Starting phenix.real_space_refine on Sat Sep 12 11:34:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rkv_4912/09_2026/6rkv_4912.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rkv_4912/09_2026/6rkv_4912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rkv_4912/09_2026/6rkv_4912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rkv_4912/09_2026/6rkv_4912.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rkv_4912/09_2026/6rkv_4912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rkv_4912/09_2026/6rkv_4912.map" } resolution = 4.6 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= 0.002 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: 5 Type Number sf(0) Gaussians P 64 5.49 5 S 54 5.16 5 C 9522 2.51 5 N 2750 2.21 5 O 3070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15460 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4022 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 21, 'TRANS': 489} Chain breaks: 2 Chain: "B" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3052 Classifications: {'peptide': 381} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 363} Chain breaks: 1 Chain: "C" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4022 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 21, 'TRANS': 489} Chain breaks: 2 Chain: "D" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3052 Classifications: {'peptide': 381} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 363} Chain breaks: 1 Chain: "F" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "E" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "G" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 368 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "H" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 368 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Time building chain proxies: 3.57, per 1000 atoms: 0.23 Number of scatterers: 15460 At special positions: 0 Unit cell: (122.32, 146.96, 123.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 64 15.00 O 3070 8.00 N 2750 7.00 C 9522 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 645.5 milliseconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3340 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 22 sheets defined 50.0% alpha, 10.4% beta 32 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 15 through 32 removed outlier: 3.934A pdb=" N SER A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 56 Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 95 through 98 removed outlier: 3.635A pdb=" N LEU A 98 " --> pdb=" O PRO A 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 98' Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.604A pdb=" N HIS A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 235 removed outlier: 4.451A pdb=" N ILE A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 283 Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 346 through 389 removed outlier: 3.518A pdb=" N ALA A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 402 through 413 Processing helix chain 'A' and resid 451 through 460 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.765A pdb=" N LYS A 465 " --> pdb=" O ARG A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 494 Processing helix chain 'A' and resid 494 through 513 removed outlier: 3.931A pdb=" N LEU A 498 " --> pdb=" O SER A 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 removed outlier: 4.415A pdb=" N SER B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 Processing helix chain 'B' and resid 500 through 518 Processing helix chain 'B' and resid 518 through 524 removed outlier: 4.023A pdb=" N VAL B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 577 through 598 Processing helix chain 'B' and resid 602 through 609 removed outlier: 4.061A pdb=" N LEU B 606 " --> pdb=" O PRO B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 621 removed outlier: 3.670A pdb=" N SER B 621 " --> pdb=" O ALA B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 641 removed outlier: 3.680A pdb=" N VAL B 626 " --> pdb=" O ASP B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 Processing helix chain 'B' and resid 684 through 699 Processing helix chain 'B' and resid 718 through 732 Processing helix chain 'B' and resid 741 through 745 removed outlier: 4.242A pdb=" N MET B 745 " --> pdb=" O LEU B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 772 through 778 removed outlier: 4.205A pdb=" N THR B 778 " --> pdb=" O ASP B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 786 Processing helix chain 'C' and resid 15 through 32 removed outlier: 3.933A pdb=" N SER C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 56 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 82 through 94 Processing helix chain 'C' and resid 95 through 98 removed outlier: 3.636A pdb=" N LEU C 98 " --> pdb=" O PRO C 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 95 through 98' Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 204 through 212 removed outlier: 3.605A pdb=" N HIS C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 235 removed outlier: 4.451A pdb=" N ILE C 229 " --> pdb=" O GLY C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 283 Processing helix chain 'C' and resid 313 through 324 Processing helix chain 'C' and resid 346 through 389 removed outlier: 3.518A pdb=" N ALA C 382 " --> pdb=" O HIS C 378 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 402 through 413 Processing helix chain 'C' and resid 451 through 460 Processing helix chain 'C' and resid 462 through 466 removed outlier: 3.765A pdb=" N LYS C 465 " --> pdb=" O ARG C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 494 Processing helix chain 'C' and resid 494 through 513 removed outlier: 3.931A pdb=" N LEU C 498 " --> pdb=" O SER C 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 436 removed outlier: 4.415A pdb=" N SER D 431 " --> pdb=" O SER D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 472 Processing helix chain 'D' and resid 500 through 518 Processing helix chain 'D' and resid 518 through 524 removed outlier: 4.023A pdb=" N VAL D 522 " --> pdb=" O MET D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 Processing helix chain 'D' and resid 577 through 598 Processing helix chain 'D' and resid 602 through 609 removed outlier: 4.061A pdb=" N LEU D 606 " --> pdb=" O PRO D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 621 removed outlier: 3.669A pdb=" N SER D 621 " --> pdb=" O ALA D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 641 removed outlier: 3.680A pdb=" N VAL D 626 " --> pdb=" O ASP D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 684 Processing helix chain 'D' and resid 684 through 699 Processing helix chain 'D' and resid 718 through 732 Processing helix chain 'D' and resid 741 through 745 removed outlier: 4.241A pdb=" N MET D 745 " --> pdb=" O LEU D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 755 Processing helix chain 'D' and resid 772 through 778 removed outlier: 4.205A pdb=" N THR D 778 " --> pdb=" O ASP D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 780 through 786 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 3.702A pdb=" N LYS A 64 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 174 Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 239 removed outlier: 3.730A pdb=" N GLY A 238 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 245 