 15408 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31930 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 12129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 12129 Classifications: {'peptide': 742} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 727} Chain breaks: 1 Chain: "R" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 282 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "F" Number of atoms: 12969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 12969 Classifications: {'peptide': 805} Link IDs: {'PTRANS': 30, 'TRANS': 774} Chain breaks: 1 Chain: "S" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 2532 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "X" Number of atoms: 1429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 1429 Classifications: {'DNA': 45} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 44} Chain: "A" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 658 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "B" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 472 Classifications: {'DNA': 15} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 14} Chain: "Y" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 1426 Classifications: {'DNA': 45} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 44} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24342 SG CYS F 889 66.074 83.609 109.038 1.00109.75 S ATOM 24403 SG CYS F 894 68.199 86.191 107.396 1.00126.76 S ATOM 24899 SG CYS F 925 68.535 82.638 106.376 1.00 90.41 S ATOM 24937 SG CYS F 928 69.850 83.608 109.632 1.00143.32 S Time building chain proxies: 5.30, per 1000 atoms: 0.17 Number of scatterers: 31930 At special positions: 0 Unit cell: (143.15, 149.694, 247.854, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 74 16.00 P 126 15.00 Mg 1 11.99 O 3361 8.00 N 2864 7.00 C 10095 6.00 H 15408 1.00 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: 3.07 Conformation dependent library (CDL) restraints added in 872.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F1003 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 925 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 894 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 889 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 928 " Number of angles added : 6 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3298 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 10 sheets defined 68.1% alpha, 8.0% beta 56 base pairs and 108 stacking pairs defined. Time for finding SS restraints: 5.63 Creating SS restraints... Processing helix chain 'C' and resid 16 through 33 removed outlier: 3.639A pdb=" N ILE C 20 " --> pdb=" O GLY C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 54 Processing helix chain 'C' and resid 77 through 108 Processing helix chain 'C' and resid 111 through 137 removed outlier: 3.537A pdb=" N LEU C 116 " --> pdb=" O ASP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 152 removed outlier: 4.196A pdb=" N VAL C 145 " --> pdb=" O ASN C 141 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ARG C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'C' and resid 171 through 193 removed outlier: 4.760A pdb=" N LYS C 177 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLN C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 removed outlier: 3.925A pdb=" N ILE C 201 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 232 through 255 Processing helix chain 'C' and resid 256 through 279 removed outlier: 3.506A pdb=" N TYR C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 296 removed outlier: 4.620A pdb=" N GLU C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 314 removed outlier: 3.825A pdb=" N PHE C 303 " --> pdb=" O HIS C 299 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR C 305 " --> pdb=" O GLU C 301 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN C 308 " --> pdb=" O HIS C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 328 removed outlier: 3.827A pdb=" N LEU C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY C 320 " --> pdb=" O ASN C 316 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG C 321 " --> pdb=" O GLU C 317 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 356 removed outlier: 4.191A pdb=" N LEU C 336 " --> pdb=" O GLY C 332 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY C 356 " --> pdb=" O ILE C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 362 through 385 Processing helix chain 'C' and resid 388 through 404 removed outlier: 3.630A pdb=" N ASN C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 416 through 431 Processing helix chain 'C' and resid 438 through 455 removed outlier: 4.137A pdb=" N TYR C 455 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 477 removed outlier: 3.627A pdb=" N PHE C 462 " --> pdb=" O ASP C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 