Starting phenix.real_space_refine on Thu May 1 02:01:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5d_44208/05_2025/9b5d_44208.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5d_44208/05_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_44208/05_2025/9b5d_44208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5d_44208/05_2025/9b5d_44208.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5d_44208/05_2025/9b5d_44208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5d_44208/05_2025/9b5d_44208.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 6.49, per 1000 atoms: 0.64 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: 2.75 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.51 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: 3.39 Time building geometry restraints manager: 3.06 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: 3.700 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.750 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.180 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (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 TRP 0.004 0.001 TRP A 669 HIS 0.003 0.001 HIS C 75 PHE 0.011 0.001 PHE A 237 TYR 0.008 0.001 TYR A 544 ARG 0.003 0.000 ARG A 409 Details of bonding type rmsd hydrogen bonds : bond 0.14631 ( 474) hydrogen bonds : angle 5.78126 ( 1323) SS BOND : bond 0.87708 ( 1) SS BOND : angle 34.52814 ( 2) covalent geometry : bond 0.00351 (10344) covalent geometry : angle 0.46635 (14009) 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 : 1.082 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: 1.4236 time to fit residues: 248.9687 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 : 1.097 ------------------------------------------------------------------------------- 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 106 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 0.0770 chunk 60 optimal weight: 0.8980 chunk 73 optimal weight: 0.0470 chunk 114 optimal weight: 0.4980 overall best weight: 0.3436 ------------------------------------------------------------------------------- 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 = 0.150660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.097849 restraints weight = 12737.035| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.53 r_work: 0.2989 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10347 Z= 0.113 Angle : 0.478 7.714 14011 Z= 0.248 Chirality : 0.042 0.153 1568 Planarity : 0.004 0.039 1812 Dihedral : 6.085 80.920 1416 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.59 % Allowed : 8.23 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.24), residues: 1273 helix: 1.78 (0.24), residues: 511 sheet: 0.97 (0.35), residues: 206 loop : 0.60 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.002 0.001 HIS A 458 PHE 0.010 0.001 PHE A 842 TYR 0.009 0.001 TYR A 736 ARG 0.006 0.000 ARG C 5 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 474) hydrogen bonds : angle 4.50276 ( 1323) SS BOND : bond 0.01662 ( 1) SS BOND : angle 5.90924 ( 2) covalent geometry : bond 0.00259 (10344) covalent geometry : angle 0.47277 (14009) Misc. bond : bond 0.00216 ( 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 141 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7804 (tp30) cc_final: 0.7388 (tp30) REVERT: A 32 MET cc_start: 0.8555 (mtp) cc_final: 0.8352 (mtp) REVERT: A 33 LYS cc_start: 0.8326 (ttpt) cc_final: 0.8014 (ttmm) REVERT: A 184 MET cc_start: 0.8502 (mtp) cc_final: 0.8179 (mtt) REVERT: A 196 MET cc_start: 0.8993 (mmp) cc_final: 0.8667 (mmp) REVERT: A 216 LYS cc_start: 0.7242 (mtmm) cc_final: 0.6856 (pttp) REVERT: A 286 MET cc_start: 0.8931 (mmm) cc_final: 0.8243 (pmt) REVERT: A 543 MET cc_start: 0.8929 (mmt) cc_final: 0.8667 (mmt) REVERT: A 841 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7553 (mtp180) REVERT: A 869 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: A 879 LYS cc_start: 0.8845 (mmmm) cc_final: 0.8297 (mmtt) REVERT: A 981 LYS cc_start: 0.8606 (mtpp) cc_final: 0.8171 (mptm) REVERT: B 11 LYS cc_start: 0.8514 (tttt) cc_final: 0.8154 (tttm) REVERT: B 51 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8354 (mt-10) REVERT: B 58 ASP cc_start: 0.8018 (m-30) cc_final: 0.7300 (m-30) REVERT: C 8 ARG cc_start: 0.8116 (mtt-85) cc_final: 0.7764 (ttp-170) REVERT: C 135 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: C 136 LEU cc_start: 0.8160 (mm) cc_final: 0.7795 (tp) REVERT: C 143 ARG cc_start: 0.8471 (ttp80) cc_final: 0.8178 (mtm110) REVERT: C 144 LYS cc_start: 0.8467 (ttmt) cc_final: 0.8148 (ttmt) REVERT: D 1 MET cc_start: 0.5763 (OUTLIER) cc_final: 0.5432 (mtm) outliers start: 18 outliers final: 7 residues processed: 132 average time/residue: 1.3719 time to fit residues: 193.6986 Evaluate side-chains 115 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 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 C residue 135 GLU 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 4 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.149414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.096576 restraints weight = 13021.387| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.55 r_work: 0.2966 rms_B_bonded: 2.95 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: 0.8263 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10347 Z= 0.143 Angle : 0.476 7.648 14011 Z= 0.248 Chirality : 0.042 0.161 1568 Planarity : 0.004 0.045 1812 Dihedral : 6.112 85.024 1412 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.24), residues: 1273 helix: 1.74 (0.24), residues: 511 sheet: 1.01 (0.35), residues: 206 loop : 0.59 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS C 75 PHE 0.011 0.001 PHE A 237 TYR 0.008 0.001 TYR A 736 ARG 0.012 0.000 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 474) hydrogen bonds : angle 4.37803 ( 1323) SS BOND : bond 0.01255 ( 1) SS BOND : angle 5.69876 ( 2) covalent geometry : bond 0.00353 (10344) covalent geometry : angle 0.47088 (14009) Misc. bond : bond 0.00120 ( 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 134 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7860 (tp30) cc_final: 0.7418 (tp30) REVERT: A 32 MET cc_start: 0.8551 (mtp) cc_final: 0.8306 (mtp) REVERT: A 33 LYS cc_start: 0.8390 (ttpt) cc_final: 0.7978 (ttmm) REVERT: A 184 MET cc_start: 0.8531 (mtp) cc_final: 0.8238 (mtt) REVERT: A 196 MET cc_start: 0.9003 (mmp) cc_final: 0.8664 (mmp) REVERT: A 216 LYS cc_start: 0.7305 (mtmm) cc_final: 0.6953 (pttp) REVERT: A 286 MET cc_start: 0.8900 (mmm) cc_final: 0.8210 (pmt) REVERT: A 869 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: A 879 LYS cc_start: 0.8853 (mmmm) cc_final: 0.8334 (mmtt) REVERT: A 980 LYS cc_start: 0.7963 (ptmt) cc_final: 0.7388 (ptpt) REVERT: A 981 LYS cc_start: 0.8644 (mtpp) cc_final: 0.8201 (mptm) REVERT: A 1011 LYS cc_start: 0.8888 (ttmm) cc_final: 0.8572 (ttmm) REVERT: B 11 LYS cc_start: 0.8461 (tttt) cc_final: 0.8175 (tttm) REVERT: B 51 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8332 (mt-10) REVERT: B 58 ASP cc_start: 0.8082 (m-30) cc_final: 0.7387 (m-30) REVERT: B 71 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8959 (pp) REVERT: C 8 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.7835 (ttp-170) REVERT: C 92 GLN cc_start: 0.6174 (OUTLIER) cc_final: 0.5961 (tm-30) REVERT: C 136 LEU cc_start: 0.8176 (mm) cc_final: 0.7793 (tp) REVERT: C 143 ARG cc_start: 0.8326 (ttp80) cc_final: 0.8014 (mtm110) REVERT: D 1 MET cc_start: 0.5764 (OUTLIER) cc_final: 0.5401 (mtm) outliers start: 26 outliers final: 12 residues processed: 125 average time/residue: 1.5931 time to fit residues: 213.5664 Evaluate side-chains 127 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 1003 VAL 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 D residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 77 optimal weight: 0.0980 chunk 49 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.150188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.097533 restraints weight = 12844.909| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.53 r_work: 0.2980 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10347 Z= 0.115 Angle : 0.451 6.999 14011 Z= 0.236 Chirality : 0.042 0.158 1568 Planarity : 0.004 0.058 1812 Dihedral : 5.993 85.188 1411 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.39 % Allowed : 9.20 