through 250 removed outlier: 6.961A pdb=" N ARG A 245 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 247 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU A 257 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A 306 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA A 291 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 335 through 337 removed outlier: 3.827A pdb=" N ALA A 336 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 441 through 446 removed outlier: 6.158A pdb=" N GLU B 419 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU B 444 " --> pdb=" O GLU B 419 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N TYR B 421 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU B 446 " --> pdb=" O TYR B 421 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 423 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU B 420 " --> pdb=" O ILE B 494 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 542 through 546 Processing sheet with id=AB1, first strand: chain 'B' and resid 565 through 566 removed outlier: 3.664A pdb=" N THR B 565 " --> pdb=" O GLU B 708 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B 708 " --> pdb=" O THR B 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 653 removed outlier: 3.537A pdb=" N VAL B 664 " --> pdb=" O TYR B 675 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.701A pdb=" N LYS C 64 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB5, first strand: chain 'C' and resid 172 through 174 Processing sheet with id=AB6, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AB7, first strand: chain 'C' and resid 237 through 239 removed outlier: 3.730A pdb=" N GLY C 238 " --> pdb=" O ILE C 332 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 245 through 250 removed outlier: 6.960A pdb=" N ARG C 245 " --> pdb=" O HIS C 262 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 247 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLU C 257 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU C 306 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA C 291 " --> pdb=" O GLU C 306 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 335 through 337 removed outlier: 3.828A pdb=" N ALA C 336 " --> pdb=" O LYS C 343 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 441 through 446 removed outlier: 6.158A pdb=" N GLU D 419 " --> pdb=" O ALA D 442 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LEU D 444 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR D 421 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU D 446 " --> pdb=" O TYR D 421 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL D 423 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU D 420 " --> pdb=" O ILE D 494 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 542 through 546 Processing sheet with id=AC3, first strand: chain 'D' and resid 565 through 566 removed outlier: 3.664A pdb=" N THR D 565 " --> pdb=" O GLU D 708 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU D 708 " --> pdb=" O THR D 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 646 through 653 removed outlier: 3.536A pdb=" N VAL D 664 " --> pdb=" O TYR D 675 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 1992 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 3.36 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4540 1.34 - 1.45: 2427 1.45 - 1.57: 8655 1.57 - 1.69: 124 1.69 - 1.81: 102 Bond restraints: 15848 Sorted by residual: bond pdb=" C3' DT G 27 " pdb=" C2' DT G 27 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.96e+00 bond pdb=" C3' DA E 6 " pdb=" C2' DA E 6 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.95e+00 bond pdb=" C3' DT H 27 " pdb=" C2' DT H 27 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.83e+00 bond pdb=" C3' DG H 24 " pdb=" C2' DG H 24 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.49e+00 bond pdb=" C3' DA F 6 " pdb=" C2' DA F 6 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.27e+00 ... (remaining 15843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 21199 1.76 - 3.53: 445 3.53 - 5.29: 31 5.29 - 7.06: 11 7.06 - 8.82: 6 Bond angle restraints: 21692 Sorted by residual: angle pdb=" O4' DA H 17 " pdb=" C4' DA H 17 " pdb=" C3' DA H 17 " ideal model delta sigma weight residual 106.00 102.56 3.44 6.00e-01 2.78e+00 3.28e+01 angle pdb=" O4' DA G 17 " pdb=" C4' DA G 17 " pdb=" C3' DA G 17 " ideal model delta sigma weight residual 106.00 102.58 3.42 6.00e-01 2.78e+00 3.24e+01 angle pdb=" O4' DC G 19 " pdb=" C4' DC G 19 " pdb=" C3' DC G 19 " ideal model delta sigma weight residual 106.00 102.63 3.37 6.00e-01 2.78e+00 3.16e+01 angle pdb=" O4' DC H 19 " pdb=" C4' DC H 19 " pdb=" C3' DC H 19 " ideal model delta sigma weight residual 106.00 102.66 3.34 6.00e-01 2.78e+00 3.09e+01 angle pdb=" O4' DC H 25 " pdb=" C4' DC H 25 " pdb=" C3' DC H 25 " ideal model delta sigma weight residual 106.00 103.02 2.98 6.00e-01 2.78e+00 2.47e+01 ... (remaining 21687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.11: 9148 28.11 - 56.23: 366 56.23 - 84.34: 34 84.34 - 112.45: 0 112.45 - 140.56: 4 Dihedral angle restraints: 9552 sinusoidal: 4376 harmonic: 5176 Sorted by residual: dihedral pdb=" CA ALA D 655 " pdb=" C ALA D 655 " pdb=" N GLU D 656 " pdb=" CA GLU D 656 " ideal model delta harmonic sigma weight residual 180.00 160.88 19.12 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ALA B 655 " pdb=" C ALA B 655 " pdb=" N GLU B 656 " pdb=" CA GLU B 656 " ideal model delta harmonic sigma weight residual 180.00 160.92 19.08 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" C4' DT H 26 " pdb=" C3' DT H 26 " pdb=" O3' DT H 26 " pdb=" P DT H 27 " ideal model delta sinusoidal sigma weight residual 220.00 79.44 140.56 1 3.50e+01 8.16e-04 1.39e+01 ... (remaining 9549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1814 0.040 - 0.080: 468 0.080 - 0.121: 158 0.121 - 0.161: 2 0.161 - 0.201: 2 Chirality restraints: 2444 Sorted by residual: chirality pdb=" CA ASN D 484 " pdb=" N ASN D 484 " pdb=" C ASN D 484 " pdb=" CB ASN D 484 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ASN B 484 " pdb=" N ASN B 484 " pdb=" C ASN B 484 " pdb=" CB ASN B 484 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" C3' DA G 21 " pdb=" C4' DA G 21 " pdb=" O3' DA G 21 " pdb=" C2' DA G 21 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 2441 not shown) Planarity restraints: 2610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 780 " -0.016 2.00e-02 2.50e+03 3.13e-02 9.79e+00 pdb=" C LEU B 780 " 0.054 2.00e-02 2.50e+03 pdb=" O LEU B 780 " -0.020 2.00e-02 2.50e+03 pdb=" N MET B 781 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 780 " 0.016 2.00e-02 2.50e+03 3.12e-02 9.74e+00 pdb=" C LEU D 780 " -0.054 2.00e-02 2.50e+03 pdb=" O LEU D 780 " 0.020 2.00e-02 2.50e+03 pdb=" N MET D 781 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 182 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO C 183 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 183 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 183 " -0.023 5.00e-02 4.00e+02 ... (remaining 2607 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2771 2.78 - 3.31: 14085 3.31 - 3.84: 23957 3.84 - 4.37: 25913 4.37 - 4.90: 44911 Nonbonded interactions: 111637 Sorted by model distance: nonbonded pdb=" OE2 GLU D 454 " pdb=" NH1 ARG D 516 " model vdw 2.246 3.120 nonbonded pdb=" OE2 GLU B 454 " pdb=" NH1 ARG B 516 " model vdw 