Starting phenix.real_space_refine on Tue Mar 3 17:40:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yai_33713/03_2026/7yai_33713.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yai_33713/03_2026/7yai_33713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yai_33713/03_2026/7yai_33713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yai_33713/03_2026/7yai_33713.map" model { file = "/net/cci-nas-00/data/ceres_data/7yai_33713/03_2026/7yai_33713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yai_33713/03_2026/7yai_33713.cif" } resolution = 3.14 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= 0.005 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 3 5.49 5 S 55 5.16 5 C 4880 2.51 5 N 1287 2.21 5 O 1452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7678 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 6704 Classifications: {'peptide': 878} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 35, 'TRANS': 842} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.71, per 1000 atoms: 0.22 Number of scatterers: 7678 At special positions: 0 Unit cell: (85.695, 84.71, 135.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 55 16.00 P 3 15.00 O 1452 8.00 N 1287 7.00 C 4880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 128 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 324.0 milliseconds 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1850 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 11 sheets defined 50.8% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 30 through 38 Processing helix chain 'A' and resid 47 through 59 removed outlier: 3.570A pdb=" N HIS A 53 " --> pdb=" O CYS A 49 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 77 Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 99 through 135 Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.752A pdb=" N SER A 239 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 removed outlier: 3.653A pdb=" N GLN A 249 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 288 Processing helix chain 'A' and resid 290 through 306 Processing helix chain 'A' and resid 309 through 327 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.154A pdb=" N GLY A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 411 Processing helix chain 'A' and resid 424 through 438 removed outlier: 3.575A pdb=" N LEU A 430 " --> pdb=" O THR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 482 through 489 removed outlier: 3.647A pdb=" N TYR A 489 " --> pdb=" O GLN A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 520 Processing helix chain 'A' and resid 551 through 562 Processing helix chain 'A' and resid 573 through 585 Processing helix chain 'A' and resid 596 through 602 Processing helix chain 'A' and resid 603 through 611 removed outlier: 3.663A pdb=" N GLN A 609 " --> pdb=" O GLN A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 635 Processing helix chain 'A' and resid 649 through 655 Processing helix chain 'A' and resid 666 through 673 Processing helix chain 'A' and resid 682 through 723 removed outlier: 3.795A pdb=" N MET A 686 " --> pdb=" O PHE A 682 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 696 " --> pdb=" O GLY A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 743 Processing helix chain 'A' and resid 743 through 748 Processing helix chain 'A' and resid 756 through 761 removed outlier: 3.731A pdb=" N ARG A 760 " --> pdb=" O LYS A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 799 Processing helix chain 'A' and resid 804 through 826 removed outlier: 3.761A pdb=" N THR A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 837 Processing helix chain 'A' and resid 841 through 861 Processing helix chain 'A' and resid 861 through 869 Processing helix chain 'A' and resid 874 through 904 removed outlier: 4.120A pdb=" N SER A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N VAL A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 123 removed outlier: 3.648A pdb=" N ASP C 122 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR C 123 " --> pdb=" O PRO C 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 119 through 123' Processing sheet with id=AA1, first strand: chain 'A' and resid 147 through 151 removed outlier: 4.087A pdb=" N HIS A 140 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS A 229 " --> pdb=" O PHE A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 195 through 