497 Processing helix chain 'C' and resid 497 through 527 removed outlier: 3.676A pdb=" N THR C 501 " --> pdb=" O GLY C 497 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LYS C 503 " --> pdb=" O GLU C 499 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU C 504 " --> pdb=" O TYR C 500 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS C 523 " --> pdb=" O GLU C 519 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS C 524 " --> pdb=" O GLN C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 574 removed outlier: 4.609A pdb=" N ARG C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N SER C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 586 Processing helix chain 'C' and resid 604 through 613 removed outlier: 3.550A pdb=" N GLN C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 616 No H-bonds generated for 'chain 'C' and resid 614 through 616' Processing helix chain 'C' and resid 622 through 630 Processing helix chain 'C' and resid 632 through 646 removed outlier: 3.577A pdb=" N SER C 646 " --> pdb=" O ILE C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 723 removed outlier: 3.939A pdb=" N GLN C 692 " --> pdb=" O MET C 688 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS C 693 " --> pdb=" O GLU C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 739 Processing helix chain 'C' and resid 745 through 759 Processing helix chain 'F' and resid 137 through 141 Processing helix chain 'F' and resid 142 through 151 Processing helix chain 'F' and resid 154 through 161 Processing helix chain 'F' and resid 162 through 165 Processing helix chain 'F' and resid 166 through 175 Processing helix chain 'F' and resid 179 through 190 Processing helix chain 'F' and resid 192 through 206 Processing helix chain 'F' and resid 214 through 227 Processing helix chain 'F' and resid 233 through 242 Processing helix chain 'F' and resid 246 through 258 Processing helix chain 'F' and resid 258 through 263 Processing helix chain 'F' and resid 269 through 281 Processing helix chain 'F' and resid 283 through 295 removed outlier: 3.691A pdb=" N ILE F 287 " --> pdb=" O SER F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 300 removed outlier: 4.372A pdb=" N THR F 300 " --> pdb=" O PRO F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 324 Processing helix chain 'F' and resid 329 through 344 Processing helix chain 'F' and resid 368 through 377 Processing helix chain 'F' and resid 394 through 406 Processing helix chain 'F' and resid 417 through 428 Processing helix chain 'F' and resid 437 through 445 Processing helix chain 'F' and resid 445 through 452 removed outlier: 3.940A pdb=" N TYR F 449 " --> pdb=" O ILE F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 469 removed outlier: 3.584A pdb=" N VAL F 465 " --> pdb=" O THR F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 492 Processing helix chain 'F' and resid 498 through 502 Processing helix chain 'F' and resid 517 through 537 Processing helix chain 'F' and resid 543 through 547 removed outlier: 3.885A pdb=" N GLN F 547 " --> pdb=" O GLU F 544 " (cutoff:3.500A) Processing helix chain 'F' and resid 549 through 560 removed outlier: 3.685A pdb=" N LEU F 554 " --> pdb=" O HIS F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 578 Processing helix chain 'F' and resid 579 through 588 Processing helix chain 'F' and resid 598 through 602 Processing helix chain 'F' and resid 604 through 608 Processing helix chain 'F' and resid 611 through 616 removed outlier: 3.556A pdb=" N THR F 615 " --> pdb=" O ASN F 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 647 Processing helix chain 'F' and resid 676 through 689 Processing helix chain 'F' and resid 706 through 718 Processing helix chain 'F' and resid 719 through 727 Processing helix chain 'F' and resid 732 through 738 removed outlier: 3.904A pdb=" N TRP F 738 " --> pdb=" O PHE F 734 " (cutoff:3.500A) Processing helix chain 'F' and resid 743 through 755 Processing helix chain 'F' and resid 756 through 770 Processing helix chain 'F' and resid 772 through 784 Processing helix chain 'F' and resid 787 through 791 Processing helix chain 'F' and resid 798 through 802 Processing helix chain 'F' and resid 821 through 828 Proline residue: F 826 - end of helix Processing helix chain 'F' and resid 832 through 836 Processing helix chain 'F' and resid 837 through 850 removed outlier: 3.902A pdb=" N TRP F 841 " --> pdb=" O SER F 837 " (cutoff:3.500A) Processing helix chain 'F' and resid 858 through 868 removed outlier: 3.748A pdb=" N ALA F 868 " --> pdb=" O ILE F 864 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 882 Processing helix chain 'F' and resid 925 through 934 Processing helix chain 'F' and resid 935 through 940 Processing helix chain 'F' and resid 942 through 948 Processing helix chain 'S' and resid 18 through 22 Processing helix chain 'S' and resid 24 