Starting phenix.real_space_refine on Fri Jan 17 00:28:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5e_44209/01_2025/9b5e_44209.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5e_44209/01_2025/9b5e_44209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5e_44209/01_2025/9b5e_44209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5e_44209/01_2025/9b5e_44209.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5e_44209/01_2025/9b5e_44209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5e_44209/01_2025/9b5e_44209.cif" } resolution = 2.81 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= 0.072 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 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 7.29, per 1000 atoms: 0.72 Number of scatterers: 10128 At special positions: 0 Unit cell: (92.568, 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=2.92 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: 2.78 Conformation dependent library (CDL) restraints added in 1.7 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 46.4% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.758A 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: 3.643A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.331A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.646A pdb=" N LYS A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.645A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.570A pdb=" N ASP A 223 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.388A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.647A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.617A 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: 4.356A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.549A 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: 3.644A 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: 3.776A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.830A pdb=" N LYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.587A pdb=" N ARG A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.544A pdb=" N SER A 581 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.824A 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: 3.571A pdb=" N THR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) removed outlier: 3.794A 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: 3.711A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.504A pdb=" N GLN A 683 " --> pdb=" O ASN A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 737 Processing helix chain 'A' and resid 743 through 753 removed outlier: 3.935A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 removed outlier: 3.795A pdb=" N GLN A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 818 through 835 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.518A pdb=" N THR A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.706A pdb=" N GLU A 882 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.787A 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 938 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 146 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 37 through 41 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: 6.851A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.308A 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: 4.097A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.320A 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: 4.097A 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: 6.507A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.264A 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: 6.316A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.381A 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: 6.316A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.423A 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: 3.850A pdb=" N ARG B 42 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.625A pdb=" N GLY C 24 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 6.182A 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 removed outlier: 4.130A pdb=" N SER D 65 " --> pdb=" O GLN D 2 " (cutoff:3.500A) 491 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: 3.78 Time building geometry restraints manager: 3.23 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: 5989 1.54 - 1.67: 156 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 1.526 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.66e+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 8.97e-01 bond pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " ideal model delta sigma weight residual 1.531 1.520 0.011 1.20e-02 6.94e+03 8.42e-01 ... (remaining 