Starting phenix.real_space_refine on Sat Feb 7 11:42:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xzj_72358/02_2026/9xzj_72358_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xzj_72358/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9xzj_72358/02_2026/9xzj_72358_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xzj_72358/02_2026/9xzj_72358_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xzj_72358/02_2026/9xzj_72358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xzj_72358/02_2026/9xzj_72358.map" } 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-2.0-5952/lib/python3.9/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: 5.22, per 1000 atoms: 0.16 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: 2.93 Conformation dependent library (CDL) restraints added in 870.2 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: 6.09 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: 8.11 Time building geometry restraints manager: 3.91 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 1.531 1.606 -0.075 1.60e-02 3.91e+03 2.20e+01 bond pdb=" C6 AGS F1001 " pdb=" N6 AGS F1001 " ideal model delta sigma weight residual 1.335 1.382 -0.047 1.00e-02 1.00e+04 2.19e+01 bond pdb=" O2B AGS F1001 " pdb=" PB AGS F1001 " ideal model delta sigma weight residual 1.531 1.605 -0.074 1.60e-02 3.91e+03 2.11e+01 bond pdb=" PG AGS F1001 " pdb=" S1G AGS F1001 " ideal model delta sigma weight residual 1.949 1.861 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C5 AGS F1001 " pdb=" N7 AGS F1001 " ideal model delta sigma weight residual 1.387 1.352 0.035 1.00e-02 1.00e+04 1.25e+01 ... (remaining 32503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 58744 2.64 - 5.29: 109 5.29 - 7.93: 4 7.93 - 10.57: 1 10.57 - 13.21: 2 Bond angle restraints: 58860 Sorted by residual: angle pdb=" C5 AGS F1001 " pdb=" N7 AGS F1001 " pdb=" C8 AGS F1001 " ideal model delta sigma weight residual 103.67 109.27 -5.60 4.26e-01 5.51e+00 1.72e+02 angle pdb=" C5 AGS F1001 " pdb=" C4 AGS F1001 " pdb=" N3 AGS F1001 " ideal model delta sigma weight residual 126.80 119.15 7.65 7.41e-01 1.82e+00 1.07e+02 angle pdb=" C4 AGS F1001 " pdb=" C5 AGS F1001 " pdb=" N7 AGS F1001 " ideal model delta sigma weight residual 110.73 107.27 3.46 4.52e-01 4.89e+00 5.85e+01 angle pdb=" N1 AGS F1001 " pdb=" C2 AGS F1001 " pdb=" N3 AGS F1001 " ideal model delta sigma weight residual 128.80 122.43 6.37 8.41e-01 1.41e+00 5.75e+01 angle pdb=" N3 AGS F1001 " pdb=" C4 AGS F1001 " pdb=" N9 AGS F1001 " ideal model delta sigma weight residual 127.16 134.74 -7.58 1.06e+00 8.92e-01 5.13e+01 ... (remaining 58855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.52: 13643 32.52 - 65.04: 1047 65.04 - 97.55: 10 97.55 - 130.07: 0 130.07 - 162.59: 1 Dihedral angle restraints: 14701 sinusoidal: 8759 harmonic: 5942 Sorted by residual: dihedral pdb=" O1A AGS F1001 " pdb=" O3A AGS F1001 " pdb=" PA AGS F1001 " pdb=" PB AGS F1001 " ideal model delta sinusoidal sigma weight residual -67.73 94.86 -162.59 1 3.00e+01 1.11e-03 2.08e+01 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=" N ARG F 536 " pdb=" CA ARG F 536 " pdb=" CB ARG F 536 " pdb=" CG ARG F 536 " ideal model delta sinusoidal sigma weight residual -60.00 -118.21 58.21 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 14698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1872 0.035 - 0.069: 604 0.069 - 0.104: 131 0.104 - 0.139: 52 0.139 - 0.173: 3 Chirality restraints: 2662 Sorted by residual: chirality pdb=" C1' AGS F1001 " pdb=" C2' AGS F1001 " pdb=" N9 AGS F1001 " pdb=" O4' AGS F1001 " both_signs ideal model delta sigma weight residual False 2.41 2.58 -0.17 2.00e-01 2.50e+01 7.49e-01 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 -2.49 -2.65 0.16 2.00e-01 2.50e+01 6.61e-01 chirality pdb=" CA ILE C 669 " pdb=" N ILE C 669 " pdb=" C ILE C 669 " pdb=" CB ILE C 669 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 2659 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: 10.200 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: 0.230 Extract box with map and model: 0.750 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 41.760 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 : 0.004 0.088 17104 Z= 0.186 Angle : 0.518 13.213 23661 Z= 0.330 Chirality : 0.037 0.173 2662 Planarity : 0.003 0.033 2577 Dihedral : 19.326 162.590 6718 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 covalent geometry : bond 0.00384 (17100) covalent geometry : angle 0.51718 (23655) hydrogen bonds : bond 0.11487 ( 971) hydrogen bonds : angle 5.15248 ( 2703) metal coordination : bond 0.04000 ( 4) metal coordination : angle 2.21478 ( 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 : 0.867 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: 0.4765 time to fit residues: 77.6730 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 : 0.827 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4565 r_free = 0.4565 target = 