through 34 Processing helix chain 'S' and resid 51 through 65 Processing helix chain 'S' and resid 86 through 93 Processing helix chain 'S' and resid 96 through 111 Processing helix chain 'S' and resid 112 through 128 Processing helix chain 'S' and resid 131 through 140 Processing helix chain 'S' and resid 146 through 158 Processing helix chain 'S' and resid 159 through 161 No H-bonds generated for 'chain 'S' and resid 159 through 161' Processing sheet with id=AA1, first strand: chain 'C' and resid 534 through 541 removed outlier: 4.024A pdb=" N ALA R 31 " --> pdb=" O GLN C 538 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 534 through 541 removed outlier: 4.024A pdb=" N ALA R 31 " --> pdb=" O GLN C 538 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL R 24 " --> pdb=" O VAL C 591 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL C 591 " --> pdb=" O VAL R 24 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS R 26 " --> pdb=" O GLU C 589 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 619 through 621 Processing sheet with id=AA4, first strand: chain 'C' and resid 724 through 726 Processing sheet with id=AA5, first strand: chain 'F' and resid 432 through 436 removed outlier: 6.615A pdb=" N PHE F 411 " --> pdb=" O ILE F 433 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LYS F 435 " --> pdb=" O PHE F 411 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR F 413 " --> pdb=" O LYS F 435 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE F 570 " --> pdb=" O ILE F 594 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL F 596 " --> pdb=" O ILE F 570 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL F 572 " --> pdb=" O VAL F 596 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL F 384 " --> pdb=" O HIS F 620 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE F 622 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LYS F 386 " --> pdb=" O PHE F 622 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU F 624 " --> pdb=" O LYS F 386 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N MET F 388 " --> pdb=" O LEU F 624 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 505 through 507 Processing sheet with id=AA7, first strand: chain 'F' and resid 696 through 698 removed outlier: 6.116A pdb=" N HIS F 697 " --> pdb=" O LEU F 795 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N THR F 797 " --> pdb=" O HIS F 697 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY F 796 " --> pdb=" O LEU F 672 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA F 671 " --> pdb=" O HIS F 810 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP F 807 " --> pdb=" O ARG F 854 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ILE F 856 " --> pdb=" O ASP F 807 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL F 809 " --> pdb=" O ILE F 856 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 873 through 877 removed outlier: 4.389A pdb=" N MET F 906 " --> pdb=" O LEU F 924 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 911 through 912 Processing sheet with id=AB1, first strand: chain 'S' and resid 13 through 17 removed outlier: 9.592A pdb=" N VAL S 45 " --> pdb=" O SER S 3 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LYS S 5 " --> pdb=" O VAL S 45 " (cutoff:3.500A) 834 hydrogen bonds defined for protein. 2415 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 144 hydrogen bonds 288 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 108 stacking parallelities Total time for adding SS restraints: 8.21 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 15373 1.04 - 1.25: 2063 1.25 - 1.45: 5651 1.45 - 1.66: 9313 1.66 - 1.86: 108 Bond restraints: 32508 Sorted by residual: bond pdb=" O2A AGS F1001 " pdb=" PA AGS F1001 " ideal model delta sigma weight residual 1.505 1.606 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" O2B AGS F1001 " pdb=" PB AGS F1001 " ideal model delta sigma weight residual 1.518 1.605 -0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C1' DC X 18 " pdb=" N1 DC X 18 " ideal model delta sigma weight residual 1.468 1.524 -0.056 1.40e-02 5.10e+03 1.58e+01 bond pdb=" PG AGS F1001 " pdb=" S1G AGS F1001 " ideal model delta sigma weight residual 1.936 1.861 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C3' DG Y 32 " pdb=" C2' DG Y 32 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.34e+01 ... (remaining 32503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 58594 2.54 - 5.08: 253 5.08 - 7.63: 8 7.63 - 10.17: 2 10.17 - 12.71: 3 Bond angle restraints: 58860 Sorted by residual: angle pdb=" O1A AGS F1001 " pdb=" PA AGS F1001 " pdb=" O2A AGS F1001 " ideal model delta sigma weight residual 122.09 109.38 12.71 3.00e+00 1.11e-01 1.80e+01 angle pdb=" O4' DT X 42 " pdb=" C1' DT X 42 " pdb=" N1 DT X 42 " ideal model delta sigma weight residual 108.00 110.94 -2.94 7.00e-01 2.04e+00 1.77e+01 