Starting phenix.real_space_refine on Sat Aug 23 05:57:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5d_44208/08_2025/9b5d_44208.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5d_44208/08_2025/9b5d_44208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5d_44208/08_2025/9b5d_44208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5d_44208/08_2025/9b5d_44208.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5d_44208/08_2025/9b5d_44208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5d_44208/08_2025/9b5d_44208.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.071 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 P 3 5.49 5 Mg 2 5.21 5 S 43 5.16 5 C 6449 2.51 5 N 1678 2.21 5 O 1953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10128 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7734 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928} Chain breaks: 1 Chain: "B" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "C" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1158 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "D" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 596 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'A1AIV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.58, per 1000 atoms: 0.25 Number of scatterers: 10128 At special positions: 0 Unit cell: (100.016, 98.952, 119.168, 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) S 43 16.00 P 3 15.00 Mg 2 11.99 O 1953 8.00 N 1678 7.00 C 6449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS C 85 " distance=2.91 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 315.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2404 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 11 sheets defined 45.9% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.750A pdb=" N TYR A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 73 through 79 removed outlier: 3.681A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 4.014A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.326A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 removed outlier: 3.607A pdb=" N ASN A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.711A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.691A pdb=" N ASP A 223 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.291A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.652A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 389 through 392 Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.406A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.555A pdb=" N SER A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.619A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 486 through 499 Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.847A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.839A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.568A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.538A pdb=" N SER A 581 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 582 " --> pdb=" O TYR A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 578 through 582' Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 601 through 618 Processing helix chain 'A' and resid 618 through 628 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.674A pdb=" N LYS A 639 " --> pdb=" O GLU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 662 through 679 removed outlier: 3.564A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 Processing helix chain 'A' and resid 718 through 737 Processing helix chain 'A' and resid 743 through 753 removed outlier: 3.982A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 4.015A pdb=" N GLN A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 794 " --> pdb=" O ILE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 834 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.521A pdb=" N THR A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.691A pdb=" N GLU A 882 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 883 " --> pdb=" O ILE A 880 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 879 through 883' Processing helix chain 'A' and resid 926 through 937 Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 98 through 112 Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 130 through 145 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.806A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TYR A 385 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.242A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL A 193 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.242A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.447A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER A 559 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 905 through 908 Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 922 removed outlier: 6.352A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 920 through 922 removed outlier: 6.352A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 12 through 16 removed outlier: 3.889A pdb=" N ARG B 42 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 26 removed outlier: 3.631A pdb=" N GLY C 24 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 12 through 16 487 hydrogen bonds defined for protein. 