2.247 3.120 nonbonded pdb=" OD2 ASP A 39 " pdb=" NH2 ARG A 46 " model vdw 2.259 3.120 nonbonded pdb=" OD2 ASP C 39 " pdb=" NH2 ARG C 46 " model vdw 2.259 3.120 nonbonded pdb=" O LYS B 538 " pdb=" OG SER B 735 " model vdw 2.282 3.040 ... (remaining 111632 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'E' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 4 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'F' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.230 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 : 0.003 0.026 15848 Z= 0.235 Angle : 0.575 8.819 21692 Z= 0.413 Chirality : 0.039 0.201 2444 Planarity : 0.005 0.041 2610 Dihedral : 13.181 140.565 6212 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -1.73 (0.19), residues: 1764 helix: 0.55 (0.17), residues: 836 sheet: -1.81 (0.35), residues: 210 loop : -3.10 (0.20), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 46 TYR 0.011 0.001 TYR A 266 PHE 0.013 0.001 PHE B 514 TRP 0.011 0.001 TRP C 415 HIS 0.005 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.23 (15848) covalent geometry : angle 0.57497 / 0.41 (21692) hydrogen bonds : bond 0.16646 / 10.95 ( 770) hydrogen bonds : angle 5.39648 / 3.82 ( 2148) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.165 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: A 113 ASP cc_start: 0.8785 (m-30) cc_final: 0.7539 (p0) REVERT: A 306 GLU cc_start: 0.8142 (tt0) cc_final: 0.7845 (tm-30) REVERT: A 307 VAL cc_start: 0.9030 (t) cc_final: 0.8790 (t) REVERT: A 326 LEU cc_start: 0.9131 (mt) cc_final: 0.8799 (tt) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1002 time to fit residues: 10.9230 Evaluate side-chains 42 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.165 Evaluate side-chains 65 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 439 LYS cc_start: 0.9127 (tttp) cc_final: 0.8838 (tptp) REVERT: B 660 PHE cc_start: 0.8181 (m-10) cc_final: 0.7574 (m-10) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1184 time to fit residues: 8.6829 Evaluate side-chains 31 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.126 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0051 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0063 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 ------------------------------------------------------------------------------- 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: 0.0020 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.0030 chunk 91 optimal weight: 0.0570 chunk 149 optimal weight: 0.0020 overall best weight: 0.0924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 HIS A 224 ASN A 357 HIS A 378 HIS A 456 GLN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS B 652 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.044557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.037715 restraints weight = 35039.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.038806 restraints weight = 21290.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.039573 restraints weight = 14743.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.040141 restraints weight = 11133.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.040564 restraints weight = 8771.445| |-----------------------------------------------------------------------------| r_work (final): 0.2873 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.056209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.046134 restraints weight = 28185.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.047086 restraints weight = 21526.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.047842 restraints weight = 17509.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.048242 restraints weight = 14834.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.048790 restraints weight = 13215.316| |-----------------------------------------------------------------------------| r_work (final): 0.3215 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.058885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.056931 restraints weight = 4063.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.057315 restraints weight = 1015.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.057535 restraints weight = 534.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.057579 restraints weight = 375.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.057606 restraints weight = 354.389| |-----------------------------------------------------------------------------| r_work (final): 0.3127 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.069014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.063237 restraints weight = 5196.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.064498 restraints weight = 1813.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.065037 restraints weight = 1114.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.065291 restraints weight = 867.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.065292 restraints weight = 786.019| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15848 Z= 0.137 Angle : 0.628 7.743 21692 Z= 0.335 Chirality : 0.043 0.193 2444 Planarity : 0.005 0.048 2610 Dihedral : 17.207 142.547 2668 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.20), residues: 1764 helix: 1.50 (0.18), residues: 826 sheet: -1.44 (0.35), residues: 208 loop : -3.02 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 438 TYR 0.016 0.001 TYR C 478 PHE 0.006 0.001 PHE A 513 TRP 0.013 0.001 TRP A 415 HIS 0.006 0.001 HIS C 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (15848) covalent geometry : angle 0.62763 / 0.34 (21692) hydrogen bonds : bond 0.07214 / 4.69 ( 770) hydrogen bonds : angle 4.94564 / 3.48 ( 2148) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8767 (m-30) cc_final: 0.7747 (p0) REVERT: A 375 ASP cc_start: 0.9391 (m-30) cc_final: 0.9188 (m-30) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0945 time to fit residues: 5.7102 Evaluate side-chains 32 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.170 Evaluate side-chains 33 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 439 LYS cc_start: 0.9162 (tttp) cc_final: 0.8846 (tptp) REVERT: B 447 LYS cc_start: 0.9014 (mtpt) cc_final: 0.8812 (mmmt) REVERT: B 496 MET cc_start: 0.9066 (ttm) cc_final: 0.8830 (tpp) REVERT: B 535 TYR cc_start: 0.8435 (m-10) cc_final: 0.8048 (m-10) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1024 time to fit residues: 3.9661 Evaluate side-chains 24 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.114 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0051 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0065 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 82 optimal weight: 2.9990 chunk 71 optimal weight: 0.0050 chunk 33 optimal weight: 0.0050 chunk 163 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.1412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN B 721 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.043596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.036967 restraints weight = 34305.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.037976 restraints weight = 21894.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.038710 restraints weight = 15508.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.039241 restraints weight = 11841.