angle pdb=" N3 DT X 22 " pdb=" C4 DT X 22 " pdb=" O4 DT X 22 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT Y 13 " pdb=" C4 DT Y 13 " pdb=" O4 DT Y 13 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT Y 24 " pdb=" C4 DT Y 24 " pdb=" O4 DT Y 24 " ideal model delta sigma weight residual 119.90 122.29 -2.39 6.00e-01 2.78e+00 1.58e+01 ... (remaining 58855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 12881 17.17 - 34.34: 832 34.34 - 51.51: 633 51.51 - 68.68: 358 68.68 - 85.85: 15 Dihedral angle restraints: 14719 sinusoidal: 8777 harmonic: 5942 Sorted by residual: dihedral pdb=" CA LEU F 812 " pdb=" C LEU F 812 " pdb=" N ASP F 813 " pdb=" CA ASP F 813 " ideal model delta harmonic sigma weight residual -180.00 -163.82 -16.18 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" O2' AGS F1001 " pdb=" C2' AGS F1001 " pdb=" C3' AGS F1001 " pdb=" O3' AGS F1001 " ideal model delta sinusoidal sigma weight residual 48.13 -37.72 85.85 1 3.00e+01 1.11e-03 9.89e+00 dihedral pdb=" C1' AGS F1001 " pdb=" C2' AGS F1001 " pdb=" C3' AGS F1001 " pdb=" O3' AGS F1001 " ideal model delta sinusoidal sigma weight residual 164.95 79.89 85.06 1 3.00e+01 1.11e-03 9.75e+00 ... (remaining 14716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2411 0.074 - 0.148: 237 0.148 - 0.222: 10 0.222 - 0.295: 1 0.295 - 0.369: 1 Chirality restraints: 2660 Sorted by residual: chirality pdb=" C3' AGS F1001 " pdb=" C2' AGS F1001 " pdb=" C4' AGS F1001 " pdb=" O3' AGS F1001 " both_signs ideal model delta sigma weight residual False -2.37 -2.74 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C4' AGS F1001 " pdb=" C3' AGS F1001 " pdb=" C5' AGS F1001 " pdb=" O4' AGS F1001 " both_signs ideal model delta sigma weight residual False -2.41 -2.65 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" C3' DA X 19 " pdb=" C4' DA X 19 " pdb=" O3' DA X 19 " pdb=" C2' DA X 19 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.48e-01 ... (remaining 2657 not shown) Planarity restraints: 4341 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET F 303 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO F 304 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO F 304 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 304 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 461 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO F 462 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO F 462 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 462 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT Y 24 " -0.013 2.00e-02 2.50e+03 7.14e-03 1.53e+00 pdb=" N1 DT Y 24 " 0.021 2.00e-02 2.50e+03 pdb=" C2 DT Y 24 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT Y 24 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DT Y 24 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DT Y 24 " -0.001 2.00e-02 2.50e+03 pdb=" O4 DT Y 24 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DT Y 24 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT Y 24 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DT Y 24 " -0.001 2.00e-02 2.50e+03 pdb=" H3 DT Y 24 " -0.001 2.00e-02 2.50e+03 pdb=" H6 DT Y 24 " 0.000 2.00e-02 2.50e+03 ... (remaining 4338 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.40: 13125 2.40 - 2.95: 72077 2.95 - 3.50: 82194 3.50 - 4.05: 110274 4.05 - 4.60: 166742 Nonbonded interactions: 444412 Sorted by model distance: nonbonded pdb=" H ASN C 406 " pdb=" HG1 THR C 409 " model vdw 1.849 2.100 nonbonded pdb=" HG SER S 24 " pdb=" H ILE S 27 " model vdw 1.875 2.100 nonbonded pdb=" HG1 THR C 592 " pdb=" H TYR C 599 " model vdw 1.880 2.100 nonbonded pdb=" H THR F 393 " pdb=" HG1 THR F 393 " model vdw 1.901 2.100 nonbonded pdb=" HE ARG C 274 " pdb=" HH TYR C 278 " model vdw 1.902 2.100 ... (remaining 444407 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: 12.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.220 Extract box with map and model: 0.740 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 42.070 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 0.005 0.101 17104 Z= 0.357 Angle : 0.603 12.711 23661 Z= 0.455 Chirality : 0.043 0.369 2660 Planarity : 0.003 0.033 2577 Dihedral : 19.512 85.845 6736 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.22), residues: 1711 helix: 2.48 (0.16), residues: 1054 sheet: 0.35 (0.55), residues: 94 loop : 0.62 (0.30), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 932 TYR 0.014 0.001 TYR C 377 PHE 0.010 0.001 PHE C 402 TRP 0.012 0.001 TRP F 271 HIS 0.003 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.36 (17100) covalent geometry : angle 0.60208 / 0.45 (23655) hydrogen bonds : bond 0.11487 / 7.68 ( 971) hydrogen bonds : angle 5.15248 / 3.73 ( 2703) metal coordination : bond 0.04000 / 2.24 ( 4) metal coordination : angle 2.21478 / 1.