1323 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: 1.94 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1723 1.27 - 1.40: 2410 1.40 - 1.54: 6015 1.54 - 1.67: 130 1.67 - 1.81: 66 Bond restraints: 10344 Sorted by residual: bond pdb=" C04 A1AIV D 101 " pdb=" C05 A1AIV D 101 " ideal model delta sigma weight residual 1.453 1.525 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.78e+00 bond pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " ideal model delta sigma weight residual 1.531 1.518 0.013 1.20e-02 6.94e+03 1.17e+00 bond pdb=" C05 A1AIV D 101 " pdb=" N06 A1AIV D 101 " ideal model delta sigma weight residual 1.151 1.132 0.019 2.00e-02 2.50e+03 9.05e-01 ... (remaining 10339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 13908 1.90 - 3.79: 88 3.79 - 5.69: 8 5.69 - 7.58: 4 7.58 - 9.48: 1 Bond angle restraints: 14009 Sorted by residual: angle pdb=" C LYS A 381 " pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta sigma weight residual 121.70 128.14 -6.44 1.80e+00 3.09e-01 1.28e+01 angle pdb=" C03 A1AIV D 101 " pdb=" C02 A1AIV D 101 " pdb=" N01 A1AIV D 101 " ideal model delta sigma weight residual 111.06 101.58 9.48 3.00e+00 1.11e-01 9.98e+00 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.30 3.23 1.18e+00 7.24e-01 7.56e+00 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 104.51 7.32 2.67e+00 1.40e-01 7.52e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.48 4.71 1.76e+00 3.23e-01 7.18e+00 ... (remaining 14004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 6051 17.32 - 34.64: 200 34.64 - 51.95: 44 51.95 - 69.27: 9 69.27 - 86.59: 4 Dihedral angle restraints: 6308 sinusoidal: 2587 harmonic: 3721 Sorted by residual: dihedral pdb=" CB CYS A 593 " pdb=" SG CYS A 593 " pdb=" SG CYS C 85 " pdb=" CB CYS C 85 " ideal model delta sinusoidal sigma weight residual -86.00 -147.30 61.30 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" CA LYS A 884 " pdb=" C LYS A 884 " pdb=" N ASN A 885 " pdb=" CA ASN A 885 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" N CYS C 85 " pdb=" CA CYS C 85 " pdb=" CB CYS C 85 " pdb=" SG CYS C 85 " ideal model delta sinusoidal sigma weight residual -180.00 -122.72 -57.28 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 6305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1384 0.060 - 0.120: 162 0.120 - 0.179: 19 0.179 - 0.239: 1 0.239 - 0.299: 2 Chirality restraints: 1568 Sorted by residual: chirality pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O2' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C3' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" O3' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C4' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" C5' ATP A1103 " pdb=" O4' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.49 -2.73 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1565 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 118 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C GLU A 118 " 0.033 2.00e-02 2.50e+03 pdb=" O GLU A 118 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR A 119 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 75 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO C 76 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.021 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO C 95 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.018 5.00e-02 4.00e+02 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 69 2.59 - 3.17: 8500 3.17 - 3.74: 14717 3.74 - 4.32: 22137 4.32 - 4.90: 37575 Nonbonded interactions: 82998 Sorted by model distance: nonbonded pdb="MG MG A1101 " pdb=" O2B ATP A1103 " model vdw 2.012 2.170 nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.044 2.170 nonbonded pdb=" OD2 ASP A 537 " pdb="MG MG A1101 " model vdw 2.052 2.170 nonbonded pdb=" OD2 ASP A 463 " pdb=" O3' ATP A1103 " model vdw 2.098 3.040 nonbonded pdb=" OD1 ASN D 25 " pdb=" NZ LYS D 29 " model vdw 2.116 3.120 ... (remaining 82993 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 1 through 75) selection = (chain 'D' and resid 1 through 75) } 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: 5.100 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.980 Find NCS groups from input model: 0.060 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:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 : 0.009 0.877 10347 Z= 0.468 Angle : 0.623 46.388 14011 Z= 0.308 Chirality : 0.043 0.299 1568 Planarity : 0.003 0.034 1812 Dihedral : 9.737 86.589 3901 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.06 % Allowed : 3.10 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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 aren not related in a simple