Starting phenix.real_space_refine on Wed Feb 12 09:12:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yai_33713/02_2025/7yai_33713.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yai_33713/02_2025/7yai_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_33713/02_2025/7yai_33713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yai_33713/02_2025/7yai_33713.map" model { file = "/net/cci-nas-00/data/ceres_data/7yai_33713/02_2025/7yai_33713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yai_33713/02_2025/7yai_33713.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.51, per 1000 atoms: 0.59 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: 1.96 Conformation dependent library (CDL) restraints added in 852.8 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: 1.02 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: 3.10 Time building geometry restraints manager: 2.25 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.120 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.700 ------------------------------------------------------------------------------- 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 7806 Z= 0.295 Angle : 0.779 15.091 10574 Z= 0.430 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (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 TRP 0.008 0.001 TRP C 149 HIS 0.002 0.001 HIS C 86 PHE 0.017 0.001 PHE A 454 TYR 0.013 0.001 TYR C 70 ARG 0.004 0.000 ARG A 760 *********************** 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 : 0.860 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: 0.1900 time to fit residues: 31.9962 Evaluate side-chains 120 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 83 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 20.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4332 r_free = 0.4332 target = 0.204338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.157563 restraints weight = 8249.853| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.97 r_work: 0.3549 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7806 Z= 0.167 Angle : 0.529 10.300 10574 Z= 0.272 Chirality : 0.041 0.183 1250 Planarity : 0.004 0.044 1331 Dihedral : 8.384 112.136 1096 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.60 % Allowed : 19.01 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 991 helix: 1.71 (0.23), residues: 486 sheet: -0.16 (0.45), residues: 119 loop : -0.11 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 285 HIS 0.001 0.000 HIS A 364 PHE 0.010 0.001 PHE A 383 TYR 0.009 0.001 TYR C 112 ARG 0.002 0.000 ARG A 523 *********************** 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 150 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.714 Fit side-chains REVERT: A 149 HIS cc_start: 0.7377 (OUTLIER) cc_final: 0.7155 (m-70) REVERT: A 262 MET cc_start: 0.7461 (mmt) cc_final: 0.7189 (mmt) REVERT: A 691 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6489 (mp0) outliers start: 22 outliers final: 11 residues processed: 138 average time/residue: 0.1848 time to fit residues: 35.2961 Evaluate side-chains 125 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 420 THR 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 67 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.4292 r_free = 0.4292 target = 0.200451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.155107 restraints weight = 8389.207| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.02 r_work: 0.3526 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7806 Z= 0.282 Angle : 0.575 10.105 10574 Z= 0.292 Chirality : 0.043 0.202 1250 Planarity : 0.004 0.048 1331 Dihedral : 8.197 117.879 1092 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.42 % Allowed : 19.13 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 991 helix: 1.48 (0.23), residues: 491 sheet: -0.13 (0.43), residues: 130 loop : -0.12 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 60 HIS 0.002 0.001 HIS A 364 PHE 0.013 0.001 PHE A 383 TYR 0.009 0.001 TYR C 143 ARG 0.004 0.000 ARG A 174 *********************** 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 : 0.893 Fit side-chains revert: symmetry clash REVERT: A 149 HIS cc_start: 0.7531 (OUTLIER) cc_final: 0.7185 (m-70) REVERT: A 262 MET cc_start: 0.7653 (mmt) cc_final: 0.7374 (mmt) REVERT: A 464 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.6877 (mppt) REVERT: A 691 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6609 (mp0) outliers start: 29 outliers final: 19 residues processed: 135 average time/residue: 0.1927 time to fit residues: 35.9863 Evaluate side-chains 136 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 55 CYS Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 20.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.201060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.153373 restraints weight = 8257.018| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.25 r_work: 0.3494 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7806 Z= 0.236 Angle : 0.549 10.155 10574 Z= 0.278 Chirality : 0.042 0.180 1250 Planarity : 0.004 0.047 1331 Dihedral : 8.104 116.314 1092 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.42 % Allowed : 19.36 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 991 helix: 1.56 (0.23), residues: 491 sheet: -0.27 (0.44), residues: 119 loop : -0.21 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 149 HIS 0.001 0.000 HIS A 364 PHE 0.015 0.001 PHE A 383 TYR 0.007 0.001 TYR C 127 ARG 0.004 0.000 ARG A 174 *********************** 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 155 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 149 HIS cc_start: 0.7528 (OUTLIER) cc_final: 0.7211 (m-70) REVERT: A 277 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8527 (mt) REVERT: A 464 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.6825 (mppt) REVERT: A 691 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: C 53 LEU cc_start: 0.7722 (tp) cc_final: 0.7493 (pp) outliers start: 29 outliers final: 22 residues processed: 145 average time/residue: 0.1789 time to fit residues: 36.6958 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 : 0.826 ------------------------------------------------------------------------------- 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 251 GLU Chi-restraints excluded: chain A residue 277 ILE 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 420 THR 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 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 Chi-restraints excluded: chain C residue 130 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.200817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.154272 restraints weight = 8297.427| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.16 r_work: 0.3475 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7806 Z= 0.241 Angle : 0.562 