10339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 13840 1.32 - 2.65: 89 2.65 - 3.97: 70 3.97 - 5.29: 6 5.29 - 6.61: 4 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 121.70 128.18 -6.48 1.80e+00 3.09e-01 1.29e+01 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.40 3.13 1.18e+00 7.24e-01 7.09e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.51 4.68 1.76e+00 3.23e-01 7.08e+00 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 105.26 6.57 2.67e+00 1.40e-01 6.06e+00 angle pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" O2' ATP A1103 " ideal model delta sigma weight residual 110.58 103.97 6.61 2.79e+00 1.28e-01 5.60e+00 ... (remaining 14004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 6043 16.31 - 32.63: 204 32.63 - 48.94: 46 48.94 - 65.26: 12 65.26 - 81.57: 3 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 -138.95 52.95 1 1.00e+01 1.00e-02 3.82e+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 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" N GLN A 80 " pdb=" CA GLN A 80 " pdb=" CB GLN A 80 " pdb=" CG GLN A 80 " ideal model delta sinusoidal sigma weight residual -180.00 -122.88 -57.12 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: 1390 0.060 - 0.119: 154 0.119 - 0.179: 21 0.179 - 0.238: 1 0.238 - 0.298: 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 2.22e+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 -2.91 0.28 2.00e-01 2.50e+01 1.91e+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 1.35e+00 ... (remaining 1565 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO C 95 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 120 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO C 121 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 17 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO C 18 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO C 18 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 18 " 0.016 5.00e-02 4.00e+02 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 76 2.61 - 3.18: 8766 3.18 - 3.75: 14660 3.75 - 4.33: 22165 4.33 - 4.90: 37204 Nonbonded interactions: 82871 Sorted by model distance: nonbonded pdb="MG MG A1101 " pdb=" O2B ATP A1103 " model vdw 2.037 2.170 nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.043 2.170 nonbonded pdb=" OD2 ASP A 537 " pdb="MG MG A1101 " model vdw 2.078 2.170 nonbonded pdb=" O PRO C 18 " pdb=" OG SER C 19 " model vdw 2.171 3.040 nonbonded pdb=" OD2 ASP A 463 " pdb=" O3' ATP A1103 " model vdw 2.188 3.040 ... (remaining 82866 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.210 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10344 Z= 0.169 Angle : 0.442 6.614 14009 Z= 0.223 Chirality : 0.042 0.298 1568 Planarity : 0.003 0.039 1812 Dihedral : 9.403 81.569 3901 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.15 % Allowed : 1.77 % Favored : 97.08 % 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: 1.33 (0.24), residues: 1273 helix: 1.63 (0.24), residues: 501 sheet: 0.67 (0.34), residues: 207 loop : 0.42 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.002 0.000 HIS C 75 PHE 0.011 0.001 PHE A 360 TYR 0.007 0.001 TYR A 732 ARG 0.002 0.000 ARG A 409 *********************** 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 172 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.6708 (mtp85) cc_final: 0.6036 (mtm-85) REVERT: A 85 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7656 (mp0) REVERT: A 114 GLU cc_start: 0.8066 (pt0) cc_final: 0.7849 (pt0) REVERT: A 184 MET cc_start: 0.8244 (mtp) cc_final: 0.7836 (mtt) REVERT: A 191 ASP cc_start: 0.8097 (m-30) cc_final: 0.7717 (p0) REVERT: A 218 MET cc_start: 0.7520 (mtt) cc_final: 0.7300 (mtt) REVERT: A 235 TYR cc_start: 0.8284 (m-80) cc_final: 0.7971 (m-80) REVERT: A 274 ASP cc_start: 0.7507 (t70) cc_final: 0.6991 (p0) REVERT: A 353 ASP cc_start: 0.7930 (t0) cc_final: 0.7436 (t0) REVERT: A 442 MET cc_start: 0.8059 (tpp) cc_final: 0.7605 (mmm) REVERT: A 540 GLU cc_start: 0.7531 (tt0) cc_final: 0.7041 (mp0) REVERT: A 558 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7742 (tm-30) REVERT: A 601 ARG cc_start: 0.7457 (mtp85) cc_final: 0.6977 (mtp180) REVERT: A 668 MET cc_start: 0.7197 (mmm) cc_final: 0.6796 (mpp) REVERT: A 723 ASP cc_start: 0.7168 (m-30) cc_final: 0.6862 (m-30) REVERT: A 879 LYS cc_start: 0.8133 (mmmm) cc_final: 0.7398 (mtmt) REVERT: A 909 ASN cc_start: 0.7583 (t0) cc_final: 0.7189 (t0) REVERT: A 937 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: A 1011 LYS cc_start: 0.8274 (ttmm) cc_final: 0.8042 (ttmm) REVERT: B 39 ASP cc_start: 0.8348 (m-30) cc_final: 0.8031 (p0) REVERT: C 34 GLN cc_start: 0.8535 (tt0) cc_final: 0.8155 (tt0) REVERT: C 66 