way. whole: 1.46 (0.24), residues: 1273 helix: 1.66 (0.24), residues: 506 sheet: 0.78 (0.35), residues: 208 loop : 0.55 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 409 TYR 0.008 0.001 TYR A 544 PHE 0.011 0.001 PHE A 237 TRP 0.004 0.001 TRP A 669 HIS 0.003 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00351 (10344) covalent geometry : angle 0.46635 (14009) SS BOND : bond 0.87708 ( 1) SS BOND : angle 34.52814 ( 2) hydrogen bonds : bond 0.14631 ( 474) hydrogen bonds : angle 5.78126 ( 1323) Misc. bond : bond 0.07788 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7419 (tp30) cc_final: 0.7011 (tp30) REVERT: A 32 MET cc_start: 0.8377 (mtp) cc_final: 0.8091 (mtp) REVERT: A 33 LYS cc_start: 0.7993 (ttpt) cc_final: 0.7714 (ttmm) REVERT: A 184 MET cc_start: 0.8383 (mtp) cc_final: 0.8111 (mtt) REVERT: A 196 MET cc_start: 0.8952 (mmp) cc_final: 0.8701 (mmp) REVERT: A 216 LYS cc_start: 0.7147 (mtmm) cc_final: 0.6817 (pttp) REVERT: A 262 LYS cc_start: 0.8936 (ttpp) cc_final: 0.8735 (tmtt) REVERT: A 286 MET cc_start: 0.8394 (mmm) cc_final: 0.7830 (pmt) REVERT: A 448 MET cc_start: 0.8910 (mmp) cc_final: 0.8620 (mmp) REVERT: A 596 LYS cc_start: 0.8578 (tmtt) cc_final: 0.8374 (mmmm) REVERT: A 611 ASP cc_start: 0.7233 (m-30) cc_final: 0.7033 (m-30) REVERT: A 652 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7941 (tmm-80) REVERT: A 832 MET cc_start: 0.8503 (mtp) cc_final: 0.8250 (mtp) REVERT: A 869 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: A 879 LYS cc_start: 0.8723 (mmmm) cc_final: 0.8350 (mmtt) REVERT: A 1011 LYS cc_start: 0.8666 (ttmm) cc_final: 0.8343 (ttmm) REVERT: B 51 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8235 (mt-10) REVERT: B 58 ASP cc_start: 0.8146 (m-30) cc_final: 0.7552 (m-30) REVERT: C 8 ARG cc_start: 0.7996 (mtt-85) cc_final: 0.7687 (ttp-170) REVERT: C 136 LEU cc_start: 0.8285 (mm) cc_final: 0.7947 (tp) REVERT: C 143 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8168 (mtm110) outliers start: 12 outliers final: 5 residues processed: 164 average time/residue: 0.6589 time to fit residues: 114.6016 Evaluate side-chains 119 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 91 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.0270 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.149378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.096427 restraints weight = 12818.543| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.53 r_work: 0.2967 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10347 Z= 0.147 Angle : 0.500 8.099 14011 Z= 0.261 Chirality : 0.043 0.157 1568 Planarity : 0.004 0.042 1812 Dihedral : 6.214 82.645 1416 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.77 % Allowed : 8.41 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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 aren not related in a simple way. whole: 1.53 (0.24), residues: 1273 helix: 1.70 (0.24), residues: 511 sheet: 0.95 (0.35), residues: 203 loop : 0.54 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 5 TYR 0.009 0.001 TYR A 250 PHE 0.011 0.001 PHE A 237 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00357 (10344) covalent geometry : angle 0.49508 (14009) SS BOND : bond 0.01929 ( 1) SS BOND : angle 6.16271 ( 2) hydrogen bonds : bond 0.04366 ( 474) hydrogen bonds : angle 4.58664 ( 1323) Misc. bond : bond 0.00175 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7815 (tp30) cc_final: 0.7407 (tp30) REVERT: A 32 MET cc_start: 0.8588 (mtp) cc_final: 0.8349 (mtp) REVERT: A 33 LYS cc_start: 0.8348 (ttpt) cc_final: 0.8033 (ttmm) REVERT: A 184 MET cc_start: 0.8563 (mtp) cc_final: 0.8247 (mtt) REVERT: A 196 MET cc_start: 0.9019 (mmp) cc_final: 0.8708 (mmp) REVERT: A 216 LYS cc_start: 0.7249 (mtmm) cc_final: 0.6860 (pttp) REVERT: A 286 MET cc_start: 0.8959 (mmm) cc_final: 0.8239 (pmt) REVERT: A 448 MET cc_start: 0.9193 (mmp) cc_final: 0.8962 (mmp) REVERT: A 540 GLU cc_start: 0.8340 (tt0) cc_final: 0.8114 (mp0) REVERT: A 596 LYS cc_start: 0.8588 (tmtt) cc_final: 0.8388 (mmmm) REVERT: A 869 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: A 879 LYS cc_start: 0.8858 (mmmm) cc_final: 0.8332 (mmtt) REVERT: A 919 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8571 (pmm-80) REVERT: A 981 LYS cc_start: 0.8615 (mtpp) cc_final: 0.8176 (mptm) REVERT: A 1011 LYS cc_start: 0.8864 (ttmm) cc_final: 0.8543 (ttmm) REVERT: B 11 LYS cc_start: 0.8488 (tttt) cc_final: 0.8143 (tttm) REVERT: B 51 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8377 (mt-10) REVERT: B 58 ASP cc_start: 0.8030 (m-30) cc_final: 0.7325 (m-30) REVERT: C 8 ARG cc_start: 0.8137 (mtt-85) cc_final: 0.7766 (ttp-170) REVERT: C 136 LEU cc_start: 0.8168 (mm) cc_final: 0.7810 (tp) REVERT: C 143 ARG cc_start: 0.8478 (ttp80) cc_final: 0.8190 (mtm110) REVERT: C 144 LYS cc_start: 0.8461 (ttmt) cc_final: 0.8246 (ttmt) REVERT: D 1 MET cc_start: 0.5773 (OUTLIER) cc_final: 0.5449 (mtm) outliers start: 20 outliers final: 7 residues processed: 133 average time/residue: 0.6466 time to