0.150590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.097311 restraints weight = 109352.405| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.23 r_work: 0.3336 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17104 Z= 0.159 Angle : 0.491 6.624 23661 Z= 0.286 Chirality : 0.037 0.144 2662 Planarity : 0.004 0.040 2577 Dihedral : 25.002 169.563 3237 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.71 % Allowed : 3.57 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.21), residues: 1711 helix: 2.42 (0.16), residues: 1061 sheet: -0.05 (0.60), residues: 84 loop : 0.56 (0.29), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 947 TYR 0.017 0.001 TYR F 553 PHE 0.010 0.001 PHE C 402 TRP 0.010 0.001 TRP F 271 HIS 0.006 0.001 HIS C 524 Details of bonding type rmsd covalent geometry : bond 0.00348 (17100) covalent geometry : angle 0.48902 (23655) hydrogen bonds : bond 0.04386 ( 971) hydrogen bonds : angle 4.36104 ( 2703) metal coordination : bond 0.00432 ( 4) metal coordination : angle 2.71565 ( 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 92 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.839 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: symmetry clash REVERT: C 261 MET cc_start: 0.7788 (mtm) cc_final: 0.7569 (mtm) REVERT: C 322 MET cc_start: 0.7975 (ttm) cc_final: 0.7512 (tpp) REVERT: F 895 ASN cc_start: 0.8458 (m-40) cc_final: 0.8166 (p0) outliers start: 11 outliers final: 7 residues processed: 87 average time/residue: 0.3878 time to fit residues: 47.3167 Evaluate side-chains 83 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 828 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 156 optimal weight: 0.7980 chunk 54 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 518 ASN F 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.148222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.094695 restraints weight = 108604.447| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.18 r_work: 0.3245 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1554 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= 0.234 Angle : 0.516 5.131 23661 Z= 0.299 Chirality : 0.038 0.146 2662 Planarity : 0.004 0.037 2577 Dihedral : 24.567 177.760 3237 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.78 % Allowed : 4.09 % Favored : 95.14 % 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: 2.22 (0.21), residues: 1711 helix: 2.18 (0.16), residues: 1054 sheet: -0.06 (0.57), residues: 91 loop : 0.49 (0.29), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 321 TYR 0.020 0.002 TYR F 553 PHE 0.014 0.001 PHE S 92 TRP 0.010 0.001 TRP F 271 HIS 0.007 0.001 HIS F 926 Details of bonding type rmsd covalent geometry : bond 0.00524 (17100) covalent geometry : angle 0.51340 (23655) hydrogen bonds : bond 0.04280 ( 971) hydrogen bonds : angle 4.24179 ( 2703) metal coordination : bond 0.00925 ( 4) metal coordination : angle 3.40880 ( 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: 12 poor density : 74 time to evaluate : 0.737 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: 0.7980 (ttm) cc_final: 0.7751 (tpp) REVERT: C 368 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8521 (pp30) REVERT: F 498 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7959 (p) REVERT: F 515 MET cc_start: 0.8520 (tpp) cc_final: 0.8202 (mmm) REVERT: F 895 ASN cc_start: 0.8542 (m-40) cc_final: 0.8209 (p0) REVERT: S 152 GLN cc_start: 0.8918 (tp40) cc_final: 0.8588 (tm-30) outliers start: 12 outliers final: 8 residues processed: 82 average time/residue: 0.3612 time to fit residues: 42.2640 Evaluate side-chains 81 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 C residue 608 MET 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 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: 9.9990 chunk 116 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 518 ASN F 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.148680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.095368 restraints weight = 108454.187| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.17 r_work: 0.3269 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17104 Z= 0.163 Angle : 0.475 6.630 23661 Z= 0.276 Chirality : 0.037 0.146 2662 Planarity : 0.004 0.052 2577 Dihedral : 24.361 176.026 3237 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: 2.27 (0.21), residues: 1711 helix: 2.26 (0.16), residues: 1049 sheet: -0.19 (0.57), residues: 91 loop : 0.47 (0.29), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 21 TYR 0.016 0.001 TYR C 377 PHE 0.011 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 covalent geometry : bond 0.00362 (17100) covalent geometry : angle 0.47331 (23655) hydrogen bonds : bond 0.03867 ( 971) hydrogen bonds : angle 4.10186 ( 2703) metal coordination : bond 0.00537 ( 4) metal coordination : angle 2.75642 ( 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 83 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.846 