10.413 10574 Z= 0.284 Chirality : 0.042 0.179 1250 Planarity : 0.004 0.047 1331 Dihedral : 8.089 116.397 1092 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.13 % Allowed : 19.48 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 991 helix: 1.57 (0.23), residues: 491 sheet: 0.08 (0.47), residues: 110 loop : -0.23 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 736 HIS 0.001 0.000 HIS A 364 PHE 0.014 0.001 PHE A 383 TYR 0.008 0.001 TYR A 696 ARG 0.002 0.000 ARG A 174 *********************** 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 156 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 HIS cc_start: 0.7513 (OUTLIER) cc_final: 0.7191 (m-70) REVERT: A 277 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8513 (mt) REVERT: A 464 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6821 (mppt) REVERT: A 691 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: A 902 ARG cc_start: 0.6428 (OUTLIER) cc_final: 0.5846 (ttp80) REVERT: C 53 LEU cc_start: 0.7762 (tp) cc_final: 0.7505 (pp) outliers start: 35 outliers final: 27 residues processed: 144 average time/residue: 0.2037 time to fit residues: 41.3878 Evaluate side-chains 151 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 251 GLU Chi-restraints excluded: chain A residue 277 ILE 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 420 THR 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 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 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 Chi-restraints excluded: chain C residue 130 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 50 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.4309 r_free = 0.4309 target = 0.201790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.155921 restraints weight = 8177.775| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.18 r_work: 0.3498 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7806 Z= 0.244 Angle : 0.563 9.867 10574 Z= 0.283 Chirality : 0.042 0.177 1250 Planarity : 0.004 0.047 1331 Dihedral : 8.092 116.851 1092 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 5.08 % Allowed : 19.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 991 helix: 1.56 (0.23), residues: 491 sheet: 0.05 (0.47), residues: 110 loop : -0.25 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 736 HIS 0.002 0.000 HIS A 364 PHE 0.014 0.001 PHE A 383 TYR 0.007 0.001 TYR A 696 ARG 0.002 0.000 ARG A 174 *********************** 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 165 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 122 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 277 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8506 (mt) REVERT: A 464 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.6884 (mppt) REVERT: A 691 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6637 (mp0) REVERT: A 693 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7227 (mmtp) REVERT: A 704 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8420 (ptm-80) REVERT: A 902 ARG cc_start: 0.6544 (OUTLIER) cc_final: 0.5982 (ttp80) outliers start: 43 outliers final: 32 residues processed: 153 average time/residue: 0.1920 time to fit residues: 40.2643 Evaluate side-chains 157 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU 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 251 GLU Chi-restraints excluded: chain A residue 277 ILE 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 420 THR 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 492 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 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 693 LYS 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 Chi-restraints excluded: chain C residue 130 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 0 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.201418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.154870 restraints weight = 8246.648| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.05 r_work: 0.3524 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7806 Z= 0.236 Angle : 0.587 11.030 10574 Z= 0.291 Chirality : 0.043 0.175 1250 Planarity : 0.004 0.046 1331 Dihedral : 8.084 116.481 1092 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 5.08 % Allowed : 20.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 991 helix: 1.60 (0.23), residues: 491 sheet: 0.25 (0.47), residues: 113 loop : -0.20 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 736 HIS 0.001 0.000 HIS A 364 PHE 0.015 0.001 PHE A 383 TYR 0.009 0.001 TYR C 112 ARG 0.004 0.000 ARG C 52 *********************** 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 161 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 277 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8475 (mt) REVERT: A 464 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6866 (mppt) REVERT: A 691 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6511 (mp0) REVERT: A 693 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7169 (mmtp) REVERT: A 704 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8404 (ptm-80) REVERT: A 879 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8024 (mt) REVERT: A 902 ARG cc_start: 0.6535 (OUTLIER) cc_final: 0.5973 (ttp80) outliers start: 43 outliers final: 33 residues processed: 148 average time/residue: 0.1942 time to fit residues: 39.7993 Evaluate side-chains 157 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 251 GLU Chi-restraints excluded: chain A residue 277 ILE 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 420 THR 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 492 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 621 SER 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 693 LYS Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 772 THR 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 Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 43 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 88 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 71 optimal weight: 0.3980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4310 r_free = 0.4310 target = 0.202266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.155778 restraints weight = 8322.587| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.18 r_work: 0.3534 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7806 Z= 0.179 Angle : 0.544 10.675 10574 Z= 0.272 Chirality : 0.041 0.167 1250 Planarity : 0.004 0.043 1331 Dihedral : 7.895 113.200 1092 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.78 % Allowed : 22.31 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.26), residues: 991 helix: 1.93 (0.23), residues: 485 sheet: -0.03 (0.45), residues: 115 loop : -0.22 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 149 HIS 0.001 0.000 HIS A 364 PHE 0.016 0.001 PHE A 383 TYR 0.008 0.001 TYR C 112 ARG 0.002 