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 261 MET cc_start: 0.7724 (mtm) cc_final: 0.7484 (mtm) REVERT: C 322 MET cc_start: 0.7976 (ttm) cc_final: 0.7505 (tpp) REVERT: F 789 ASP cc_start: 0.8794 (m-30) cc_final: 0.8586 (m-30) REVERT: F 895 ASN cc_start: 0.8398 (m-40) cc_final: 0.8136 (p0) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.4477 time to fit residues: 74.7268 Evaluate side-chains 78 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 518 ASN C 524 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.152566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.099048 restraints weight = 109153.019| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.26 r_work: 0.3336 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17104 Z= 0.150 Angle : 0.500 6.385 23661 Z= 0.293 Chirality : 0.039 0.160 2660 Planarity : 0.004 0.034 2577 Dihedral : 25.201 66.238 3255 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.58 % Allowed : 3.63 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.21), residues: 1711 helix: 2.38 (0.16), residues: 1061 sheet: 0.25 (0.56), residues: 94 loop : 0.53 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 749 TYR 0.014 0.001 TYR C 377 PHE 0.010 0.001 PHE C 402 TRP 0.010 0.001 TRP F 271 HIS 0.005 0.001 HIS C 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (17100) covalent geometry : angle 0.49802 / 0.29 (23655) hydrogen bonds : bond 0.04601 / 3.06 ( 971) hydrogen bonds : angle 4.44410 / 3.18 ( 2703) metal coordination : bond 0.00527 / 0.27 ( 4) metal coordination : angle 2.49731 / 1.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 261 MET cc_start: 0.7762 (mtm) cc_final: 0.7537 (mtm) REVERT: C 322 MET cc_start: 0.8014 (ttm) cc_final: 0.7542 (tpp) REVERT: F 194 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8326 (mp10) REVERT: F 895 ASN cc_start: 0.8388 (m-40) cc_final: 0.8144 (p0) outliers start: 9 outliers final: 5 residues processed: 85 average time/residue: 0.3691 time to fit residues: 44.8388 Evaluate side-chains 84 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 573 ARG Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 194 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 156 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 chunk 73 optimal weight: 40.0000 chunk 37 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.150148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.096124 restraints weight = 108579.179| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.21 r_work: 0.3323 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17104 Z= 0.215 Angle : 0.508 6.259 23661 Z= 0.294 Chirality : 0.038 0.145 2660 Planarity : 0.004 0.035 2577 Dihedral : 24.779 66.019 3255 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.58 % Allowed : 3.96 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.21), residues: 1711 helix: 2.25 (0.16), residues: 1054 sheet: 0.00 (0.57), residues: 91 loop : 0.55 (0.29), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 749 TYR 0.019 0.002 TYR F 553 PHE 0.013 0.001 PHE S 92 TRP 0.010 0.001 TRP F 271 HIS 0.005 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.22 (17100) covalent geometry : angle 0.50599 / 0.29 (23655) hydrogen bonds : bond 0.04278 / 2.83 ( 971) hydrogen bonds : angle 4.30006 / 3.08 ( 2703) metal coordination : bond 0.00634 / 0.34 ( 4) metal coordination : angle 3.05639 / 1.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 322 MET cc_start: 0.7974 (ttm) cc_final: 0.7710 (tpp) REVERT: R 36 ASP cc_start: 0.3636 (p0) cc_final: 0.3422 (p0) REVERT: F 515 MET cc_start: 0.8426 (tpp) cc_final: 0.8116 (mmm) REVERT: F 895 ASN cc_start: 0.8531 (m-40) cc_final: 0.8211 (p0) outliers start: 9 outliers final: 9 residues processed: 82 average time/residue: 0.3512 time to fit residues: 41.8170 Evaluate side-chains 83 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 508 PHE Chi-restraints excluded: chain C residue 573 ARG Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 583 MET Chi-restraints excluded: chain F residue 660 SER Chi-restraints excluded: chain F residue 828 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 66 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.149076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.095874 restraints weight = 108560.629| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.58 r_work: 0.3261 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17104 Z= 0.156 Angle : 0.481 6.763 23661 Z= 0.277 Chirality : 0.037 0.145 2660 Planarity : 0.004 0.052 2577 Dihedral : 24.511 66.290 3255 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.65 % Allowed : 4.41 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.21), residues: 1711 helix: 2.26 (0.16), residues: 1052 sheet: -0.12 (0.56), residues: 91 loop : 0.52 (0.29), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 21 TYR 0.016 0.001 TYR F 553 PHE 0.020 0.001 PHE C 465 TRP 0.009 0.001 TRP F 271 HIS 0.003 0.001 HIS