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.24), residues: 1273 helix: 1.76 (0.24), residues: 511 sheet: 1.06 (0.34), residues: 212 loop : 0.66 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.001 0.000 HIS C 32 PHE 0.010 0.001 PHE A 360 TYR 0.007 0.001 TYR A 250 ARG 0.009 0.000 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 474) hydrogen bonds : angle 4.25116 ( 1323) SS BOND : bond 0.01287 ( 1) SS BOND : angle 5.11834 ( 2) covalent geometry : bond 0.00277 (10344) covalent geometry : angle 0.44724 (14009) Misc. bond : bond 0.00232 ( 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 140 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7849 (tp30) cc_final: 0.7254 (tp30) REVERT: A 32 MET cc_start: 0.8529 (mtp) cc_final: 0.8324 (mtp) REVERT: A 33 LYS cc_start: 0.8390 (ttpt) cc_final: 0.7965 (ttmm) REVERT: A 184 MET cc_start: 0.8444 (mtp) cc_final: 0.8108 (mtt) REVERT: A 196 MET cc_start: 0.8985 (mmp) cc_final: 0.8625 (mmp) REVERT: A 216 LYS cc_start: 0.7277 (mtmm) cc_final: 0.6924 (pttp) REVERT: A 286 MET cc_start: 0.8888 (mmm) cc_final: 0.8221 (pmt) REVERT: A 668 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7675 (mpt) REVERT: A 869 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: A 879 LYS cc_start: 0.8842 (mmmm) cc_final: 0.8333 (mmtt) REVERT: A 980 LYS cc_start: 0.7981 (ptmt) cc_final: 0.7431 (ptpt) REVERT: A 981 LYS cc_start: 0.8650 (mtpp) cc_final: 0.8230 (mptm) REVERT: B 11 LYS cc_start: 0.8468 (tttt) cc_final: 0.8152 (tttm) REVERT: B 51 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8308 (mt-10) REVERT: B 58 ASP cc_start: 0.8098 (m-30) cc_final: 0.7376 (m-30) REVERT: B 71 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8962 (pp) REVERT: C 8 ARG cc_start: 0.8251 (mtt-85) cc_final: 0.7879 (ttp-170) REVERT: C 135 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: C 136 LEU cc_start: 0.8128 (mm) cc_final: 0.7753 (tp) REVERT: C 143 ARG cc_start: 0.8317 (ttp80) cc_final: 0.8004 (mtm110) REVERT: C 144 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8160 (ttmt) REVERT: D 1 MET cc_start: 0.5805 (OUTLIER) cc_final: 0.5335 (mtm) outliers start: 27 outliers final: 11 residues processed: 128 average time/residue: 1.4309 time to fit residues: 196.2560 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 : 1.221 ------------------------------------------------------------------------------- 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 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 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 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 113 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 111 optimal weight: 0.0070 chunk 96 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.150064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.097279 restraints weight = 12873.193| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.54 r_work: 0.2979 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10347 Z= 0.129 Angle : 0.467 9.024 14011 Z= 0.242 Chirality : 0.043 0.369 1568 Planarity : 0.004 0.047 1812 Dihedral : 5.920 81.252 1411 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.74 % Allowed : 9.56 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.24), residues: 1273 helix: 1.75 (0.24), residues: 510 sheet: 1.07 (0.34), residues: 212 loop : 0.65 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS C 75 PHE 0.010 0.001 PHE A 237 TYR 0.007 0.001 TYR A 736 ARG 0.008 0.000 ARG C 5 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 474) hydrogen bonds : angle 4.22245 ( 1323) SS BOND : bond 0.02061 ( 1) SS BOND : angle 4.36288 ( 2) covalent geometry : bond 0.00314 (10344) covalent geometry : angle 0.46446 (14009) Misc. bond : bond 0.00221 ( 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 130 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7859 (tp30) cc_final: 0.7244 (tp30) REVERT: A 32 MET cc_start: 0.8534 (mtp) cc_final: 0.8298 (mtp) REVERT: A 33 LYS cc_start: 0.8393 (ttpt) cc_final: 0.7959 (ttmm) REVERT: A 184 MET cc_start: 0.8529 (mtp) cc_final: 0.8228 (mtt) REVERT: A 216 LYS cc_start: 0.7310 (mtmm) cc_final: 0.6954 (pttp) REVERT: A 286 MET cc_start: 