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.039634 restraints weight = 9518.425| |-----------------------------------------------------------------------------| r_work (final): 0.2847 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.054788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.045480 restraints weight = 28108.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.046286 restraints weight = 22298.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.046928 restraints weight = 18555.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.047410 restraints weight = 15944.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.047718 restraints weight = 14109.010| |-----------------------------------------------------------------------------| r_work (final): 0.3186 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.058503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.056452 restraints weight = 4170.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.056891 restraints weight = 980.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.057087 restraints weight = 487.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.057275 restraints weight = 340.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.057292 restraints weight = 272.290| |-----------------------------------------------------------------------------| r_work (final): 0.2922 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.068638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.063096 restraints weight = 5050.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.064361 restraints weight = 1857.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.064889 restraints weight = 1127.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.065080 restraints weight = 890.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.065195 restraints weight = 807.150| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15848 Z= 0.134 Angle : 0.611 8.990 21692 Z= 0.329 Chirality : 0.042 0.176 2444 Planarity : 0.005 0.058 2610 Dihedral : 17.112 143.477 2668 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.20), residues: 1764 helix: 1.78 (0.18), residues: 828 sheet: -1.10 (0.37), residues: 208 loop : -2.88 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 256 TYR 0.017 0.001 TYR A 21 PHE 0.008 0.001 PHE D 458 TRP 0.017 0.001 TRP D 629 HIS 0.005 0.001 HIS C 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (15848) covalent geometry : angle 0.61145 / 0.33 (21692) hydrogen bonds : bond 0.06921 / 4.44 ( 770) hydrogen bonds : angle 4.84602 / 3.42 ( 2148) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9273 (t0) cc_final: 0.9000 (t0) REVERT: A 113 ASP cc_start: 0.8809 (m-30) cc_final: 0.8078 (p0) REVERT: A 375 ASP cc_start: 0.9375 (m-30) cc_final: 0.9175 (m-30) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0901 time to fit residues: 4.4132 Evaluate side-chains 32 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.101 Evaluate side-chains 27 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 439 LYS cc_start: 0.9146 (tttp) cc_final: 0.8857 (tptp) REVERT: B 447 LYS cc_start: 0.9025 (mtpt) cc_final: 0.8811 (mmmt) REVERT: B 496 MET cc_start: 0.8729 (ttm) cc_final: 0.8520 (tpp) REVERT: B 535 TYR cc_start: 0.8285 (m-10) cc_final: 0.7902 (m-10) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0786 time to fit residues: 2.6384 Evaluate side-chains 22 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.122 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0050 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0063 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 26 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 chunk 78 optimal weight: 0.0010 chunk 148 optimal weight: 0.0370 chunk 162 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 40 optimal weight: 0.3980 chunk 141 optimal weight: 7.9990 overall best weight: 0.8466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 389 ASN B 721 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.043417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.036794 restraints weight = 35116.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.037794 restraints weight = 22331.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.038546 restraints weight = 15793.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.039074 restraints weight = 12009.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.039390 restraints weight = 9637.146| |-----------------------------------------------------------------------------| r_work (final): 0.2839 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.054184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.045083 restraints weight = 27706.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.045886 restraints weight = 21858.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.046535 restraints weight = 18132.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.046872 restraints weight = 15538.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.047387 restraints weight = 13966.129| |-----------------------------------------------------------------------------| r_work (final): 0.3188 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.059033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.056953 restraints weight = 4163.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.057411 restraints weight = 957.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.057706 restraints weight = 494.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.057711 restraints weight = 353.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.057711 restraints weight = 350.016| |-----------------------------------------------------------------------------| r_work (final): 0.2917 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.068706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.062751 restraints weight = 5394.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.064126 restraints weight = 2150.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.064769 restraints weight = 1405.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.064983 restraints weight = 1101.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.065016 restraints weight = 1003.108| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15848 Z= 0.117 Angle : 0.563 7.315 21692 Z= 0.305 Chirality : 0.041 0.171 2444 Planarity : 0.004 0.052 2610 Dihedral : 17.047 143.748 2668 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.20), residues: 1764 helix: 1.97 (0.19), residues: 828 sheet: -0.74 (0.39), residues: 186 loop : -2.78 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 764 TYR 0.011 0.001 TYR B 528 PHE 0.005 0.001 PHE D 660 TRP 0.011 0.001 TRP A 415 HIS 0.003 0.001 HIS C 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.12 (15848) covalent geometry : angle 0.56269 / 0.31 (21692) hydrogen bonds : bond 0.06774 / 4.34 ( 770) hydrogen bonds : angle 4.70370 / 3.28 ( 2148) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.170 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: A 104 ASP cc_start: 0.9265 (t0) cc_final: 0.8972 (t0) REVERT: A 113 ASP cc_start: 0.8799 (m-30) cc_final: 0.8077 (p0) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0869 time to fit residues: 3.7516 Evaluate side-chains 29 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.189 Evaluate side-chains 26 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 439 LYS cc_start: 0.9119 (tttp) cc_final: 0.8816 (tptp) REVERT: B 447 LYS cc_start: 0.9074 (mtpt) cc_final: 0.8849 (mmmt) REVERT: B 535 TYR cc_start: 0.8234 (m-10) cc_final: 0.7870 (m-10) REVERT: B 583 LEU cc_start: 0.8618 (mm) cc_final: 0.8081 (pp) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0703 time to fit residues: 2.3497 Evaluate side-chains 22 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.076 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0032 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0069 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 136 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 147 optimal weight: 0.0070 chunk 143 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 0.0570 chunk 122 optimal weight: 0.0040 chunk 116 optimal weight: 0.0060 chunk 64 optimal weight: 2.9990 overall best weight: 0.