fit residues: 91.5423 Evaluate side-chains 118 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 91 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 0.0370 chunk 83 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 121 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.6060 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.149419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.096514 restraints weight = 12863.054| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.53 r_work: 0.2966 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10347 Z= 0.138 Angle : 0.477 7.586 14011 Z= 0.249 Chirality : 0.042 0.162 1568 Planarity : 0.004 0.050 1812 Dihedral : 6.151 85.034 1412 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.30 % Allowed : 8.76 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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 aren not related in a simple way. whole: 1.56 (0.24), residues: 1273 helix: 1.69 (0.24), residues: 511 sheet: 0.98 (0.35), residues: 206 loop : 0.59 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 645 TYR 0.008 0.001 TYR A 250 PHE 0.011 0.001 PHE A 237 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00338 (10344) covalent geometry : angle 0.47268 (14009) SS BOND : bond 0.01181 ( 1) SS BOND : angle 5.66951 ( 2) hydrogen bonds : bond 0.04036 ( 474) hydrogen bonds : angle 4.40965 ( 1323) Misc. bond : bond 0.00146 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7873 (tp30) cc_final: 0.7437 (tp30) REVERT: A 32 MET cc_start: 0.8580 (mtp) cc_final: 0.8322 (mtp) REVERT: A 33 LYS cc_start: 0.8418 (ttpt) cc_final: 0.8010 (ttmm) REVERT: A 184 MET cc_start: 0.8530 (mtp) cc_final: 0.8222 (mtt) REVERT: A 196 MET cc_start: 0.9013 (mmp) cc_final: 0.8736 (mmp) REVERT: A 216 LYS cc_start: 0.7289 (mtmm) cc_final: 0.6938 (pttp) REVERT: A 286 MET cc_start: 0.8922 (mmm) cc_final: 0.8216 (pmt) REVERT: A 448 MET cc_start: 0.9131 (mmp) cc_final: 0.8922 (mmp) REVERT: A 540 GLU cc_start: 0.8347 (tt0) cc_final: 0.8129 (mp0) REVERT: A 543 MET cc_start: 0.8993 (mmt) cc_final: 0.8782 (mmt) REVERT: A 596 LYS cc_start: 0.8553 (tmtt) cc_final: 0.8196 (ttpt) REVERT: A 869 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: A 879 LYS cc_start: 0.8871 (mmmm) cc_final: 0.8361 (mmtt) REVERT: A 980 LYS cc_start: 0.7962 (ptmt) cc_final: 0.7390 (ptpt) REVERT: A 981 LYS cc_start: 0.8621 (mtpp) cc_final: 0.8205 (mptm) REVERT: B 51 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8367 (mt-10) REVERT: B 58 ASP cc_start: 0.8086 (m-30) cc_final: 0.7387 (m-30) REVERT: B 71 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8957 (pp) REVERT: C 8 ARG cc_start: 0.8192 (mtt-85) cc_final: 0.7835 (ttp-170) REVERT: C 92 GLN cc_start: 0.6192 (OUTLIER) cc_final: 0.5985 (tm-30) REVERT: C 135 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: C 136 LEU cc_start: 0.8135 (mm) cc_final: 0.7764 (tp) REVERT: C 143 ARG cc_start: 0.8352 (ttp80) cc_final: 0.8046 (mtm110) REVERT: D 1 MET cc_start: 0.5764 (OUTLIER) cc_final: 0.5387 (mtm) outliers start: 26 outliers final: 12 residues processed: 127 average time/residue: 0.6762 time to fit residues: 91.3834 Evaluate side-chains 118 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain D residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 11 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 109 optimal weight: 0.0970 chunk 112 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.149710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.096912 restraints weight = 13014.976| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.55 r_work: 0.2972 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10347 Z= 0.128 Angle : 0.461 6.430 14011 Z= 0.242 Chirality : 0.042 0.160 1568 Planarity : 0.004 0.049 1812 Dihedral : 6.071 86.669 1411 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.57 % Allowed : 9.12 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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 aren not related in a simple way. whole: 1.58 (0.24), residues: 1273 helix: 1.70 (0.24), residues: 511 sheet: 0.97 (0.34), residues: 220 loop : 0.59 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 645 TYR 0.008 0.001 TYR A 250 PHE 0.010 0.001 PHE A 237 TRP 0.004 0.001 TRP A 669 HIS 0.002 0.000 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00313 (10344) covalent geometry : angle 0.45783 (14009) SS BOND : bond 0.00556 ( 1) SS BOND : angle 4.84277 ( 2) hydrogen bonds : bond 0.03785 ( 474) hydrogen bonds : angle 4.30712 ( 1323) Misc. bond : bond 0.00156 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7890 (tp30) cc_final: 0.7280 (tp30) REVERT: A 32 MET cc_start: 0.8544 (mtp) cc_final: 0.8317 (mtp) REVERT: A 33 LYS cc_start: 0.8413 (ttpt) cc_final: 0.7985 (ttmm) REVERT: A 184 MET cc_start: 0.8454 (mtp) cc_final: 0.8113 (mtt) REVERT: A 196 MET cc_start: 0.8999 (mmp) cc_final: 0.8711 (mmp) REVERT: A 216 LYS cc_start: 0.7280 (mtmm) cc_final: 0.6920 (pttp) REVERT: A 250 TYR cc_start: 0.8267 (m-10) cc_final: 