0.8878 (mmm) cc_final: 0.8236 (pmt) REVERT: A 869 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: A 879 LYS cc_start: 0.8851 (mmmm) cc_final: 0.8344 (mmtt) REVERT: A 919 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8589 (pmm-80) REVERT: A 980 LYS cc_start: 0.7980 (ptmt) cc_final: 0.7429 (ptpt) REVERT: A 981 LYS cc_start: 0.8638 (mtpp) cc_final: 0.8228 (mptm) REVERT: B 51 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8332 (mt-10) REVERT: B 58 ASP cc_start: 0.8110 (m-30) cc_final: 0.7410 (m-30) REVERT: B 71 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8939 (pp) REVERT: C 8 ARG cc_start: 0.8264 (mtt-85) cc_final: 0.7890 (ttp-170) REVERT: C 135 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: C 136 LEU cc_start: 0.8092 (mm) cc_final: 0.7735 (tp) REVERT: C 143 ARG cc_start: 0.8304 (ttp80) cc_final: 0.7974 (mtm110) REVERT: D 1 MET cc_start: 0.5720 (OUTLIER) cc_final: 0.5273 (mtm) outliers start: 31 outliers final: 16 residues processed: 118 average time/residue: 1.8839 time to fit residues: 239.0311 Evaluate side-chains 118 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 3.193 ------------------------------------------------------------------------------- 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 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 110 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 47 optimal weight: 0.0670 chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.149699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.097035 restraints weight = 12927.173| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.53 r_work: 0.2976 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10347 Z= 0.135 Angle : 0.467 8.225 14011 Z= 0.243 Chirality : 0.042 0.172 1568 Planarity : 0.004 0.048 1812 Dihedral : 5.900 76.033 1411 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.39 % Allowed : 10.18 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.24), residues: 1273 helix: 1.73 (0.24), residues: 510 sheet: 1.12 (0.34), residues: 211 loop : 0.64 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS C 75 PHE 0.014 0.001 PHE A 237 TYR 0.007 0.001 TYR A 81 ARG 0.008 0.000 ARG C 5 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 474) hydrogen bonds : angle 4.20358 ( 1323) SS BOND : bond 0.00899 ( 1) SS BOND : angle 4.07459 ( 2) covalent geometry : bond 0.00333 (10344) covalent geometry : angle 0.46479 (14009) Misc. bond : bond 0.00009 ( 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 123 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7936 (tp30) cc_final: 0.7317 (tp30) REVERT: A 32 MET cc_start: 0.8540 (mtp) cc_final: 0.8286 (mtp) REVERT: A 33 LYS cc_start: 0.8385 (ttpt) cc_final: 0.7963 (ttmm) REVERT: A 184 MET cc_start: 0.8437 (mtp) cc_final: 0.8195 (mtt) REVERT: A 196 MET cc_start: 0.8818 (tpp) cc_final: 0.8553 (mmp) REVERT: A 216 LYS cc_start: 0.7325 (mtmm) cc_final: 0.6956 (pttp) REVERT: A 286 MET cc_start: 0.8854 (mmm) cc_final: 0.8202 (pmt) REVERT: A 869 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: A 879 LYS cc_start: 0.8848 (mmmm) cc_final: 0.8334 (mmtt) REVERT: A 980 LYS cc_start: 0.8021 (ptmt) cc_final: 0.7455 (ptpt) REVERT: B 11 LYS cc_start: 0.8444 (tttt) cc_final: 0.8165 (tttm) REVERT: B 58 ASP cc_start: 0.8122 (m-30) cc_final: 0.7388 (m-30) REVERT: B 71 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8947 (pp) REVERT: C 8 ARG cc_start: 0.8277 (mtt-85) cc_final: 0.7888 (ttp-170) REVERT: C 92 GLN cc_start: 0.6066 (OUTLIER) cc_final: 0.5834 (tm-30) REVERT: C 135 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: C 136 LEU cc_start: 0.8119 (mm) cc_final: 0.7752 (tp) REVERT: C 143 ARG cc_start: 0.8303 (ttp80) cc_final: 0.7963 (mtm110) REVERT: C 144 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8278 (ttpt) REVERT: D 1 MET cc_start: 0.5761 (OUTLIER) cc_final: 0.5356 (mtm) outliers start: 27 outliers final: 14 residues processed: 114 average time/residue: 1.8403 time to fit residues: 225.2900 Evaluate side-chains 114 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 2.936 ------------------------------------------------------------------------------- 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 