LYS cc_start: 0.8044 (mtmt) cc_final: 0.7840 (mttp) REVERT: C 72 ARG cc_start: 0.8280 (mmm-85) cc_final: 0.7625 (tpt170) REVERT: C 92 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7603 (tm-30) REVERT: C 117 ASP cc_start: 0.8409 (t0) cc_final: 0.8089 (t0) outliers start: 13 outliers final: 2 residues processed: 167 average time/residue: 1.4854 time to fit residues: 264.5148 Evaluate side-chains 121 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 118 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.0470 chunk 95 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 0.0010 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 0.3980 chunk 114 optimal weight: 3.9990 overall best weight: 0.3084 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.139884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098306 restraints weight = 12036.741| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.10 r_work: 0.2964 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10344 Z= 0.167 Angle : 0.481 5.902 14009 Z= 0.252 Chirality : 0.042 0.156 1568 Planarity : 0.004 0.039 1812 Dihedral : 6.071 78.010 1411 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.86 % Allowed : 6.73 % Favored : 91.42 % 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: 1.86 (0.24), residues: 503 sheet: 1.02 (0.36), residues: 193 loop : 0.49 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 669 HIS 0.002 0.001 HIS C 32 PHE 0.010 0.001 PHE A 360 TYR 0.010 0.001 TYR A 736 ARG 0.005 0.000 ARG C 143 *********************** 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 147 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7739 (mtp85) cc_final: 0.7158 (mtm-85) REVERT: A 184 MET cc_start: 0.8497 (mtp) cc_final: 0.8160 (mtt) REVERT: A 191 ASP cc_start: 0.8111 (m-30) cc_final: 0.7794 (p0) REVERT: A 218 MET cc_start: 0.7828 (mtt) cc_final: 0.7586 (mtt) REVERT: A 235 TYR cc_start: 0.8862 (m-80) cc_final: 0.8646 (m-80) REVERT: A 353 ASP cc_start: 0.8101 (t0) cc_final: 0.7757 (t0) REVERT: A 442 MET cc_start: 0.8852 (tpp) cc_final: 0.8641 (mmm) REVERT: A 465 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8187 (t70) REVERT: A 540 GLU cc_start: 0.8450 (tt0) cc_final: 0.8208 (mp0) REVERT: A 668 MET cc_start: 0.8215 (mmm) cc_final: 0.7875 (mpp) REVERT: A 723 ASP cc_start: 0.8144 (m-30) cc_final: 0.7896 (m-30) REVERT: A 879 LYS cc_start: 0.8802 (mmmm) cc_final: 0.8279 (mtmt) REVERT: A 944 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7319 (tmt) REVERT: A 983 GLU cc_start: 0.8506 (mp0) cc_final: 0.8062 (mp0) REVERT: B 39 ASP cc_start: 0.8569 (m-30) cc_final: 0.8251 (p0) REVERT: C 92 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7797 (tm-30) outliers start: 21 outliers final: 8 residues processed: 137 average time/residue: 1.3111 time to fit residues: 192.8251 Evaluate side-chains 120 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 4 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.142021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.094875 restraints weight = 12554.567| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.45 r_work: 0.2913 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10344 Z= 0.264 Angle : 0.497 5.924 14009 Z= 0.258 Chirality : 0.043 0.157 1568 Planarity : 0.004 0.043 1812 Dihedral : 5.857 81.050 1408 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.77 % Allowed : 8.85 % Favored : 89.38 % 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: 1.55 (0.24), residues: 1273 helix: 1.76 (0.24), residues: 502 sheet: 1.03 (0.35), residues: 206 loop : 0.49 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS C 125 PHE 0.012 0.001 PHE A 360 TYR 0.009 0.001 TYR C 145 ARG 0.006 0.000 ARG C 143 *********************** 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: 20 poor density : 115 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7545 (mtp85) cc_final: 0.6812 (mtm-85) REVERT: A 184 MET cc_start: 0.8653 (mtp) cc_final: 0.8280 (mtt) REVERT: A 191 ASP cc_start: 0.8181 (m-30) cc_final: 0.7781 (p0) REVERT: A 235 TYR cc_start: 0.8759 (m-80) cc_final: 0.8535 (m-80) REVERT: A 353 ASP cc_start: 0.8250 (t0) cc_final: 0.7779 (t0) REVERT: A 465 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8257 (t70) REVERT: A 540 GLU cc_start: 0.8432 (tt0) cc_final: 0.7922 (mp0) REVERT: A 668 MET cc_start: 0.8088 (mmm) cc_final: 0.7686 (mpp) REVERT: A 723 ASP cc_start: 0.8118 (m-30) cc_final: 0.7903 (m-30) REVERT: A 762 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8512 (pttt) REVERT: A 879 LYS cc_start: 0.8740 (mmmm) cc_final: 0.8160 (mtmt) REVERT: A 937 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7925 (mp0) REVERT: A 944 