0.8054 (m-10) REVERT: A 286 MET cc_start: 0.8897 (mmm) cc_final: 0.8195 (pmt) REVERT: A 540 GLU cc_start: 0.8365 (tt0) cc_final: 0.8142 (mp0) REVERT: A 543 MET cc_start: 0.8983 (mmt) cc_final: 0.8730 (mmt) REVERT: A 668 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7681 (mpt) REVERT: A 869 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: A 879 LYS cc_start: 0.8850 (mmmm) cc_final: 0.8334 (mmtt) REVERT: A 980 LYS cc_start: 0.7978 (ptmt) cc_final: 0.7413 (ptpt) REVERT: B 51 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8342 (mt-10) REVERT: B 58 ASP cc_start: 0.8103 (m-30) cc_final: 0.7380 (m-30) REVERT: B 71 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8942 (pp) REVERT: C 8 ARG cc_start: 0.8269 (mtt-85) cc_final: 0.7881 (ttp-170) REVERT: C 135 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: C 136 LEU cc_start: 0.8171 (mm) cc_final: 0.7779 (tp) REVERT: C 143 ARG cc_start: 0.8318 (ttp80) cc_final: 0.8011 (mtm110) REVERT: C 144 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8159 (ttmt) REVERT: D 1 MET cc_start: 0.5813 (OUTLIER) cc_final: 0.5476 (mtm) outliers start: 29 outliers final: 14 residues processed: 125 average time/residue: 0.6454 time to fit residues: 86.1523 Evaluate side-chains 121 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain D residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 81 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.149607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.096721 restraints weight = 12957.582| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.55 r_work: 0.2969 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10347 Z= 0.137 Angle : 0.468 6.454 14011 Z= 0.243 Chirality : 0.042 0.167 1568 Planarity : 0.004 0.048 1812 Dihedral : 6.025 85.195 1411 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.39 % Allowed : 9.65 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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 aren not related in a simple way. whole: 1.59 (0.24), residues: 1273 helix: 1.72 (0.24), residues: 510 sheet: 0.99 (0.34), residues: 220 loop : 0.58 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 5 TYR 0.007 0.001 TYR A 736 PHE 0.011 0.001 PHE A 237 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00338 (10344) covalent geometry : angle 0.46507 (14009) SS BOND : bond 0.01478 ( 1) SS BOND : angle 4.19091 ( 2) hydrogen bonds : bond 0.03796 ( 474) hydrogen bonds : angle 4.26251 ( 1323) Misc. bond : bond 0.00244 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7883 (tp30) cc_final: 0.7279 (tp30) REVERT: A 32 MET cc_start: 0.8547 (mtp) cc_final: 0.8291 (mtp) REVERT: A 33 LYS cc_start: 0.8413 (ttpt) cc_final: 0.7980 (ttmm) REVERT: A 184 MET cc_start: 0.8535 (mtp) cc_final: 0.8207 (mtt) REVERT: A 196 MET cc_start: 0.8993 (mmp) cc_final: 0.8780 (tpp) REVERT: A 216 LYS cc_start: 0.7294 (mtmm) cc_final: 0.6945 (pttp) REVERT: A 286 MET cc_start: 0.8879 (mmm) cc_final: 0.8189 (pmt) REVERT: A 540 GLU cc_start: 0.8365 (tt0) cc_final: 0.8139 (mp0) REVERT: A 668 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7701 (mpt) REVERT: A 869 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7934 (mp0) REVERT: A 879 LYS cc_start: 0.8850 (mmmm) cc_final: 0.8336 (mmtt) REVERT: A 919 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8574 (pmm-80) REVERT: A 980 LYS cc_start: 0.7981 (ptmt) cc_final: 0.7428 (ptpt) REVERT: A 981 LYS cc_start: 0.8579 (mtpp) cc_final: 0.8227 (mptm) REVERT: B 51 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8335 (mt-10) REVERT: B 58 ASP cc_start: 0.8113 (m-30) cc_final: 0.7397 (m-30) REVERT: B 71 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8939 (pp) REVERT: C 8 ARG cc_start: 0.8280 (mtt-85) cc_final: 0.7892 (ttp-170) REVERT: C 135 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: C 136 LEU cc_start: 0.8162 (mm) cc_final: 0.7778 (tp) REVERT: C 143 ARG cc_start: 0.8309 (ttp80) cc_final: 0.7981 (mtm110) REVERT: C 144 LYS cc_start: 0.8465 (ttmt) cc_final: 0.8146 (ttpt) REVERT: D 1 MET cc_start: 0.5800 (OUTLIER) cc_final: 0.5333 (mtm) outliers start: 27 outliers final: 12 residues processed: 116 average time/residue: 0.6463 time to fit residues: 79.8801 Evaluate side-chains 116 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain D residue 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 86 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.149731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.096950 restraints weight = 12995.738| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.54 r_work: 0.2973 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 0.034 10347 Z= 0.128 Angle : 0.469 9.307 14011 Z= 0.242 Chirality : 0.043 0.415 1568 Planarity : 0.004 0.048 1812 Dihedral : 5.972 81.828 1411 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.57 % Allowed : 9.91 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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 aren not related in a simple way. whole: 