1003 VAL 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 85 CYS Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 110 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.148932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.096107 restraints weight = 13016.031| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.55 r_work: 0.2959 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10347 Z= 0.163 Angle : 0.493 11.236 14011 Z= 0.252 Chirality : 0.043 0.293 1568 Planarity : 0.004 0.049 1812 Dihedral : 5.944 72.908 1411 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.30 % Allowed : 10.53 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.24), residues: 1273 helix: 1.63 (0.24), residues: 510 sheet: 0.97 (0.34), residues: 222 loop : 0.60 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.001 HIS C 75 PHE 0.012 0.001 PHE A 237 TYR 0.009 0.001 TYR A 81 ARG 0.006 0.000 ARG C 5 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 474) hydrogen bonds : angle 4.26198 ( 1323) SS BOND : bond 0.00893 ( 1) SS BOND : angle 4.33894 ( 2) covalent geometry : bond 0.00411 (10344) covalent geometry : angle 0.48983 (14009) Misc. bond : bond 0.00045 ( 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 125 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7950 (tp30) cc_final: 0.7422 (tp30) REVERT: A 32 MET cc_start: 0.8548 (mtp) cc_final: 0.8264 (mtp) REVERT: A 33 LYS cc_start: 0.8408 (ttpt) cc_final: 0.7965 (ttmm) REVERT: A 184 MET cc_start: 0.8557 (mtp) cc_final: 0.8347 (mtt) REVERT: A 216 LYS cc_start: 0.7381 (mtmm) cc_final: 0.7016 (pttp) REVERT: A 286 MET cc_start: 0.8870 (mmm) cc_final: 0.8217 (pmt) REVERT: A 869 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: A 879 LYS cc_start: 0.8860 (mmmm) cc_final: 0.8347 (mmtt) REVERT: A 980 LYS cc_start: 0.8117 (ptmt) cc_final: 0.7513 (ptpt) REVERT: A 981 LYS cc_start: 0.8613 (mtpp) cc_final: 0.8285 (mptm) REVERT: B 11 LYS cc_start: 0.8457 (tttt) cc_final: 0.8219 (tttm) REVERT: B 58 ASP cc_start: 0.8133 (m-30) cc_final: 0.7391 (m-30) REVERT: B 71 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8946 (pp) REVERT: C 8 ARG cc_start: 0.8258 (mtt-85) cc_final: 0.7963 (ttp-170) REVERT: C 135 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: C 136 LEU cc_start: 0.8098 (mm) cc_final: 0.7736 (tp) REVERT: C 143 ARG cc_start: 0.8316 (ttp80) cc_final: 0.7996 (mtm110) REVERT: D 1 MET cc_start: 0.5831 (mtm) cc_final: 0.5431 (mtm) outliers start: 26 outliers final: 15 residues processed: 115 average time/residue: 1.3391 time to fit residues: 165.0958 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 : 1.063 ------------------------------------------------------------------------------- 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 1003 VAL 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 91 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 144 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 58 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 68 optimal weight: 0.1980 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 = 0.3886 r_free = 0.3886 target = 0.149254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.096536 restraints weight = 13001.535| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.56 r_work: 0.2960 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10347 Z= 0.139 Angle : 0.488 9.623 14011 Z= 0.252 Chirality : 0.043 0.178 1568 Planarity : 0.004 0.049 1812 Dihedral : 5.932 72.994 1411 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.12 % Allowed : 11.