F 926 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (17100) covalent geometry : angle 0.47886 / 0.28 (23655) hydrogen bonds : bond 0.03953 / 2.62 ( 971) hydrogen bonds : angle 4.18445 / 2.99 ( 2703) metal coordination : bond 0.00550 / 0.29 ( 4) metal coordination : angle 2.83992 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 322 MET cc_start: 0.8018 (ttm) cc_final: 0.7763 (tpp) REVERT: F 498 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7870 (p) REVERT: F 515 MET cc_start: 0.8487 (tpp) cc_final: 0.8215 (mmm) REVERT: F 895 ASN cc_start: 0.8530 (m-40) cc_final: 0.8191 (p0) REVERT: S 81 ARG cc_start: 0.6382 (mtt-85) cc_final: 0.5864 (mtp180) REVERT: S 152 GLN cc_start: 0.8925 (tp40) cc_final: 0.8599 (tm-30) outliers start: 10 outliers final: 7 residues processed: 83 average time/residue: 0.3420 time to fit residues: 41.6336 Evaluate side-chains 82 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 508 PHE Chi-restraints excluded: chain C residue 573 ARG Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 660 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 39 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 126 optimal weight: 0.0970 chunk 115 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.149174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.095808 restraints weight = 108530.672| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.59 r_work: 0.3246 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17104 Z= 0.155 Angle : 0.471 6.052 23661 Z= 0.271 Chirality : 0.036 0.145 2660 Planarity : 0.004 0.037 2577 Dihedral : 24.187 66.609 3255 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.65 % Allowed : 4.47 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.21), residues: 1711 helix: 2.31 (0.16), residues: 1047 sheet: -0.10 (0.56), residues: 91 loop : 0.53 (0.29), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 749 TYR 0.017 0.001 TYR F 553 PHE 0.029 0.001 PHE C 465 TRP 0.009 0.001 TRP F 271 HIS 0.004 0.001 HIS F 926 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (17100) covalent geometry : angle 0.46853 / 0.27 (23655) hydrogen bonds : bond 0.03821 / 2.53 ( 971) hydrogen bonds : angle 4.11445 / 2.94 ( 2703) metal coordination : bond 0.00470 / 0.25 ( 4) metal coordination : angle 2.76331 / 1.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 322 MET cc_start: 0.7975 (ttm) cc_final: 0.7737 (tpp) REVERT: F 498 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7886 (p) REVERT: F 515 MET cc_start: 0.8538 (tpp) cc_final: 0.8254 (mmm) REVERT: F 895 ASN cc_start: 0.8612 (m-40) cc_final: 0.8250 (p0) outliers start: 10 outliers final: 8 residues processed: 81 average time/residue: 0.3094 time to fit residues: 37.4041 Evaluate side-chains 82 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 508 PHE Chi-restraints excluded: chain C residue 573 ARG Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 566 SER Chi-restraints excluded: chain F residue 660 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 138 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 70 optimal weight: 30.0000 chunk 64 optimal weight: 20.0000 chunk 131 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 177 optimal weight: 50.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 378 ASN C 518 ASN F 344 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.146775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.092928 restraints weight = 108392.898| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.17 r_work: 0.3198 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 17104 Z= 0.385 Angle : 0.588 6.423 23661 Z= 0.333 Chirality : 0.042 0.162 2660 Planarity : 0.004 0.047 2577 Dihedral : 24.021 67.055 3255 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.84 % Allowed : 4.67 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.21), residues: 1711 helix: 1.84 (0.16), residues: 1047 sheet: 0.19 (0.61), residues: 81 loop : 0.10 (0.28), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 779 TYR 0.020 0.002 TYR C 260 PHE 0.018 0.002 PHE S 92 TRP 0.010 0.001 TRP C 167 HIS 0.007 0.002 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00861 / 0.38 (17100) covalent geometry : angle 0.58492 / 0.33 (23655) hydrogen bonds : bond 0.04513 / 2.96 ( 971) hydrogen bonds : angle 4.35133 / 3.11 ( 2703) metal coordination : bond 0.01318 / 0.75 ( 4) metal coordination : angle 3.52284 / 1.