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: C 368 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8528 (pp30) REVERT: F 498 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7942 (p) REVERT: F 515 MET cc_start: 0.8516 (tpp) cc_final: 0.8153 (mmm) REVERT: S 152 GLN cc_start: 0.8908 (tp40) cc_final: 0.8593 (tm-30) outliers start: 10 outliers final: 8 residues processed: 81 average time/residue: 0.3664 time to fit residues: 42.2212 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 : 1.029 ------------------------------------------------------------------------------- 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 194 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 39 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.148306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.094997 restraints weight = 108685.913| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.17 r_work: 0.3263 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17104 Z= 0.175 Angle : 0.476 7.519 23661 Z= 0.277 Chirality : 0.037 0.145 2662 Planarity : 0.004 0.041 2577 Dihedral : 24.190 176.132 3237 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.65 % Allowed : 4.67 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.21), residues: 1711 helix: 2.29 (0.16), residues: 1045 sheet: -0.24 (0.57), residues: 91 loop : 0.45 (0.29), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 888 TYR 0.016 0.001 TYR F 553 PHE 0.010 0.001 PHE C 402 TRP 0.008 0.001 TRP F 271 HIS 0.005 0.001 HIS F 926 Details of bonding type rmsd covalent geometry : bond 0.00390 (17100) covalent geometry : angle 0.47428 (23655) hydrogen bonds : bond 0.03823 ( 971) hydrogen bonds : angle 4.07785 ( 2703) metal coordination : bond 0.00583 ( 4) metal coordination : angle 2.69947 ( 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 : 0.935 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: F 515 MET cc_start: 0.8507 (tpp) cc_final: 0.8159 (mmm) REVERT: F 895 ASN cc_start: 0.8608 (t0) cc_final: 0.8196 (p0) REVERT: F 906 MET cc_start: 0.8988 (mmt) cc_final: 0.8787 (mmt) REVERT: S 152 GLN cc_start: 0.8908 (tp40) cc_final: 0.8597 (tm-30) outliers start: 10 outliers final: 7 residues processed: 81 average time/residue: 0.3299 time to fit residues: 38.2914 Evaluate side-chains 79 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 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: 30.0000 chunk 38 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 131 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 177 optimal weight: 20.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 378 ASN C 386 ASN C 518 ASN F 194 GLN F 344 ASN S 108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.146038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.092032 restraints weight = 108718.990| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.18 r_work: 0.3187 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 17104 Z= 0.385 Angle : 0.585 6.005 23661 Z= 0.336 Chirality : 0.043 0.194 2662 Planarity : 0.005 0.052 2577 Dihedral : 23.973 178.900 3237 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.91 % Allowed : 4.73 % Favored : 94.36 % 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: 1.59 (0.21), residues: 1711 helix: 1.75 (0.16), residues: 1046 sheet: 0.06 (0.62), residues: 81 loop : 0.04 (0.28), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 321 TYR 0.020 0.002 TYR C 260 PHE 0.018 0.002 PHE S 92 TRP 0.011 0.002 TRP F 532 HIS 0.007 0.002 HIS F 926 Details of bonding type rmsd covalent geometry : bond 0.00868 (17100) covalent geometry : angle 0.58179 (23655) hydrogen bonds : bond 0.04568 ( 971) hydrogen bonds : angle 4.35927 ( 2703) metal coordination : bond 0.01840 ( 4) metal coordination : angle 3.72747 ( 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: 14 poor density : 69 time to evaluate : 0.755 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: 0.8832 (OUTLIER) cc_final: 0.8557 (pp30) REVERT: F 515 MET cc_start: 0.8518 (tpp) cc_final: 0.8225 (mmm) REVERT: F 895 ASN cc_start: 0.8811 (t0) cc_final: 0.8302 (p0) REVERT: S 152 GLN cc_start: 0.8892 (tp40) cc_final: 0.8604 (tm-30) outliers start: 14 outliers final: 8 residues processed: 81 average time/residue: 0.3199 time to fit residues: 37.9157 Evaluate side-chains 76 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 453 PHE Chi-restraints excluded: chain C residue 508 PHE Chi-restraints excluded: chain C residue 573 ARG Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 566 SER Chi-restraints excluded: chain F residue 660 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.1980 chunk 39 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 177 optimal weight: 20.0000 chunk 155 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.148053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.094482 restraints weight = 108560.427| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.16 r_work: 0.3243 