0.000 ARG C 78 *********************** 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: 32 poor density : 123 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 149 HIS cc_start: 0.7535 (OUTLIER) cc_final: 0.7245 (m-70) REVERT: A 277 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8467 (mt) REVERT: A 383 PHE cc_start: 0.7714 (m-80) cc_final: 0.7457 (m-80) REVERT: A 464 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.6864 (mppt) REVERT: A 691 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6491 (mp0) REVERT: A 704 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8383 (ptm-80) REVERT: A 879 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8024 (mt) REVERT: A 902 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.5987 (ttp80) REVERT: C 69 TRP cc_start: 0.8393 (m-90) cc_final: 0.7291 (m-10) outliers start: 32 outliers final: 23 residues processed: 147 average time/residue: 0.2380 time to fit residues: 48.3854 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 : 0.896 ------------------------------------------------------------------------------- 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 251 GLU Chi-restraints excluded: chain A residue 277 ILE 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 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 621 SER 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 710 SER Chi-restraints excluded: chain A residue 772 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 95 optimal weight: 0.0070 chunk 72 optimal weight: 0.0270 chunk 10 optimal weight: 2.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.202703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.157155 restraints weight = 8327.455| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.24 r_work: 0.3514 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7806 Z= 0.181 Angle : 0.563 10.512 10574 Z= 0.282 Chirality : 0.041 0.169 1250 Planarity : 0.004 0.043 1331 Dihedral : 7.902 113.353 1092 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.90 % Allowed : 22.20 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.26), residues: 991 helix: 1.97 (0.23), residues: 485 sheet: 0.07 (0.46), residues: 115 loop : -0.16 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 736 HIS 0.001 0.000 HIS A 364 PHE 0.015 0.001 PHE A 383 TYR 0.008 0.001 TYR C 112 ARG 0.002 0.000 ARG C 78 *********************** 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 151 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8213 (pp30) cc_final: 0.7868 (mm110) REVERT: A 149 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.7216 (m-70) REVERT: A 262 MET cc_start: 0.7733 (mmt) cc_final: 0.7510 (mmt) REVERT: A 383 PHE cc_start: 0.7597 (m-80) cc_final: 0.7353 (m-80) REVERT: A 464 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6840 (mppt) REVERT: A 691 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6507 (mp0) REVERT: A 704 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8376 (ptm-80) REVERT: A 879 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8043 (mt) REVERT: A 902 ARG cc_start: 0.6515 (OUTLIER) cc_final: 0.5939 (ttp80) REVERT: C 69 TRP cc_start: 0.8432 (m-90) cc_final: 0.7262 (m-10) outliers start: 33 outliers final: 24 residues processed: 145 average time/residue: 0.1858 time to fit residues: 37.1008 Evaluate side-chains 147 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 251 GLU 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 621 SER 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 683 GLN Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 710 SER 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 68 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 73 optimal weight: 0.0040 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 0.0970 chunk 28 optimal weight: 0.5980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 855 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.205491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.158741 restraints weight = 8270.364| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.21 r_work: 0.3535 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 7806 Z= 0.160 Angle : 0.553 10.387 10574 Z= 0.277 Chirality : 0.041 0.164 1250 Planarity : 0.004 0.042 1331 Dihedral : 7.819 110.858 1092 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.78 % Allowed : 22.43 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.26), residues: 991 helix: 2.11 (0.23), residues: 485 sheet: 1.01 (0.52), residues: 93 loop : -0.22 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 149 HIS 0.001 0.000 HIS A 98 PHE 0.013 0.001 PHE A 383 TYR 0.008 0.001 TYR C 112 ARG 0.003 0.000 ARG C 78 ********************** 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 150 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8217 (pp30) cc_final: 0.7950 (mm110) REVERT: A 149 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.7291 (m-70) REVERT: A 383 PHE cc_start: 0.7629 (m-80) cc_final: 0.7413 (m-80) REVERT: A 691 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6523 (mp0) REVERT: A 704 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8349 (ptm-80) REVERT: A 879 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7919 (mt) REVERT: A 902 ARG cc_start: 0.6561 (OUTLIER) cc_final: 0.5985 (ttp80) REVERT: C 69 TRP cc_start: 0.8446 (m-90) cc_final: 0.7277 (m-10) outliers start: 32 outliers final: 25 residues processed: 141 average time/residue: 0.1988 time to fit residues: 38.4630 Evaluate side-chains 147 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 251 GLU 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 637 SER 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 683 GLN Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 710 SER 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 28 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 87 optimal weight: 8.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.4348 r_free = 0.4348 target = 0.205833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.161032 restraints weight = 8250.085| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.17 r_work: 0.3555 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 7806 Z= 0.159 Angle : 0.548 10.247 10574 Z= 0.275 Chirality : 0.041 0.164 1250 Planarity : 0.004 0.042 1331 Dihedral : 7.803 111.034 1092 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.78 % Allowed : 22.55 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.27), residues: 991 helix: 2.13 (0.23), residues: 485 sheet: 0.56 (0.49), residues: 103 loop : -0.18 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 149 HIS 0.000 0.000 HIS A 364 PHE 0.012 0.001 PHE A 383 TYR 0.008 0.001 TYR C 112 ARG 0.003 0.000 ARG C 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3704.10 seconds wall clock time: 66 minutes 30.12 seconds (3990.12 seconds total)