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 721 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.043586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.036822 restraints weight = 34350.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.037842 restraints weight = 21645.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.038591 restraints weight = 15338.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.039127 restraints weight = 11722.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.039528 restraints weight = 9421.893| |-----------------------------------------------------------------------------| r_work (final): 0.2850 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.054466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.045126 restraints weight = 28339.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.046005 restraints weight = 22268.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.046690 restraints weight = 18372.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.047197 restraints weight = 15733.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.047454 restraints weight = 13880.276| |-----------------------------------------------------------------------------| r_work (final): 0.3184 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.059147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.056874 restraints weight = 4250.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.057384 restraints weight = 1049.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.057670 restraints weight = 522.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.057716 restraints weight = 384.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.057878 restraints weight = 368.804| |-----------------------------------------------------------------------------| r_work (final): 0.3138 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.068875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.063363 restraints weight = 5090.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.064752 restraints weight = 1955.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.065267 restraints weight = 1179.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.065472 restraints weight = 923.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.065587 restraints weight = 829.902| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15848 Z= 0.109 Angle : 0.558 7.505 21692 Z= 0.301 Chirality : 0.042 0.168 2444 Planarity : 0.004 0.053 2610 Dihedral : 16.991 143.242 2668 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.21), residues: 1764 helix: 2.08 (0.19), residues: 840 sheet: -0.55 (0.39), residues: 186 loop : -2.72 (0.19), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 764 TYR 0.010 0.001 TYR C 21 PHE 0.006 0.001 PHE D 660 TRP 0.011 0.001 TRP A 415 HIS 0.002 0.001 HIS C 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.11 (15848) covalent geometry : angle 0.55760 / 0.30 (21692) hydrogen bonds : bond 0.06684 / 4.29 ( 770) hydrogen bonds : angle 4.60873 / 3.21 ( 2148) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.9408 (mt0) cc_final: 0.9020 (mp10) REVERT: A 104 ASP cc_start: 0.9245 (t0) cc_final: 0.8995 (t0) REVERT: A 113 ASP cc_start: 0.8788 (m-30) cc_final: 0.8057 (p0) REVERT: A 375 ASP cc_start: 0.9356 (m-30) cc_final: 0.9153 (m-30) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0777 time to fit residues: 3.5152 Evaluate side-chains 30 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.166 Evaluate side-chains 26 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 439 LYS cc_start: 0.9118 (tttp) cc_final: 0.8814 (tptp) REVERT: B 447 LYS cc_start: 0.9107 (mtpt) cc_final: 0.8886 (mmmt) REVERT: B 535 TYR cc_start: 0.8168 (m-10) cc_final: 0.7832 (m-10) REVERT: B 583 LEU cc_start: 0.8571 (mm) cc_final: 0.8054 (pp) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0719 time to fit residues: 2.3865 Evaluate side-chains 22 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.121 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0050 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0060 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 25 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 44 optimal weight: 0.0770 chunk 79 optimal weight: 5.9990 chunk 140 optimal weight: 0.0030 chunk 26 optimal weight: 4.9990 chunk 96 optimal weight: 0.4980 chunk 90 optimal weight: 7.9990 overall best weight: 1.5152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 721 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.042939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.036151 restraints weight = 35209.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.037140 restraints weight = 22207.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.037872 restraints weight = 15838.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.038404 restraints weight = 12111.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.038810 restraints weight = 9820.350| |-----------------------------------------------------------------------------| r_work (final): 0.2826 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.053191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.044224 restraints weight = 28036.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.045062 restraints weight = 22131.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.045705 restraints weight = 18309.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.046249 restraints weight = 15712.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.046620 restraints weight = 13807.248| |-----------------------------------------------------------------------------| r_work (final): 0.3161 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.058890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.056588 restraints weight = 4151.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.057051 restraints weight = 1013.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.057350 restraints weight = 529.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.057533 restraints weight = 388.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.057533 restraints weight = 307.331| |-----------------------------------------------------------------------------| r_work (final): 0.2906 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.068557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.062288 restraints weight = 5239.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.063723 restraints weight = 2357.