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 368 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8558 (pp30) REVERT: F 498 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.8071 (p) REVERT: F 515 MET cc_start: 0.8444 (tpp) cc_final: 0.8153 (mmm) REVERT: S 152 GLN cc_start: 0.8929 (tp40) cc_final: 0.8602 (tm-30) outliers start: 13 outliers final: 7 residues processed: 79 average time/residue: 0.2755 time to fit residues: 32.5103 Evaluate side-chains 78 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 508 PHE Chi-restraints excluded: chain C residue 573 ARG Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 566 SER Chi-restraints excluded: chain F residue 660 SER Chi-restraints excluded: chain S residue 84 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.0980 chunk 39 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 177 optimal weight: 50.0000 chunk 155 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 173 optimal weight: 2.9990 chunk 55 optimal weight: 30.0000 chunk 97 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 118 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.148672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.094331 restraints weight = 110277.423| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.22 r_work: 0.3244 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17104 Z= 0.156 Angle : 0.486 6.308 23661 Z= 0.280 Chirality : 0.037 0.146 2660 Planarity : 0.004 0.046 2577 Dihedral : 23.858 67.269 3255 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.52 % Allowed : 5.06 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.21), residues: 1711 helix: 2.02 (0.16), residues: 1046 sheet: 0.10 (0.62), residues: 81 loop : 0.22 (0.28), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 749 TYR 0.016 0.001 TYR C 377 PHE 0.024 0.001 PHE C 465 TRP 0.010 0.001 TRP F 271 HIS 0.004 0.001 HIS S 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (17100) covalent geometry : angle 0.48380 / 0.28 (23655) hydrogen bonds : bond 0.04038 / 2.67 ( 971) hydrogen bonds : angle 4.19289 / 2.99 ( 2703) metal coordination : bond 0.00573 / 0.31 ( 4) metal coordination : angle 2.91776 / 1.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 368 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8549 (pp30) REVERT: C 688 MET cc_start: -0.4482 (mmt) cc_final: -0.4844 (mmt) REVERT: F 498 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.8025 (p) REVERT: F 515 MET cc_start: 0.8505 (tpp) cc_final: 0.8227 (mmm) REVERT: F 895 ASN cc_start: 0.8586 (m-40) cc_final: 0.8196 (p0) REVERT: S 152 GLN cc_start: 0.8915 (tp40) cc_final: 0.8587 (tm-30) outliers start: 8 outliers final: 5 residues processed: 79 average time/residue: 0.3365 time to fit residues: 39.3945 Evaluate side-chains 77 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 508 PHE Chi-restraints excluded: chain C residue 573 ARG Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 660 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 172 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 60 optimal weight: 30.0000 chunk 145 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 163 optimal weight: 0.7980 chunk 74 optimal weight: 30.0000 chunk 126 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.148183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.094770 restraints weight = 108312.051| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.16 r_work: 0.3252 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17104 Z= 0.166 Angle : 0.485 8.827 23661 Z= 0.277 Chirality : 0.037 0.145 2660 Planarity : 0.004 0.046 2577 Dihedral : 23.565 67.307 3255 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.58 % Allowed : 5.19 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.21), residues: 1711 helix: 2.14 (0.16), residues: 1047 sheet: 0.08 (0.61), residues: 81 loop : 0.27 (0.28), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 749 TYR 0.017 0.001 TYR C 377 PHE 0.028 0.001 PHE C 465 TRP 0.010 0.001 TRP F 271 HIS 0.004 0.001 HIS F 926 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (17100) covalent geometry : angle 0.48311 / 0.28 (23655) hydrogen bonds : bond 0.03861 / 2.55 ( 971) hydrogen bonds : angle 4.10761 / 2.93 ( 2703) metal coordination : bond 0.00518 / 0.28 ( 4) metal coordination : angle 2.68402 / 1.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 368 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8552 (pp30) REVERT: F 515 MET cc_start: 0.8502 (tpp) cc_final: 0.8236 (mmm) REVERT: S 152 GLN cc_start: 0.8891 (tp40) cc_final: 0.8591 (tm-30) outliers start: 9 outliers final: 6 residues processed: 79 average time/residue: 0.3344 time to fit residues: 39.4518 Evaluate side-chains 76 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 508 PHE Chi-restraints excluded: chain C residue 573 ARG Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 660 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 136 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 163 optimal weight: 0.0770 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.148286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.095021 restraints weight = 108157.346| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.15 r_work: 0.3264 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17104 Z= 0.147 Angle : 0.472 8.477 23661 Z= 