197 removed outlier: 4.355A pdb=" N LEU A 181 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASP A 184 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N VAL A 223 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 330 through 332 removed outlier: 6.029A pdb=" N GLY A 658 " --> pdb=" O MET A 675 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU A 677 " --> pdb=" O GLY A 658 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA A 660 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N MET A 641 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N MET A 661 " --> pdb=" O MET A 641 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 346 through 349 removed outlier: 6.076A pdb=" N ILE A 347 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE A 569 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N SER A 349 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE A 566 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N PHE A 617 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N MET A 568 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLN A 592 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N PHE A 617 " --> pdb=" O GLN A 592 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL A 594 " --> pdb=" O PHE A 617 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 393 removed outlier: 4.302A pdb=" N VAL A 386 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU A 536 " --> pdb=" O PRO A 531 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N PHE A 538 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER A 529 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 540 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA A 462 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 450 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL A 466 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ARG A 448 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 393 removed outlier: 4.302A pdb=" N VAL A 386 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N CYS A 490 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N PHE A 538 " --> pdb=" O CYS A 490 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR A 492 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N GLY A 540 " --> pdb=" O THR A 492 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N GLN A 494 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 13.745A pdb=" N VAL A 542 " --> pdb=" O GLN A 494 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 416 through 417 Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.500A pdb=" N THR C 110 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 105 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 46 removed outlier: 7.669A pdb=" N VAL C 45 " --> pdb=" O SER C 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.786A pdb=" N PHE C 80 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ARG C 71 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA C 82 " --> pdb=" O TRP C 69 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP C 66 " --> pdb=" O GLN C 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.786A pdb=" N PHE C 80 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ARG C 71 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA C 82 " --> pdb=" O TRP C 69 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP C 66 " --> pdb=" O GLN C 131 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2016 1.33 - 1.46: 1459 1.46 - 1.58: 4239 1.58 - 1.70: 2 1.70 - 1.82: 90 Bond restraints: 7806 Sorted by residual: bond pdb=" O3A ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sigma weight residual 1.698 1.607 0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C3B ACP A1001 " pdb=" PG ACP A1001 " ideal model delta sigma weight residual 1.875 1.794 0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" O5' ACP A1001 " pdb=" PA ACP A1001 " ideal model delta sigma weight residual 1.659 1.578 0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" N VAL A 31 " pdb=" CA VAL A 31 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.19e-02 7.06e+03 9.63e+00 bond pdb=" C LYS A 761 " pdb=" N PRO A 762 " ideal model delta sigma weight residual 1.329 1.365 -0.036 1.18e-02 7.18e+03 9.35e+00 ... (remaining 7801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 10455 3.02 - 6.04: 101 6.04 - 9.05: 15 9.05 - 12.07: 2 12.07 - 15.09: 1 Bond angle