1.61 (0.24), residues: 1273 helix: 1.74 (0.24), residues: 510 sheet: 0.97 (0.33), residues: 223 loop : 0.61 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 5 TYR 0.007 0.001 TYR A 736 PHE 0.010 0.001 PHE A 237 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00314 (10344) covalent geometry : angle 0.46650 (14009) SS BOND : bond 0.00856 ( 1) SS BOND : angle 4.31919 ( 2) hydrogen bonds : bond 0.03694 ( 474) hydrogen bonds : angle 4.23764 ( 1323) Misc. bond : bond 0.00081 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7951 (tp30) cc_final: 0.7348 (tp30) REVERT: A 32 MET cc_start: 0.8532 (mtp) cc_final: 0.8270 (mtp) REVERT: A 33 LYS cc_start: 0.8386 (ttpt) cc_final: 0.7969 (ttmm) REVERT: A 184 MET cc_start: 0.8549 (mtp) cc_final: 0.8240 (mtt) REVERT: A 196 MET cc_start: 0.8982 (mmp) cc_final: 0.8769 (tpp) REVERT: A 216 LYS cc_start: 0.7309 (mtmm) cc_final: 0.6952 (pttp) REVERT: A 286 MET cc_start: 0.8876 (mmm) cc_final: 0.8194 (pmt) REVERT: A 540 GLU cc_start: 0.8354 (tt0) cc_final: 0.8131 (mp0) REVERT: A 869 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: A 879 LYS cc_start: 0.8847 (mmmm) cc_final: 0.8335 (mmtt) REVERT: A 919 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8607 (pmm-80) REVERT: A 980 LYS cc_start: 0.8046 (ptmt) cc_final: 0.7474 (ptpt) REVERT: A 981 LYS cc_start: 0.8576 (mtpp) cc_final: 0.8210 (mptm) REVERT: B 58 ASP cc_start: 0.8122 (m-30) cc_final: 0.7398 (m-30) REVERT: B 71 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8942 (pp) REVERT: C 8 ARG cc_start: 0.8281 (mtt-85) cc_final: 0.7902 (ttp-170) REVERT: C 135 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: C 136 LEU cc_start: 0.8141 (mm) cc_final: 0.7776 (tp) REVERT: C 143 ARG cc_start: 0.8310 (ttp80) cc_final: 0.7976 (mtm110) REVERT: C 144 LYS cc_start: 0.8465 (ttmt) cc_final: 0.8206 (ttpt) REVERT: D 1 MET cc_start: 0.5791 (OUTLIER) cc_final: 0.5345 (mtm) outliers start: 29 outliers final: 14 residues processed: 116 average time/residue: 0.7027 time to fit residues: 86.9471 Evaluate side-chains 117 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 919 ARG Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain D residue 1 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 49 optimal weight: 0.0000 chunk 93 optimal weight: 0.0040 chunk 25 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.150690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.097998 restraints weight = 12793.531| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.53 r_work: 0.2993 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10347 Z= 0.105 Angle : 0.449 8.531 14011 Z= 0.232 Chirality : 0.041 0.170 1568 Planarity : 0.004 0.047 1812 Dihedral : 5.822 75.119 1411 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.04 % Allowed : 10.62 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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 aren not related in a simple way. whole: 1.72 (0.24), residues: 1273 helix: 1.78 (0.24), residues: 510 sheet: 1.08 (0.34), residues: 216 loop : 0.70 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 645 TYR 0.007 0.001 TYR C 74 PHE 0.009 0.001 PHE A 237 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00252 (10344) covalent geometry : angle 0.44624 (14009) SS BOND : bond 0.00490 ( 1) SS BOND : angle 4.08998 ( 2) hydrogen bonds : bond 0.03364 ( 474) hydrogen bonds : angle 4.14128 ( 1323) Misc. bond : bond 0.00008 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7944 (tp30) cc_final: 0.7357 (tp30) REVERT: A 33 LYS cc_start: 0.8372 (ttpt) cc_final: 0.7951 (ttmm) REVERT: A 184 MET cc_start: 0.8436 (mtp) cc_final: 0.8155 (mtt) REVERT: A 193 VAL cc_start: 0.8680 (t) cc_final: 0.8266 (p) REVERT: A 216 LYS cc_start: 0.7337 (mtmm) cc_final: 0.6984 (pttp) REVERT: A 286 MET cc_start: 0.8819 (mmm) cc_final: 0.8191 (pmt) REVERT: A 540 GLU cc_start: 0.8325 (tt0) cc_final: 0.8112 (mp0) REVERT: A 543 MET cc_start: 0.8984 (mmt) cc_final: 0.8745 (mmp) REVERT: A 869 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: A 879 LYS cc_start: 0.8833 (mmmm) cc_final: 0.8326 (mmtt) REVERT: A 906 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8433 (ptt) REVERT: A 980 LYS cc_start: 0.8014 (ptmt) cc_final: 0.7442 (ptpt) REVERT: A 981 LYS cc_start: 0.8573 (mtpp) cc_final: 0.8155 (mptm) REVERT: B 58 ASP cc_start: 0.8111 (m-30) cc_final: 0.7375 (m-30) REVERT: B 71 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8927 (pp) REVERT: C 8 ARG cc_start: 0.8256 (mtt-85) cc_final: 0.7967 (ttp-170) REVERT: C 135 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: C 136 LEU cc_start: 0.8085 (mm) cc_final: 0.7735 (tp) REVERT: C 143 ARG cc_start: 0.8312 (ttp80) cc_final: 0.8000 (mtm110) REVERT: C 144 LYS cc_start: 0.8468 (ttmt) cc_final: 0.8218 (ttpt) REVERT: D 1 MET cc_start: 0.5677 (mtm) cc_final: 0.5271 (mtm) outliers start: 23 outliers final: 13 residues processed: 112 average time/residue: 0.7127 time to fit residues: 85.1843 Evaluate side-chains 112 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 