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.064408 restraints weight = 1511.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.064651 restraints weight = 1195.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.064791 restraints weight = 1080.902| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15848 Z= 0.123 Angle : 0.569 7.107 21692 Z= 0.307 Chirality : 0.041 0.155 2444 Planarity : 0.004 0.053 2610 Dihedral : 17.022 144.589 2668 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.21), residues: 1764 helix: 2.29 (0.19), residues: 828 sheet: -0.51 (0.39), residues: 186 loop : -2.61 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 596 TYR 0.008 0.001 TYR A 21 PHE 0.007 0.001 PHE B 660 TRP 0.013 0.001 TRP A 415 HIS 0.002 0.001 HIS C 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (15848) covalent geometry : angle 0.56877 / 0.31 (21692) hydrogen bonds : bond 0.06700 / 4.24 ( 770) hydrogen bonds : angle 4.61493 / 3.19 ( 2148) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.167 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: A 104 ASP cc_start: 0.9286 (t0) cc_final: 0.8959 (t0) REVERT: A 113 ASP cc_start: 0.8808 (m-30) cc_final: 0.8041 (p0) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0964 time to fit residues: 3.7608 Evaluate side-chains 28 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.149 Evaluate side-chains 24 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 439 LYS cc_start: 0.9142 (tttp) cc_final: 0.8837 (tptp) REVERT: B 447 LYS cc_start: 0.9097 (mtpt) cc_final: 0.8853 (mmmt) REVERT: B 535 TYR cc_start: 0.8231 (m-10) cc_final: 0.7896 (m-10) REVERT: B 583 LEU cc_start: 0.8557 (mm) cc_final: 0.8017 (pp) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0734 time to fit residues: 2.2365 Evaluate side-chains 21 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.124 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0051 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0063 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 164 optimal weight: 0.9990 chunk 83 optimal weight: 0.0050 chunk 31 optimal weight: 5.9990 chunk 39 optimal weight: 0.0010 chunk 67 optimal weight: 0.3980 chunk 106 optimal weight: 2.9990 chunk 80 optimal weight: 0.0670 chunk 32 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.2738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 721 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.043523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.036765 restraints weight = 34125.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.037788 restraints weight = 21692.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.038501 restraints weight = 15459.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.039054 restraints weight = 11875.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.039378 restraints weight = 9615.537| |-----------------------------------------------------------------------------| r_work (final): 0.2844 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.053951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.044716 restraints weight = 28511.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.045558 restraints weight = 22303.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.046225 restraints weight = 18502.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.046716 restraints weight = 15881.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.047157 restraints weight = 14069.359| |-----------------------------------------------------------------------------| r_work (final): 0.3170 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.059926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.057453 restraints weight = 4078.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.057963 restraints weight = 1074.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.058268 restraints weight = 573.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.058357 restraints weight = 414.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.058509 restraints weight = 377.507| |-----------------------------------------------------------------------------| r_work (final): 0.3146 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.068891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.062680 restraints weight = 5584.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.064093 restraints weight = 2366.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.064793 restraints weight = 1537.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.065083 restraints weight = 1216.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.065231 restraints weight = 1082.907| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15848 Z= 0.108 Angle : 0.549 6.765 21692 Z= 0.296 Chirality : 0.041 0.157 2444 Planarity : 0.004 0.053 2610 Dihedral : 17.072 143.161 2668 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.21), residues: 1764 helix: 2.31 (0.19), residues: 840 sheet: -0.43 (0.39), residues: 186 loop : -2.51 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 46 TYR 0.008 0.001 TYR C 21 PHE 0.025 0.001 PHE D 514 TRP 0.011 0.001 TRP A 415 HIS 0.002 0.001 HIS C 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.11 (15848) covalent geometry : angle 0.54918 / 0.30 (21692) hydrogen bonds : bond 0.06623 / 4.24 ( 770) hydrogen bonds : angle 4.51191 / 3.11 ( 2148) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9225 (t0) cc_final: 0.8928 (t0) REVERT: A 113 ASP cc_start: 0.8808 (m-30) cc_final: 0.8032 (p0) REVERT: A 159 MET cc_start: 0.8859 (mmm) cc_final: 0.8434 (mmm) REVERT: A 375 ASP cc_start: 0.9348 (m-30) cc_final: 0.9146 (m-30) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0935 time to fit residues: 3.6452 Evaluate side-chains 28 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.160 Evaluate side-chains 25 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 447 LYS cc_start: 0.9070 (mtpt) cc_final: 0.8836 (mmmt) REVERT: B 535 TYR cc_start: 0.8267 (m-10) cc_final: 0.7325 (m-10) REVERT: B 583 LEU cc_start: 0.8572 (mm) cc_final: 0.8046 (pp) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0692 time to fit residues: 2.2356 Evaluate side-chains 21 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.122 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0052 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0061 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 1.9990 chunk 67 optimal weight: 0.0870 chunk 76 optimal weight: 10.0000 chunk 51 optimal weight: 0.0870 chunk 140 optimal weight: 0.0770 chunk 160 optimal weight: 0.2980 chunk 173 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 20 optimal weight: 0.0030 chunk 19 optimal weight: 4.9990 overall best weight: 0.1104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 721 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.043660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.036865 restraints weight = 34329.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.037905 restraints weight = 21803.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.038598 restraints weight = 15570.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.039195 restraints weight = 12124.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.039603 restraints weight = 9743.984| |-----------------------------------------------------------------------------| r_work (final): 0.2853 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.054469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.045354 restraints weight = 29202.