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17104 Z= 0.159 Angle : 0.493 7.672 23661 Z= 0.286 Chirality : 0.037 0.146 2662 Planarity : 0.004 0.049 2577 Dihedral : 23.798 177.467 3237 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.71 % Allowed : 5.19 % 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: 1.94 (0.21), residues: 1711 helix: 2.03 (0.16), residues: 1045 sheet: -0.01 (0.62), residues: 81 loop : 0.19 (0.28), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 21 TYR 0.017 0.001 TYR C 377 PHE 0.009 0.001 PHE C 402 TRP 0.010 0.001 TRP F 271 HIS 0.005 0.001 HIS F 697 Details of bonding type rmsd covalent geometry : bond 0.00355 (17100) covalent geometry : angle 0.49168 (23655) hydrogen bonds : bond 0.03938 ( 971) hydrogen bonds : angle 4.11554 ( 2703) metal coordination : bond 0.00537 ( 4) metal coordination : angle 2.67625 ( 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 81 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.825 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 241 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6815 (tm-30) REVERT: C 368 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8546 (pp30) REVERT: F 515 MET cc_start: 0.8497 (tpp) cc_final: 0.8212 (mmm) REVERT: F 895 ASN cc_start: 0.8764 (t0) cc_final: 0.8536 (t0) REVERT: S 152 GLN cc_start: 0.8875 (tp40) cc_final: 0.8604 (tm-30) outliers start: 11 outliers final: 8 residues processed: 79 average time/residue: 0.3571 time to fit residues: 41.4459 Evaluate side-chains 80 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 241 GLU Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 508 PHE Chi-restraints excluded: chain C residue 573 ARG Chi-restraints excluded: chain C residue 574 HIS Chi-restraints excluded: chain F residue 157 ASP 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: 4.9990 chunk 68 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 145 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 56 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 chunk 137 optimal weight: 0.0980 chunk 163 optimal weight: 0.0980 chunk 74 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 518 ASN S 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.148061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.094835 restraints weight = 108449.838| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.15 r_work: 0.3280 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17104 Z= 0.140 Angle : 0.473 6.147 23661 Z= 0.273 Chirality : 0.037 0.151 2662 Planarity : 0.003 0.048 2577 Dihedral : 23.533 176.758 3237 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.52 % Allowed : 5.64 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.21), residues: 1711 helix: 2.24 (0.16), residues: 1045 sheet: -0.11 (0.61), residues: 81 loop : 0.31 (0.29), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 536 TYR 0.016 0.001 TYR F 553 PHE 0.009 0.001 PHE C 402 TRP 0.011 0.001 TRP F 271 HIS 0.005 0.001 HIS F 926 Details of bonding type rmsd covalent geometry : bond 0.00313 (17100) covalent geometry : angle 0.47094 (23655) hydrogen bonds : bond 0.03622 ( 971) hydrogen bonds : angle 3.99430 ( 2703) metal coordination : bond 0.00414 ( 4) metal coordination : angle 2.53297 ( 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: 8 poor density : 72 time to evaluate : 0.790 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: C 368 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8567 (pp30) REVERT: F 515 MET cc_start: 0.8494 (tpp) cc_final: 0.8221 (mmm) REVERT: F 895 ASN cc_start: 0.8756 (t0) cc_final: 0.8519 (t0) REVERT: S 152 GLN cc_start: 0.8847 (tp40) cc_final: 0.8584 (tm-30) outliers start: 8 outliers final: 7 residues processed: 79 average time/residue: 0.3267 time to fit residues: 37.8296 Evaluate side-chains 79 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 574 HIS 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: 0.9980 chunk 56 optimal weight: 20.0000 chunk 163 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 518 ASN F 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.147612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.094303 restraints weight = 108511.096| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.15 r_work: 0.3252 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17104 Z= 0.173 Angle : 0.484 8.247 23661 Z= 0.279 Chirality : 0.037 0.144 2662 Planarity : 0.004 0.050 2577 Dihedral : 23.320 176.065 3237 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.71 % Allowed : 5.64 % Favored : 93.64 % 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: 2.22 (0.21), residues: 1711 helix: 2.26 (0.16), residues: 1046 sheet: -0.01 (0.61), residues: 81 loop : 0.33 (0.29), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 21 TYR 0.016 0.001 TYR C 377 PHE 0.010 0.001 PHE S 92 TRP 0.010 0.001 TRP C 21 HIS 0.004 0.001 HIS F 926 Details of bonding type rmsd covalent geometry : bond 0.00389 (17100) covalent geometry : angle 0.48263 (23655) hydrogen bonds : bond 0.03691 ( 971) hydrogen bonds : angle 3.99922 ( 2703) metal coordination : bond 0.00647 ( 4) metal coordination : angle 2.68711 ( 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 82 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.841 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: C 241 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6864 (tm-30) REVERT: C 368 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8537 (pp30) REVERT: F 895 ASN cc_start: 0.8735 (t0) cc_final: 0.8486 (t0) REVERT: F 906 MET cc_start: 0.9045 (mmt) cc_final: 0.8837 (mmt) REVERT: S 152 GLN cc_start: 0.8876 (tp40) cc_final: 0.8606 (tm-30) outliers start: 11 outliers final: 7 residues processed: 81 average time/residue: 0.3364 time to fit residues: 39.8278 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 : 0.888 ------------------------------------------------------------------------------- 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 241 GLU 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 C residue 574 HIS Chi-restraints excluded: chain F residue 566 SER Chi-restraints excluded: chain F residue 660 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 93 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 99 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 181 optimal weight: 50.0000 chunk 5 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 518 ASN F 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.148022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.094749 restraints weight = 108692.035| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.15 r_work: 0.3281 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17104 Z= 0.145 Angle : 0.473 5.930 23661 Z= 0.273 Chirality : 0.037 0.144 2662 Planarity : 0.003 0.050 2577 Dihedral : 23.199 176.030 3237 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.65 % Allowed : 5.58 % Favored : 93.77 % 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: 2.26 (0.21), residues: 1711 helix: 2.27 (0.16), residues: 1050 sheet: -0.04 (0.61), residues: 81 loop : 0.36 (0.29), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 536 TYR 0.016 0.001 TYR F 553 PHE 0.009 0.001 PHE C 402 TRP 0.011 0.001 TRP C 21 HIS 0.004 0.001 HIS F 926 Details of bonding type rmsd covalent geometry : bond 0.00323 (17100) covalent geometry : angle 0.47115 (23655) hydrogen bonds : bond 0.03581 ( 971) hydrogen bonds : angle 3.96730 ( 2703) metal coordination : bond 0.00466 ( 4) metal coordination : angle 2.41453 ( 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 80 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.885 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: C 368 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8534 (pp30) REVERT: C 719 MET cc_start: 0.1475 (ttm) cc_final: 0.1210 (ptp) REVERT: F 515 MET cc_start: 0.8447 (tpp) cc_final: 0.8103 (mmm) REVERT: F 895 ASN cc_start: 0.8699 (t0) cc_final: 0.8447 (t0) REVERT: F 906 MET cc_start: 0.9004 (mmt) cc_final: 0.8796 (mmt) REVERT: S 152 GLN cc_start: 0.8860 (tp40) cc_final: 0.8607 (tm-30) outliers start: 10 outliers final: 8 residues processed: 79 average time/residue: 0.3148 time to fit residues: 37.5928 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 : 0.891 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 574 HIS Chi-restraints excluded: chain F residue 566 SER Chi-restraints excluded: chain F residue 660 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 141 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 180 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 74 optimal weight: 30.0000 chunk 172 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 518 ASN F 194 GLN F 727 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.147830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.094530 restraints weight = 108625.939| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.15 r_work: 0.3259 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17104 Z= 0.157 Angle : 0.474 6.354 23661 Z= 0.274 Chirality : 0.037 0.142 2662 Planarity : 0.004 0.051 2577 Dihedral : 22.968 175.141 3237 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.65 % Allowed : 5.58 % Favored : 93.77 % 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: 2.26 (0.21), residues: 1711 helix: 2.30 (0.16), residues: 1049 sheet: -0.00 (0.61), residues: 81 loop : 0.30 (0.29), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 947 TYR 0.016 0.001 TYR F 553 PHE 0.009 0.001 PHE S 92 TRP 0.010 0.001 TRP C 21 HIS 0.004 0.001 HIS F 926 Details of bonding type rmsd covalent geometry : bond 0.00350 (17100) covalent geometry : angle 0.47219 (23655) hydrogen bonds : bond 0.03570 ( 971) hydrogen bonds : angle 3.95336 ( 2703) metal coordination : bond 0.00549 ( 4) metal coordination : angle 2.45693 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13345.47 seconds wall clock time: 226 minutes 3.87 seconds (13563.87 seconds total)