135 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 9 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 117 optimal weight: 0.0040 chunk 27 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.147965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.094846 restraints weight = 12979.534| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.50 r_work: 0.2987 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10347 Z= 0.112 Angle : 0.475 11.435 14011 Z= 0.243 Chirality : 0.043 0.301 1568 Planarity : 0.004 0.047 1812 Dihedral : 5.705 80.773 1410 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.68 % Allowed : 11.50 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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 aren not related in a simple way. whole: 1.71 (0.24), residues: 1273 helix: 1.79 (0.24), residues: 510 sheet: 1.07 (0.34), residues: 216 loop : 0.68 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 645 TYR 0.007 0.001 TYR A 544 PHE 0.012 0.001 PHE A 237 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00271 (10344) covalent geometry : angle 0.47470 (14009) SS BOND : bond 0.02275 ( 1) SS BOND : angle 1.35967 ( 2) hydrogen bonds : bond 0.03383 ( 474) hydrogen bonds : angle 4.12408 ( 1323) Misc. bond : bond 0.00137 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7944 (tp30) cc_final: 0.7336 (tp30) REVERT: A 33 LYS cc_start: 0.8408 (ttpt) cc_final: 0.7983 (ttmm) REVERT: A 184 MET cc_start: 0.8385 (mtp) cc_final: 0.8085 (mtt) REVERT: A 193 VAL cc_start: 0.8687 (t) cc_final: 0.8273 (p) REVERT: A 196 MET cc_start: 0.8819 (tpp) cc_final: 0.8429 (mmp) REVERT: A 216 LYS cc_start: 0.7364 (mtmm) cc_final: 0.7001 (pttp) REVERT: A 286 MET cc_start: 0.8836 (mmm) cc_final: 0.8229 (pmt) REVERT: A 540 GLU cc_start: 0.8354 (tt0) cc_final: 0.8135 (mp0) REVERT: A 543 MET cc_start: 0.9000 (mmt) cc_final: 0.8717 (mmp) REVERT: A 869 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: A 879 LYS cc_start: 0.8842 (mmmm) cc_final: 0.8337 (mmtt) REVERT: A 980 LYS cc_start: 0.8049 (ptmt) cc_final: 0.7473 (ptpt) REVERT: A 981 LYS cc_start: 0.8569 (mtpp) cc_final: 0.8146 (mptm) REVERT: B 58 ASP cc_start: 0.8179 (m-30) cc_final: 0.7483 (m-30) REVERT: B 71 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8927 (pp) REVERT: C 8 ARG cc_start: 0.8266 (mtt-85) cc_final: 0.7973 (ttp-170) REVERT: C 135 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: C 136 LEU cc_start: 0.8144 (mm) cc_final: 0.7783 (tp) REVERT: C 143 ARG cc_start: 0.8295 (ttp80) cc_final: 0.7977 (mtm110) REVERT: C 144 LYS cc_start: 0.8476 (ttmt) cc_final: 0.8229 (ttpt) REVERT: D 1 MET cc_start: 0.5668 (mtm) cc_final: 0.5255 (mtm) outliers start: 19 outliers final: 12 residues processed: 113 average time/residue: 0.7211 time to fit residues: 86.8282 Evaluate side-chains 112 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 135 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 14 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 20 optimal weight: 0.0370 chunk 91 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.147964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.094854 restraints weight = 13001.726| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.50 r_work: 0.2989 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10347 Z= 0.112 Angle : 0.469 10.979 14011 Z= 0.242 Chirality : 0.042 0.175 1568 Planarity : 0.004 0.048 1812 Dihedral : 5.673 75.693 1410 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.77 % Allowed : 11.50 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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 aren not related in a simple way. whole: 1.68 (0.24), residues: 1273 helix: 1.80 (0.24), residues: 510 sheet: 1.03 (0.34), residues: 223 loop : 0.62 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 645 TYR 0.006 0.001 TYR C 74 PHE 0.010 0.001 PHE A 237 TRP 0.005 0.001 TRP A 669 HIS 0.001 0.000 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00272 (10344) covalent geometry : angle 0.46888 (14009) SS BOND : bond 0.01670 ( 1) SS BOND : angle 2.04212 ( 2) hydrogen bonds : bond 0.03345 ( 474) hydrogen bonds : angle 4.12310 ( 1323) Misc. bond : bond 0.00066 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7936 (tp30) cc_final: 0.7331 (tp30) REVERT: A 33 LYS cc_start: 0.8456 (ttpt) cc_final: 0.8090 (ttmm) REVERT: A 184 MET cc_start: 0.8393 (mtp) cc_final: 0.8150 (mtt) REVERT: A 193 VAL cc_start: 0.8669 (t) cc_final: 0.8250 (p) REVERT: A 196 MET cc_start: 0.8807 (tpp) cc_final: 0.8557 (mmp) REVERT: A 216 LYS cc_start: 0.7368 (mtmm) cc_final: 0.7007 (pttp) REVERT: A 286 MET cc_start: 0.8815 (mmm) cc_final: 0.8229 (pmt) REVERT: A 540 GLU cc_start: 0.8373 (tt0) cc_final: 0.8154 (mp0) REVERT: A 543 MET cc_start: 0.8987 (mmt) cc_final: 0.8720 (mmp) REVERT: A 869 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: A 879 LYS cc_start: 0.8851 (mmmm) cc_final: 0.8347 (mmtt) REVERT: A 980 LYS cc_start: 0.8057 (ptmt) cc_final: 0.7482 (ptpt) REVERT: A 