restraints: 10574 Sorted by residual: angle pdb=" PA ACP A1001 " pdb=" O3A ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sigma weight residual 125.06 109.97 15.09 3.00e+00 1.11e-01 2.53e+01 angle pdb=" CA MET A 247 " pdb=" CB MET A 247 " pdb=" CG MET A 247 " ideal model delta sigma weight residual 114.10 122.05 -7.95 2.00e+00 2.50e-01 1.58e+01 angle pdb=" C LYS C 108 " pdb=" N ASN C 109 " pdb=" CA ASN C 109 " ideal model delta sigma weight residual 122.46 127.99 -5.53 1.41e+00 5.03e-01 1.54e+01 angle pdb=" CA LEU A 29 " pdb=" C LEU A 29 " pdb=" N PRO A 30 " ideal model delta sigma weight residual 117.67 121.50 -3.83 1.01e+00 9.80e-01 1.44e+01 angle pdb=" C VAL C 111 " pdb=" CA VAL C 111 " pdb=" CB VAL C 111 " ideal model delta sigma weight residual 110.91 115.37 -4.46 1.24e+00 6.50e-01 1.29e+01 ... (remaining 10569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.07: 4425 26.07 - 52.13: 281 52.13 - 78.20: 28 78.20 - 104.26: 6 104.26 - 130.33: 2 Dihedral angle restraints: 4742 sinusoidal: 1870 harmonic: 2872 Sorted by residual: dihedral pdb=" CB CYS C 55 " pdb=" SG CYS C 55 " pdb=" SG CYS C 128 " pdb=" CB CYS C 128 " ideal model delta sinusoidal sigma weight residual -86.00 -18.81 -67.19 1 1.00e+01 1.00e-02 5.88e+01 dihedral pdb=" O1A ACP A1001 " pdb=" O3A ACP A1001 " pdb=" PA ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sinusoidal sigma weight residual -48.75 81.58 -130.33 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" O1B ACP A1001 " pdb=" C3B ACP A1001 " pdb=" PB ACP A1001 " pdb=" PG ACP A1001 " ideal model delta sinusoidal sigma weight residual -52.82 60.34 -113.16 1 3.00e+01 1.11e-03 1.49e+01 ... (remaining 4739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1081 0.064 - 0.128: 156 0.128 - 0.192: 11 0.192 - 0.255: 1 0.255 - 0.319: 1 Chirality restraints: 1250 Sorted by residual: chirality pdb=" CB VAL C 111 " pdb=" CA VAL C 111 " pdb=" CG1 VAL C 111 " pdb=" CG2 VAL C 111 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CB ILE A 803 " pdb=" CA ILE A 803 " pdb=" CG1 ILE A 803 " pdb=" CG2 ILE A 803 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA LEU A 29 " pdb=" N LEU A 29 " pdb=" C LEU A 29 " pdb=" CB LEU A 29 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 1247 not shown) Planarity restraints: 1331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 760 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C ARG A 760 " 0.041 2.00e-02 2.50e+03 pdb=" O ARG A 760 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS A 761 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 648 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C ASP A 648 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP A 648 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 649 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 28 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C GLU A 28 " -0.035 2.00e-02 2.50e+03 pdb=" O GLU A 28 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 29 " 0.012 2.00e-02 2.50e+03 ... (remaining 1328 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 78 2.64 - 3.21: 6948 3.21 - 3.77: 12363 3.77 - 4.34: 16790 4.34 - 4.90: 27742 Nonbonded interactions: 63921 Sorted by model distance: nonbonded pdb=" O VAL A 303 " pdb=" OD1 ASN A 738 " model vdw 2.075 3.040 nonbonded pdb=" O ARG A 417 " pdb=" OG1 THR A 420 " model vdw 2.217 3.040 nonbonded pdb=" OE2 GLU A 308 " pdb=" ND2 ASN A 738 " model vdw 2.260 3.120 nonbonded pdb=" OG SER A 368 " pdb=" OH TYR A 510 " model vdw 2.286 3.040 nonbonded pdb=" OG SER A 27 " pdb=" OE1 GLN A 202 " model vdw 2.303 3.040 ... (remaining 63916 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.250 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 7807 Z= 0.234 Angle : 0.782 15.091 10576 Z= 0.431 Chirality : 0.046 0.319 1250 Planarity : 0.005 0.048 1331 Dihedral : 16.329 130.326 2889 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.35 % Allowed : 20.78 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.25), residues: 991 helix: 1.06 (0.22), residues: 479 sheet: 0.05 (0.45), residues: 126 loop : -0.26 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 760 TYR 0.013 0.001 TYR C 70 PHE 0.017 0.001 PHE A 454 TRP 0.008 0.001 TRP C 149 HIS 0.002 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 7806) covalent geometry : angle 0.77889 (10574) SS BOND : bond 0.00729 ( 1) SS BOND : angle 4.89403 ( 2) hydrogen bonds : bond 0.11502 ( 436) hydrogen bonds : angle 5.74658 ( 1344) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: C 69 TRP cc_start: 0.7571 (OUTLIER) cc_final: 0.7090 (m-10) outliers start: 3 outliers final: 1 residues processed: 121 average time/residue: 0.0749 time to fit residues: 12.6223 Evaluate side-chains 121 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 146 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.204569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.157548 restraints weight = 8247.507| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.96 r_work: 0.3553 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7807 Z= 0.115 Angle : 0.531 10.016 10576 Z= 0.274 Chirality : 0.041 0.179 1250 Planarity : 0.004 0.044 1331 Dihedral : 8.461 112.702 1096 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.48 % Allowed : 19.01 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 991 helix: 1.71 (0.23), residues: 486 sheet: -0.15 (0.45), residues: 119 loop : -0.10 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 523 TYR 0.008 0.001 TYR C 112 PHE 0.009 0.001 PHE A 383 TRP 0.004 0.001 TRP A 285 HIS 0.001 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7806) covalent geometry : angle 0.53009 (10574) SS BOND : bond 0.00195 ( 1) SS BOND : angle 2.50410 ( 2) hydrogen bonds : bond 0.03897 ( 436) hydrogen bonds : angle 4.44160 ( 1344) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.276 Fit side-chains REVERT: A 149 HIS cc_start: 0.7414 (OUTLIER) cc_final: 0.7170 (m-70) REVERT: A 262 MET cc_start: 0.7495 (mmt) cc_final: 0.7218 (mmt) REVERT: A 691 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6564 (mp0) REVERT: C 53 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7327 (pp) outliers start: 21 outliers final: 9 residues processed: 137 average time/residue: 0.0755 time to fit residues: 14.6461 Evaluate side-chains 123 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 5 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 94 optimal weight: 30.0000 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.201638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.154932 restraints weight = 8342.816| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.06 r_work: 0.3481 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7807 Z= 0.163 Angle : 0.557 10.062 10576 Z= 0.283 Chirality : 0.042 0.195 1250 Planarity : 0.004 0.047 1331 Dihedral : 8.160 116.887 1092 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.42 % Allowed : 18.54 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.26), residues: 991 helix: 1.58 (0.23), residues: 491 sheet: -0.12 (0.43), residues: 130 loop : -0.09 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 523 TYR 0.009 0.001 TYR C 143 PHE 0.012 0.001 PHE A 383 TRP 0.006 0.001 TRP A 60 HIS 0.002 0.001 HIS A 624 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 7806) covalent geometry : angle 0.55634 (10574) SS BOND : bond 0.00132 ( 1) SS BOND : angle 1.62077 ( 2) hydrogen bonds : bond 0.03959 ( 436) hydrogen bonds : angle 4.45803 ( 1344) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 149 HIS cc_start: 0.7506 (OUTLIER) cc_final: 0.7178 (m-70) REVERT: A 262 MET cc_start: 0.7600 (mmt) cc_final: 0.7341 (mmt) REVERT: A 464 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.6848 (mppt) REVERT: A 691 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6570 (mp0) REVERT: C 53 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7197 (pp) outliers start: 29 outliers final: 20 residues processed: 135 average time/residue: 0.0697 time to fit residues: 13.2180 Evaluate side-chains 136 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.203332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.158073 restraints weight = 8327.136| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.22 r_work: 0.3535 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7807 Z= 0.114 Angle : 0.522 10.413 10576 Z= 0.263 Chirality : 0.041 0.177 1250 Planarity : 0.004 0.043 1331 Dihedral : 7.907 112.800 1092 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.07 % Allowed : 19.36 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.26), residues: 991 helix: 1.96 (0.23), residues: 485 sheet: 0.01 (0.44), residues: 125 loop : -0.10 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 174 TYR 0.007 0.001 TYR C 112 PHE 0.013 0.001 PHE A 383 TRP 0.004 0.001 TRP A 736 HIS 