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.24), residues: 1273 helix: 1.64 (0.24), residues: 510 sheet: 0.93 (0.34), residues: 217 loop : 0.60 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS C 75 PHE 0.012 0.001 PHE A 237 TYR 0.007 0.001 TYR A 81 ARG 0.008 0.000 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 474) hydrogen bonds : angle 4.24361 ( 1323) SS BOND : bond 0.00773 ( 1) SS BOND : angle 4.11923 ( 2) covalent geometry : bond 0.00345 (10344) covalent geometry : angle 0.48546 (14009) Misc. bond : bond 0.00019 ( 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 121 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7975 (tp30) cc_final: 0.7365 (tp30) REVERT: A 33 LYS cc_start: 0.8409 (ttpt) cc_final: 0.7982 (ttmm) REVERT: A 184 MET cc_start: 0.8489 (mtp) cc_final: 0.8224 (mtt) REVERT: A 196 MET cc_start: 0.8834 (tpp) cc_final: 0.8491 (mmp) REVERT: A 216 LYS cc_start: 0.7386 (mtmm) cc_final: 0.7025 (pttp) REVERT: A 286 MET cc_start: 0.8858 (mmm) cc_final: 0.8203 (pmt) REVERT: A 869 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: A 879 LYS cc_start: 0.8846 (mmmm) cc_final: 0.8330 (mmtt) REVERT: A 980 LYS cc_start: 0.8070 (ptmt) cc_final: 0.7465 (ptpt) REVERT: A 981 LYS cc_start: 0.8604 (mtpp) cc_final: 0.8257 (mptm) REVERT: B 71 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8947 (pp) REVERT: C 8 ARG cc_start: 0.8262 (mtt-85) cc_final: 0.7964 (ttp-170) REVERT: C 135 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: C 136 LEU cc_start: 0.8107 (mm) cc_final: 0.7748 (tp) REVERT: C 143 ARG cc_start: 0.8318 (ttp80) cc_final: 0.7990 (mtm110) REVERT: D 1 MET cc_start: 0.5788 (mtm) cc_final: 0.5378 (mtm) outliers start: 24 outliers final: 16 residues processed: 113 average time/residue: 1.3801 time to fit residues: 167.4635 Evaluate side-chains 114 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 1003 VAL 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 91 ASP Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 144 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 0.4980 chunk 112 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.146292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.092901 restraints weight = 13052.432| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.54 r_work: 0.2959 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10347 Z= 0.164 Angle : 0.494 10.774 14011 Z= 0.254 Chirality : 0.043 0.236 1568 Planarity : 0.004 0.049 1812 Dihedral : 5.965 71.089 1411 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.86 % Allowed : 11.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.24), residues: 1273 helix: 1.57 (0.24), residues: 510 sheet: 0.95 (0.33), residues: 222 loop : 0.58 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS C 75 PHE 0.013 0.001 PHE A 237 TYR 0.008 0.001 TYR A 81 ARG 0.008 0.000 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 474) hydrogen bonds : angle 4.30645 ( 1323) SS BOND : bond 0.00880 ( 1) SS BOND : angle 4.31218 ( 2) covalent geometry : bond 0.00411 (10344) covalent geometry : angle 0.49090 (14009) Misc. bond : bond 0.00018 ( 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: 21 poor density : 96 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7949 (tp30) cc_final: 0.7322 (tp30) REVERT: A 33 LYS cc_start: 0.8441 (ttpt) cc_final: 0.8007 (ttmm) REVERT: A 184 MET cc_start: 0.8522 (mtp) cc_final: 0.8266 (mtt) REVERT: A 196 MET cc_start: 0.8895 (tpp) cc_final: 0.8543 (mmp) REVERT: A 216 LYS cc_start: 0.7432 (mtmm) cc_final: 0.7087 (pttp) REVERT: A 286 MET cc_start: 0.8866 (mmm) cc_final: 0.8223 (pmt) REVERT: A 869 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7957 (mp0) REVERT: A 879 LYS cc_start: 0.8857 (mmmm) cc_final: 0.8344 (mmtt) REVERT: A 980 LYS cc_start: 0.8123 (ptmt) cc_final: 0.7518 (ptpt) REVERT: A 981 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8262 (mptm) REVERT: B 71 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8946 (pp) REVERT: C 8 ARG cc_start: 0.8283 (mtt-85) cc_final: 0.7994 (ttp-170) REVERT: C 135 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: C 136 LEU cc_start: 0.8139 (mm) cc_final: 0.7775 (tp) REVERT: C 143 ARG cc_start: 0.8342 (ttp80) cc_final: 0.8020 (mtm110) REVERT: D 1 MET cc_start: 0.5631 (mtm) cc_final: 0.5183 (mtm) outliers start: 21 outliers final: 15 residues processed: 109 average time/residue: 1.3491 time to fit residues: 157.7446 Evaluate side-chains 115 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 1003 VAL 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 91 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 144 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 17 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 64 optimal weight: 0.0070 chunk 34 optimal weight: 