981 LYS cc_start: 0.8611 (mtpp) cc_final: 0.8229 (mptm) REVERT: B 71 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8928 (pp) REVERT: C 8 ARG cc_start: 0.8263 (mtt-85) cc_final: 0.7956 (ttp-170) REVERT: C 135 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: C 136 LEU cc_start: 0.8146 (mm) cc_final: 0.7786 (tp) REVERT: C 143 ARG cc_start: 0.8303 (ttp80) cc_final: 0.7976 (mtm110) REVERT: C 144 LYS cc_start: 0.8464 (ttmt) cc_final: 0.8231 (ttpt) REVERT: D 1 MET cc_start: 0.5774 (mtm) cc_final: 0.5355 (mtm) outliers start: 20 outliers final: 11 residues processed: 110 average time/residue: 0.6758 time to fit residues: 79.3296 Evaluate side-chains 108 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 135 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 108 optimal weight: 0.0870 chunk 81 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.146831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.093594 restraints weight = 12842.072| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.50 r_work: 0.2976 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10347 Z= 0.155 Angle : 0.502 10.850 14011 Z= 0.259 Chirality : 0.043 0.218 1568 Planarity : 0.004 0.049 1812 Dihedral : 5.748 75.158 1410 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.33 % Allowed : 12.04 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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 aren not related in a simple way. whole: 1.61 (0.24), residues: 1273 helix: 1.73 (0.24), residues: 510 sheet: 1.00 (0.34), residues: 223 loop : 0.60 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 645 TYR 0.009 0.001 TYR A 81 PHE 0.012 0.001 PHE A 237 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00390 (10344) covalent geometry : angle 0.50117 (14009) SS BOND : bond 0.01645 ( 1) SS BOND : angle 1.66879 ( 2) hydrogen bonds : bond 0.03735 ( 474) hydrogen bonds : angle 4.19711 ( 1323) Misc. bond : bond 0.00065 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7910 (tp30) cc_final: 0.7371 (tp30) REVERT: A 33 LYS cc_start: 0.8470 (ttpt) cc_final: 0.8087 (ttmm) REVERT: A 184 MET cc_start: 0.8418 (mtp) cc_final: 0.8087 (mtt) REVERT: A 196 MET cc_start: 0.8835 (tpp) cc_final: 0.8487 (mmp) REVERT: A 216 LYS cc_start: 0.7384 (mtmm) cc_final: 0.7025 (pttp) REVERT: A 286 MET cc_start: 0.8821 (mmm) cc_final: 0.8195 (pmt) REVERT: A 540 GLU cc_start: 0.8380 (tt0) cc_final: 0.8150 (mp0) REVERT: A 869 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: A 879 LYS cc_start: 0.8857 (mmmm) cc_final: 0.8344 (mmtt) REVERT: A 980 LYS cc_start: 0.8075 (ptmt) cc_final: 0.7489 (ptpt) REVERT: A 981 LYS cc_start: 0.8616 (mtpp) cc_final: 0.8224 (mptm) REVERT: B 71 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8936 (pp) REVERT: C 8 ARG cc_start: 0.8262 (mtt-85) cc_final: 0.7971 (ttp-170) REVERT: C 135 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: C 136 LEU cc_start: 0.8141 (mm) cc_final: 0.7772 (tp) REVERT: C 143 ARG cc_start: 0.8293 (ttp80) cc_final: 0.7985 (mtm110) REVERT: C 144 LYS cc_start: 0.8476 (ttmt) cc_final: 0.8247 (ttpt) REVERT: D 1 MET cc_start: 0.5722 (mtm) cc_final: 0.5277 (mtm) outliers start: 15 outliers final: 10 residues processed: 100 average time/residue: 0.6418 time to fit residues: 68.3444 Evaluate side-chains 103 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 135 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 50 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 75 optimal weight: 0.0070 chunk 21 optimal weight: 0.0870 chunk 90 optimal weight: 0.8980 chunk 20 optimal weight: 0.1980 chunk 67 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 94 optimal weight: 0.0980 chunk 114 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.2176 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.149005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.095943 restraints weight = 12947.745| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.51 r_work: 0.3000 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10347 Z= 0.089 Angle : 0.455 9.744 14011 Z= 0.235 Chirality : 0.041 0.227 1568 Planarity : 0.004 0.047 1812 Dihedral : 5.537 66.975 1410 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.97 % Allowed : 12.39 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % 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 aren not related in a simple way. whole: 1.74 (0.24), residues: 1273 helix: 1.84 (0.24), residues: 510 sheet: 1.08 (0.34), residues: 224 loop : 0.66 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 645 TYR 0.006 0.001 TYR A 736 PHE 0.009 0.001 PHE A 842 TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00203 (10344) covalent geometry : angle 0.45471 (14009) SS BOND : bond 0.01348 ( 1) SS BOND : angle 1.58906 ( 2) hydrogen bonds : bond 0.03066 ( 474) hydrogen bonds : angle 4.05857 ( 1323) Misc. bond : bond 0.00023 ( 2) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 4181.27 seconds wall clock time: 71 minutes 29.98 seconds (4289.98 seconds total)