0.001 0.000 HIS A 624 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7806) covalent geometry : angle 0.52190 (10574) SS BOND : bond 0.00198 ( 1) SS BOND : angle 1.50986 ( 2) hydrogen bonds : bond 0.03559 ( 436) hydrogen bonds : angle 4.21007 ( 1344) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.285 Fit side-chains REVERT: A 149 HIS cc_start: 0.7523 (OUTLIER) cc_final: 0.7211 (m-70) REVERT: A 247 MET cc_start: 0.8550 (mmm) cc_final: 0.7822 (mmm) REVERT: A 464 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.6835 (mppt) REVERT: A 691 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6624 (mp0) REVERT: C 78 ARG cc_start: 0.7745 (ttm170) cc_final: 0.7483 (ttm170) outliers start: 26 outliers final: 17 residues processed: 142 average time/residue: 0.0730 time to fit residues: 14.5495 Evaluate side-chains 135 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 82 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.203194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.156479 restraints weight = 8306.062| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.25 r_work: 0.3530 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7807 Z= 0.124 Angle : 0.536 10.490 10576 Z= 0.273 Chirality : 0.041 0.176 1250 Planarity : 0.004 0.044 1331 Dihedral : 7.885 113.264 1092 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.54 % Allowed : 19.36 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.26), residues: 991 helix: 1.97 (0.23), residues: 485 sheet: -0.19 (0.45), residues: 119 loop : -0.11 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 174 TYR 0.007 0.001 TYR C 112 PHE 0.012 0.001 PHE A 383 TRP 0.004 0.001 TRP C 149 HIS 0.001 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7806) covalent geometry : angle 0.53587 (10574) SS BOND : bond 0.00144 ( 1) SS BOND : angle 1.45397 ( 2) hydrogen bonds : bond 0.03646 ( 436) hydrogen bonds : angle 4.28557 ( 1344) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.251 Fit side-chains REVERT: A 149 HIS cc_start: 0.7569 (OUTLIER) cc_final: 0.7249 (m-70) REVERT: A 464 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6803 (mppt) REVERT: A 691 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: A 879 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8239 (mt) REVERT: A 902 ARG cc_start: 0.6481 (OUTLIER) cc_final: 0.5912 (ttp80) REVERT: C 53 LEU cc_start: 0.7720 (tp) cc_final: 0.7395 (pp) REVERT: C 69 TRP cc_start: 0.8431 (m-90) cc_final: 0.7072 (m-10) outliers start: 30 outliers final: 19 residues processed: 142 average time/residue: 0.0779 time to fit residues: 15.6341 Evaluate side-chains 140 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 94 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 0.0870 chunk 71 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 22 optimal weight: 0.0000 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.202255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.156886 restraints weight = 8331.183| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.19 r_work: 0.3512 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7807 Z= 0.139 Angle : 0.546 9.555 10576 Z= 0.277 Chirality : 0.042 0.179 1250 Planarity : 0.004 0.045 1331 Dihedral : 7.930 114.754 1092 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.54 % Allowed : 19.95 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.26), residues: 991 helix: 1.86 (0.23), residues: 485 sheet: -0.16 (0.45), residues: 120 loop : -0.17 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 174 TYR 0.007 0.001 TYR A 696 PHE 0.013 0.001 PHE A 383 TRP 0.004 0.001 TRP C 149 HIS 0.001 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7806) covalent geometry : angle 0.54606 (10574) SS BOND : bond 0.00187 ( 1) SS BOND : angle 1.48015 ( 2) hydrogen bonds : bond 0.03667 ( 436) hydrogen bonds : angle 4.28333 ( 1344) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.260 Fit side-chains REVERT: A 43 GLN cc_start: 0.8282 (pp30) cc_final: 0.8035 (mm110) REVERT: A 149 HIS cc_start: 0.7565 (OUTLIER) cc_final: 0.7244 (m-70) REVERT: A 464 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.6830 (mppt) REVERT: A 691 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6556 (mp0) REVERT: A 704 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8388 (ptm-80) REVERT: A 879 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8046 (mt) REVERT: A 902 ARG cc_start: 0.6531 (OUTLIER) cc_final: 0.5987 (ttp80) REVERT: C 53 LEU cc_start: 0.7720 (tp) cc_final: 0.7403 (pp) REVERT: C 69 TRP cc_start: 0.8436 (m-90) cc_final: 0.7103 (m-10) outliers start: 30 outliers final: 21 residues processed: 138 average time/residue: 0.0788 time to fit residues: 15.1638 Evaluate side-chains 143 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 89 optimal weight: 20.0000 chunk 84 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 22 optimal weight: 40.0000 chunk 82 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.204014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.158346 restraints weight = 8204.612| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.15 r_work: 0.3530 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7807 Z= 0.127 Angle : 0.547 10.782 10576 Z= 0.277 Chirality : 0.042 0.173 1250 Planarity : 0.004 0.044 1331 Dihedral : 7.874 113.621 1092 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.54 % Allowed : 20.43 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.26), residues: 991 helix: 1.87 (0.23), residues: 485 sheet: 0.17 (0.47), residues: 110 loop : -0.18 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 174 TYR 0.006 0.001 TYR A 696 PHE 0.014 0.001 PHE A 383 TRP 0.003 0.001 TRP A 736 HIS 0.001 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7806) covalent geometry : angle 0.54707 (10574) SS BOND : bond 0.00174 ( 1) SS BOND : angle 1.39363 ( 2) hydrogen bonds : bond 0.03591 ( 436) hydrogen bonds : angle 4.28270 ( 1344) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.270 Fit side-chains REVERT: A 149 HIS cc_start: 0.7591 (OUTLIER) cc_final: 0.7297 (m-70) REVERT: A 464 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.6925 (mppt) REVERT: A 691 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: A 704 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8386 (ptm-80) REVERT: A 879 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8026 (mt) REVERT: A 902 ARG cc_start: 0.6509 (OUTLIER) cc_final: 0.5952 (ttp80) REVERT: C 69 TRP cc_start: 0.8434 (m-90) cc_final: 0.7171 (m-10) outliers start: 30 outliers final: 22 residues processed: 138 average time/residue: 0.0865 time to fit residues: 16.4144 Evaluate side-chains 143 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.199802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.154027 restraints weight = 8321.302| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.18 r_work: 0.3463 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 7807 Z= 0.233 Angle : 0.632 10.067 10576 Z= 0.322 Chirality : 0.045 0.178 1250 Planarity : 0.004 0.048 1331 Dihedral : 8.360 121.693 1092 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.90 % Allowed : 20.66 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.26), residues: 991 helix: 1.23 (0.23), residues: 490 sheet: 0.13 (0.46), residues: 125 loop : -0.35 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 52 TYR 0.014 0.002 TYR A 483 PHE 0.019 0.002 PHE A 702 TRP 0.005 0.001 TRP C 66 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00563 ( 7806) covalent geometry : angle 0.63170 (10574) SS BOND : bond 0.00213 ( 1) SS BOND : angle 1.39075 ( 2) hydrogen bonds : bond 0.04289 ( 436) hydrogen bonds : angle 4.65312 ( 1344) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8185 (pp30) cc_final: 0.7914 (mm110) REVERT: A 383 PHE cc_start: 0.7734 (m-80) cc_final: 0.7519 (m-80) REVERT: A 464 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.6971 (mppt) REVERT: A 691 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6670 (mp0) REVERT: A 879 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8048 (mt) REVERT: A 902 ARG cc_start: 0.6540 (OUTLIER) cc_final: 0.5931 (ttp80) outliers start: 33 outliers final: 25 residues processed: 148 average time/residue: 0.0835 time to fit residues: 17.2165 Evaluate side-chains 151 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 7 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.202370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.155672 restraints weight = 8320.802| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.28 r_work: 0.3506 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7807 Z= 0.126 Angle : 0.570 10.244 10576 Z= 0.287 Chirality : 0.041 0.168 1250 Planarity : 0.004 0.045 1331 Dihedral : 8.014 113.655 1092 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.31 % Allowed : 21.72 