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.046183 restraints weight = 23058.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.046834 restraints weight = 19149.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.047359 restraints weight = 16444.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.047743 restraints weight = 14524.680| |-----------------------------------------------------------------------------| r_work (final): 0.3177 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.059928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.057426 restraints weight = 4087.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.057965 restraints weight = 1071.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.058304 restraints weight = 568.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.058349 restraints weight = 393.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.058349 restraints weight = 376.017| |-----------------------------------------------------------------------------| r_work (final): 0.3137 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.068993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.062758 restraints weight = 5486.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.064216 restraints weight = 2347.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.064832 restraints weight = 1504.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.065115 restraints weight = 1209.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.065241 restraints weight = 1088.059| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15848 Z= 0.110 Angle : 0.565 6.514 21692 Z= 0.305 Chirality : 0.041 0.162 2444 Planarity : 0.004 0.053 2610 Dihedral : 17.085 143.219 2668 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.21), residues: 1764 helix: 2.26 (0.19), residues: 830 sheet: -0.40 (0.39), residues: 186 loop : -2.44 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 356 TYR 0.008 0.001 TYR A 21 PHE 0.008 0.001 PHE B 660 TRP 0.010 0.001 TRP A 415 HIS 0.002 0.000 HIS C 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.11 (15848) covalent geometry : angle 0.56487 / 0.30 (21692) hydrogen bonds : bond 0.06644 / 4.27 ( 770) hydrogen bonds : angle 4.55869 / 3.12 ( 2148) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9240 (t0) cc_final: 0.8880 (t0) REVERT: A 113 ASP cc_start: 0.8756 (m-30) cc_final: 0.7815 (p0) REVERT: A 159 MET cc_start: 0.8916 (mmm) cc_final: 0.8562 (mmm) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0770 time to fit residues: 3.2434 Evaluate side-chains 28 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.169 Evaluate side-chains 26 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 447 LYS cc_start: 0.9053 (mtpt) cc_final: 0.8831 (mmmt) REVERT: B 583 LEU cc_start: 0.8542 (mm) cc_final: 0.8019 (pp) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0709 time to fit residues: 2.3577 Evaluate side-chains 21 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.133 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0055 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0062 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 60 optimal weight: 0.0040 chunk 53 optimal weight: 8.9990 chunk 51 optimal weight: 0.0980 chunk 101 optimal weight: 0.4980 chunk 62 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 86 optimal weight: 0.3980 chunk 88 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 721 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.043931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.037017 restraints weight = 34505.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.038034 restraints weight = 22256.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.038769 restraints weight = 16041.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.039331 restraints weight = 12451.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.039742 restraints weight = 10060.103| |-----------------------------------------------------------------------------| r_work (final): 0.2853 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.054106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.044743 restraints weight = 29378.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.045576 restraints weight = 23259.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.046222 restraints weight = 19305.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.046729 restraints weight = 16646.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.047080 restraints weight = 14775.288| |-----------------------------------------------------------------------------| r_work (final): 0.3175 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.060436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.057909 restraints weight = 4007.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.058451 restraints weight = 1082.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.058719 restraints weight = 559.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.058816 restraints weight = 404.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.058816 restraints weight = 355.297| |-----------------------------------------------------------------------------| r_work (final): 0.3145 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.069271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.062863 restraints weight = 5496.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.064385 restraints weight = 2447.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.065050 restraints weight = 1563.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.065342 restraints weight = 1233.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.065486 restraints weight = 1098.365| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15848 Z= 0.107 Angle : 0.569 6.978 21692 Z= 0.305 Chirality : 0.041 0.155 2444 Planarity : 0.004 0.052 2610 Dihedral : 17.078 143.412 2668 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.21), residues: 1764 helix: 2.29 (0.19), residues: 830 sheet: -0.30 (0.39), residues: 186 loop : -2.40 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 764 TYR 0.015 0.001 TYR B 535 PHE 0.012 0.001 PHE D 660 TRP 0.010 0.001 TRP A 415 HIS 0.002 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.11 (15848) covalent geometry : angle 0.56871 / 0.30 (21692) hydrogen bonds : bond 0.06612 / 4.25 ( 770) hydrogen bonds : angle 4.54807 / 3.10 ( 2148) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8751 (m-30) cc_final: 0.7952 (p0) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0803 time to fit residues: 3.0568 Evaluate side-chains 26 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.207 Evaluate side-chains 25 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 447 LYS cc_start: 0.9059 (mtpt) cc_final: 0.8827 (mmmt) REVERT: B 583 LEU cc_start: 0.8575 (mm) cc_final: 0.8055 (pp) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0715 time to fit residues: 2.3402 Evaluate side-chains 20 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.120 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0051 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0062 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 100 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 133 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 180 optimal weight: 30.0000 chunk 108 optimal weight: 0.0170 chunk 54 optimal weight: 7.9990 overall best weight: 1.