0.5980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 = 0.146893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.093643 restraints weight = 13066.091| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.50 r_work: 0.2974 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10347 Z= 0.133 Angle : 0.492 9.879 14011 Z= 0.254 Chirality : 0.042 0.181 1568 Planarity : 0.004 0.049 1812 Dihedral : 5.918 71.491 1411 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.86 % Allowed : 11.68 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.24), residues: 1273 helix: 1.61 (0.24), residues: 510 sheet: 0.99 (0.33), residues: 222 loop : 0.60 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS C 32 PHE 0.011 0.001 PHE A 237 TYR 0.007 0.001 TYR A 736 ARG 0.009 0.000 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 474) hydrogen bonds : angle 4.24950 ( 1323) SS BOND : bond 0.00692 ( 1) SS BOND : angle 4.04310 ( 2) covalent geometry : bond 0.00328 (10344) covalent geometry : angle 0.48937 (14009) Misc. bond : bond 0.00017 ( 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 118 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7917 (tp30) cc_final: 0.7300 (tp30) REVERT: A 33 LYS cc_start: 0.8422 (ttpt) cc_final: 0.7990 (ttmm) REVERT: A 184 MET cc_start: 0.8440 (mtp) cc_final: 0.8160 (mtt) REVERT: A 193 VAL cc_start: 0.8749 (t) cc_final: 0.8344 (p) REVERT: A 196 MET cc_start: 0.8884 (tpp) cc_final: 0.8527 (mmp) REVERT: A 216 LYS cc_start: 0.7365 (mtmm) cc_final: 0.7043 (pttp) REVERT: A 286 MET cc_start: 0.8838 (mmm) cc_final: 0.8196 (pmt) REVERT: A 869 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: A 879 LYS cc_start: 0.8840 (mmmm) cc_final: 0.8323 (mmtt) REVERT: A 980 LYS cc_start: 0.8099 (ptmt) cc_final: 0.7508 (ptpt) REVERT: A 981 LYS cc_start: 0.8607 (mtpp) cc_final: 0.8236 (mptm) REVERT: B 71 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8943 (pp) REVERT: C 8 ARG cc_start: 0.8255 (mtt-85) cc_final: 0.7970 (ttp-170) REVERT: C 135 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: C 136 LEU cc_start: 0.8147 (mm) cc_final: 0.7776 (tp) REVERT: C 143 ARG cc_start: 0.8324 (ttp80) cc_final: 0.7995 (mtm110) REVERT: C 144 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8296 (ttpt) REVERT: D 1 MET cc_start: 0.5654 (mtm) cc_final: 0.5196 (mtm) outliers start: 21 outliers final: 14 residues processed: 111 average time/residue: 1.3974 time to fit residues: 166.6648 Evaluate side-chains 119 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 855 MET Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 1003 VAL 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 91 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 144 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 6 optimal weight: 0.5980 chunk 50 optimal weight: 0.0570 chunk 123 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 37 optimal weight: 0.0570 chunk 41 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 76 optimal weight: 0.0060 chunk 85 optimal weight: 0.7980 overall best weight: 0.2632 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.150933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098483 restraints weight = 12888.028| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.54 r_work: 0.2992 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10347 Z= 0.096 Angle : 0.473 10.936 14011 Z= 0.243 Chirality : 0.042 0.221 1568 Planarity : 0.004 0.047 1812 Dihedral : 5.603 68.601 1410 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.42 % Allowed : 11.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1273 helix: 1.68 (0.24), residues: 513 sheet: 1.04 (0.33), residues: 223 loop : 0.65 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 32 PHE 0.009 0.001 PHE A 237 TYR 0.006 0.001 TYR C 74 ARG 0.009 0.000 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 474) hydrogen bonds : angle 4.13222 ( 1323) SS BOND : bond 0.01676 ( 1) SS BOND : angle 1.38442 ( 2) covalent geometry : bond 0.00221 (10344) covalent geometry : angle 0.47262 (14009) Misc. bond : bond 0.00043 ( 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: 8913.43 seconds wall clock time: 155 minutes 14.79 seconds (9314.79 seconds total)