0.271 Chirality : 0.037 0.145 2660 Planarity : 0.004 0.045 2577 Dihedral : 23.350 67.500 3255 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.45 % Allowed : 5.45 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.21), residues: 1711 helix: 2.18 (0.16), residues: 1047 sheet: 0.08 (0.61), residues: 81 loop : 0.28 (0.28), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 888 TYR 0.016 0.001 TYR F 553 PHE 0.037 0.001 PHE C 465 TRP 0.010 0.001 TRP F 271 HIS 0.005 0.001 HIS F 926 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (17100) covalent geometry : angle 0.47045 / 0.27 (23655) hydrogen bonds : bond 0.03794 / 2.51 ( 971) hydrogen bonds : angle 4.07426 / 2.91 ( 2703) metal coordination : bond 0.00511 / 0.27 ( 4) metal coordination : angle 2.73964 / 1.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 368 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8527 (pp30) REVERT: F 515 MET cc_start: 0.8482 (tpp) cc_final: 0.8235 (mmm) REVERT: F 895 ASN cc_start: 0.8795 (t0) cc_final: 0.8573 (t0) REVERT: S 152 GLN cc_start: 0.8897 (tp40) cc_final: 0.8598 (tm-30) outliers start: 7 outliers final: 4 residues processed: 76 average time/residue: 0.3057 time to fit residues: 34.9932 Evaluate side-chains 73 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 508 PHE Chi-restraints excluded: chain C residue 573 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 93 optimal weight: 0.0470 chunk 119 optimal weight: 0.4980 chunk 106 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 99 optimal weight: 0.0980 chunk 17 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 181 optimal weight: 50.0000 chunk 5 optimal weight: 0.9980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 518 ASN F 718 GLN S 64 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.148725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.095711 restraints weight = 108721.522| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.16 r_work: 0.3308 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17104 Z= 0.108 Angle : 0.461 7.065 23661 Z= 0.263 Chirality : 0.036 0.145 2660 Planarity : 0.003 0.044 2577 Dihedral : 23.015 67.747 3255 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.39 % Allowed : 5.64 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.21), residues: 1711 helix: 2.43 (0.16), residues: 1040 sheet: -0.24 (0.57), residues: 91 loop : 0.45 (0.29), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 947 TYR 0.016 0.001 TYR F 553 PHE 0.019 0.001 PHE C 465 TRP 0.012 0.001 TRP F 271 HIS 0.004 0.001 HIS F 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (17100) covalent geometry : angle 0.45935 / 0.26 (23655) hydrogen bonds : bond 0.03559 / 2.36 ( 971) hydrogen bonds : angle 3.96170 / 2.83 ( 2703) metal coordination : bond 0.00338 / 0.18 ( 4) metal coordination : angle 2.45758 / 1.23 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 368 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8562 (pp30) REVERT: F 515 MET cc_start: 0.8445 (tpp) cc_final: 0.8200 (mmm) REVERT: F 895 ASN cc_start: 0.8726 (t0) cc_final: 0.8501 (t0) REVERT: S 152 GLN cc_start: 0.8866 (tp40) cc_final: 0.8590 (tm-30) outliers start: 6 outliers final: 5 residues processed: 75 average time/residue: 0.3139 time to fit residues: 35.6904 Evaluate side-chains 75 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 508 PHE Chi-restraints excluded: chain C residue 573 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 141 optimal weight: 0.0970 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 180 optimal weight: 30.0000 chunk 16 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 172 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.148400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.095219 restraints weight = 108529.507| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.15 r_work: 0.3294 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17104 Z= 0.147 Angle : 0.467 7.628 23661 Z= 0.268 Chirality : 0.037 0.144 2660 Planarity : 0.003 0.046 2577 Dihedral : 22.878 67.924 3255 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.39 % Allowed : 5.64 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.21), residues: 1711 helix: 2.35 (0.16), residues: 1049 sheet: 0.10 (0.60), residues: 81 loop : 0.42 (0.29), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 81 TYR 0.016 0.001 TYR F 553 PHE 0.029 0.001 PHE C 465 TRP 0.010 0.001 TRP C 21 HIS 0.004 0.001 HIS F 926 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (17100) covalent geometry : angle 0.46466 / 0.27 (23655) hydrogen bonds : bond 0.03669 / 2.43 ( 971) hydrogen bonds : angle 3.97284 / 2.84 ( 2703) metal coordination : bond 0.00542 / 0.29 ( 4) metal coordination : angle 2.67627 / 1.34 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11913.00 seconds wall clock time: 202 minutes 9.71 seconds (12129.71 seconds total)