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN B 721 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.043079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.036331 restraints weight = 35099.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.037317 restraints weight = 22800.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.038053 restraints weight = 16469.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.038581 restraints weight = 12718.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.038981 restraints weight = 10326.367| |-----------------------------------------------------------------------------| r_work (final): 0.2828 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.052956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.044049 restraints weight = 29527.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.044843 restraints weight = 23076.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.045483 restraints weight = 19208.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.045997 restraints weight = 16367.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.046429 restraints weight = 14424.316| |-----------------------------------------------------------------------------| r_work (final): 0.3152 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.059628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.057204 restraints weight = 3741.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.057655 restraints weight = 1100.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.057879 restraints weight = 630.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.057879 restraints weight = 473.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.057879 restraints weight = 473.289| |-----------------------------------------------------------------------------| r_work (final): 0.3118 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.068372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.062039 restraints weight = 5753.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.063511 restraints weight = 2448.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.064135 restraints weight = 1556.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.064431 restraints weight = 1269.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.064546 restraints weight = 1105.083| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15848 Z= 0.123 Angle : 0.587 9.295 21692 Z= 0.314 Chirality : 0.041 0.158 2444 Planarity : 0.004 0.052 2610 Dihedral : 17.099 144.441 2668 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.21), residues: 1764 helix: 2.26 (0.19), residues: 830 sheet: -0.31 (0.40), residues: 186 loop : -2.34 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 764 TYR 0.040 0.001 TYR B 535 PHE 0.013 0.001 PHE B 660 TRP 0.014 0.001 TRP A 415 HIS 0.002 0.001 HIS C 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (15848) covalent geometry : angle 0.58728 / 0.31 (21692) hydrogen bonds : bond 0.06704 / 4.27 ( 770) hydrogen bonds : angle 4.63987 / 3.16 ( 2148) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.212 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: A 52 MET cc_start: 0.9392 (ttm) cc_final: 0.9183 (ttm) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0807 time to fit residues: 2.9603 Evaluate side-chains 26 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.191 Evaluate side-chains 23 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0542 time to fit residues: 1.7399 Evaluate side-chains 17 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.156 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0068 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0085 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 10 optimal weight: 9.9990 chunk 167 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 118 optimal weight: 20.0000 chunk 168 optimal weight: 4.9990 chunk 130 optimal weight: 0.0170 chunk 49 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 overall best weight: 2.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 452 ASN B 721 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.041544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.034898 restraints weight = 34792.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.035886 restraints weight = 22388.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.036568 restraints weight = 16162.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.037105 restraints weight = 12596.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.037511 restraints weight = 10215.001| |-----------------------------------------------------------------------------| r_work (final): 0.2783 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.051936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.043233 restraints weight = 30151.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.044140 restraints weight = 22860.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.044816 restraints weight = 18425.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.045356 restraints weight = 15512.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.045758 restraints weight = 13496.736| |-----------------------------------------------------------------------------| r_work (final): 0.3119 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.058875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.056191 restraints weight = 3849.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.056681 restraints weight = 1004.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.056952 restraints weight = 573.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.056952 restraints weight = 430.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.056952 restraints weight = 430.510| |-----------------------------------------------------------------------------| r_work (final): 0.3096 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.067063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.061066 restraints weight = 5392.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.062407 restraints weight = 2377.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.063150 restraints weight = 1582.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.063415 restraints weight = 1228.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.063506 restraints weight = 1063.196| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15848 Z= 0.146 Angle : 0.619 8.901 21692 Z= 0.330 Chirality : 0.041 0.165 2444 Planarity : 0.005 0.109 2610 Dihedral : 17.267 144.459 2668 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1764 helix: 2.07 (0.18), residues: 830 sheet: -0.34 (0.39), residues: 186 loop : -2.38 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 596 TYR 0.025 0.001 TYR B 535 PHE 0.035 0.002 PHE D 660 TRP 0.018 0.002 TRP A 415 HIS 0.003 0.001 HIS B 669 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (15848) covalent geometry : angle 0.61948 / 0.33 (21692) hydrogen bonds : bond 0.06908 / 4.39 ( 770) hydrogen bonds : angle 4.70696 / 3.19 ( 2148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1943.15 seconds wall clock time: 34 minutes 37.36 seconds (2077.36 seconds total)