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.26), residues: 991 helix: 1.67 (0.23), residues: 491 sheet: -0.02 (0.46), residues: 123 loop : -0.24 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 523 TYR 0.008 0.001 TYR C 112 PHE 0.020 0.001 PHE A 454 TRP 0.006 0.001 TRP A 736 HIS 0.001 0.000 HIS A 624 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7806) covalent geometry : angle 0.56846 (10574) SS BOND : bond 0.00071 ( 1) SS BOND : angle 2.57477 ( 2) hydrogen bonds : bond 0.03644 ( 436) hydrogen bonds : angle 4.33599 ( 1344) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 149 HIS cc_start: 0.7505 (OUTLIER) cc_final: 0.7195 (m-70) REVERT: A 464 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.6886 (mppt) REVERT: A 691 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6542 (mp0) REVERT: A 704 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8403 (ptm-80) REVERT: A 879 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8024 (mt) REVERT: A 902 ARG cc_start: 0.6518 (OUTLIER) cc_final: 0.5935 (ttp80) outliers start: 28 outliers final: 20 residues processed: 142 average time/residue: 0.0818 time to fit residues: 16.0861 Evaluate side-chains 144 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 69 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 88 optimal weight: 40.0000 chunk 79 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 73 optimal weight: 0.1980 chunk 41 optimal weight: 8.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.203680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.156587 restraints weight = 8311.426| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.26 r_work: 0.3484 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7807 Z= 0.117 Angle : 0.561 10.145 10576 Z= 0.281 Chirality : 0.041 0.170 1250 Planarity : 0.004 0.043 1331 Dihedral : 7.900 111.782 1092 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.42 % Allowed : 21.84 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.26), residues: 991 helix: 1.95 (0.23), residues: 485 sheet: 0.08 (0.45), residues: 123 loop : -0.19 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 78 TYR 0.009 0.001 TYR C 112 PHE 0.020 0.001 PHE A 454 TRP 0.006 0.001 TRP C 149 HIS 0.001 0.000 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7806) covalent geometry : angle 0.56048 (10574) SS BOND : bond 0.00233 ( 1) SS BOND : angle 1.97148 ( 2) hydrogen bonds : bond 0.03473 ( 436) hydrogen bonds : angle 4.23140 ( 1344) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.256 Fit side-chains REVERT: A 149 HIS cc_start: 0.7521 (OUTLIER) cc_final: 0.7226 (m-70) REVERT: A 383 PHE cc_start: 0.7657 (m-80) cc_final: 0.7437 (m-80) REVERT: A 691 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6595 (mp0) REVERT: A 704 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8376 (ptm-80) REVERT: A 879 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8044 (mt) REVERT: A 902 ARG cc_start: 0.6487 (OUTLIER) cc_final: 0.5893 (ttp80) REVERT: C 69 TRP cc_start: 0.8450 (m-90) cc_final: 0.7259 (m-10) outliers start: 29 outliers final: 21 residues processed: 136 average time/residue: 0.0811 time to fit residues: 15.2422 Evaluate side-chains 143 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 68 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.203227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.157707 restraints weight = 8318.215| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.23 r_work: 0.3541 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7807 Z= 0.123 Angle : 0.567 9.977 10576 Z= 0.284 Chirality : 0.041 0.168 1250 Planarity : 0.004 0.044 1331 Dihedral : 7.896 113.373 1092 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.19 % Allowed : 22.43 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.26), residues: 991 helix: 1.92 (0.23), residues: 485 sheet: 0.42 (0.48), residues: 111 loop : -0.28 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 78 TYR 0.008 0.001 TYR C 112 PHE 0.019 0.001 PHE A 454 TRP 0.006 0.001 TRP C 149 HIS 0.001 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7806) covalent geometry : angle 0.56707 (10574) SS BOND : bond 0.00133 ( 1) SS BOND : angle 1.64553 ( 2) hydrogen bonds : bond 0.03491 ( 436) hydrogen bonds : angle 4.22157 ( 1344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1816.78 seconds wall clock time: 31 minutes 50.22 seconds (1910.22 seconds total)