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7228 (tmt) REVERT: A 983 GLU cc_start: 0.8364 (mp0) cc_final: 0.7844 (mp0) REVERT: B 39 ASP cc_start: 0.8532 (m-30) cc_final: 0.8088 (p0) REVERT: C 92 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7499 (tm-30) outliers start: 20 outliers final: 10 residues processed: 128 average time/residue: 1.4167 time to fit residues: 194.8528 Evaluate side-chains 126 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 20 optimal weight: 5.9990 chunk 104 optimal weight: 0.3980 chunk 88 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 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 = 0.3744 r_free = 0.3744 target = 0.143320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.094653 restraints weight = 12531.429| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.47 r_work: 0.2917 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10344 Z= 0.206 Angle : 0.472 6.761 14009 Z= 0.245 Chirality : 0.042 0.170 1568 Planarity : 0.004 0.047 1812 Dihedral : 5.825 83.458 1408 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.86 % Allowed : 10.18 % 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 (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: 1.59 (0.24), residues: 1273 helix: 1.82 (0.24), residues: 501 sheet: 1.01 (0.35), residues: 206 loop : 0.51 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 125 PHE 0.011 0.001 PHE A 360 TYR 0.013 0.001 TYR C 145 ARG 0.009 0.000 ARG C 5 *********************** 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 136 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7519 (mtp85) cc_final: 0.6769 (mtm-85) REVERT: A 184 MET cc_start: 0.8484 (mtp) cc_final: 0.8119 (mtt) REVERT: A 235 TYR cc_start: 0.8756 (m-80) cc_final: 0.8532 (m-80) REVERT: A 353 ASP cc_start: 0.8231 (t0) cc_final: 0.7680 (m-30) REVERT: A 465 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8290 (t70) REVERT: A 540 GLU cc_start: 0.8395 (tt0) cc_final: 0.7865 (mp0) REVERT: A 668 MET cc_start: 0.8088 (mmm) cc_final: 0.7686 (mpp) REVERT: A 723 ASP cc_start: 0.8093 (m-30) cc_final: 0.7870 (m-30) REVERT: A 762 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8500 (pttt) REVERT: A 879 LYS cc_start: 0.8754 (mmmm) cc_final: 0.8165 (mtmt) REVERT: A 937 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: A 983 GLU cc_start: 0.8360 (mp0) cc_final: 0.7820 (mp0) REVERT: B 39 ASP cc_start: 0.8475 (m-30) cc_final: 0.8044 (p0) REVERT: C 92 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7487 (tm-30) REVERT: D 27 LYS cc_start: 0.8731 (tppp) cc_final: 0.8452 (tppp) outliers start: 21 outliers final: 11 residues processed: 129 average time/residue: 1.2905 time to fit residues: 179.7891 Evaluate side-chains 123 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.7980 chunk 27 optimal weight: 0.1980 chunk 36 optimal weight: 0.0570 chunk 111 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.143321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.096364 restraints weight = 12356.204| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.44 r_work: 0.2925 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10344 Z= 0.189 Angle : 0.463 7.132 14009 Z= 0.240 Chirality : 0.042 0.150 1568 Planarity : 0.004 0.045 1812 Dihedral : 5.785 83.791 1408 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.21 % Allowed : 10.44 % 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 (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: 1.64 (0.24), residues: 1273 helix: 1.86 (0.24), residues: 502 sheet: 0.96 (0.35), residues: 207 loop : 0.56 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.002 0.000 HIS C 125 PHE 0.011 0.001 PHE A 360 TYR 0.015 0.001 TYR C 145 ARG 0.009 0.000 ARG C 143 *********************** 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 140 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8465 (mtp) cc_final: 0.8102 (mtt) REVERT: A 213 THR cc_start: 0.7344 (OUTLIER) cc_final: 0.6944 (t) REVERT: A 235 TYR cc_start: 0.8758 (m-80) cc_final: 0.8523 (m-80) REVERT: A 250 TYR cc_start: 0.7708 (m-80) cc_final: 0.7364 (m-80) REVERT: A 353 ASP cc_start: 0.8220 (t0) cc_final: 0.7685 (m-30) REVERT: A 465 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8324 (t70) REVERT: A 540 GLU cc_start: 0.8350 (tt0) cc_final: 0.7853 (mp0) REVERT: A 668 MET cc_start: 0.8084 (mmm) cc_final: 0.7685 (mpp) REVERT: A 723 ASP cc_start: 0.8109 (m-30) cc_final: 0.7888 (m-30) REVERT: A 762 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8489 (pttt) REVERT: A 879 LYS cc_start: 0.8754 (mmmm) cc_final: 0.8160 (mtmt) REVERT: A 937 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: A 983 GLU cc_start: 0.8371 (mp0) cc_final: 0.7804 (mp0) REVERT: B 39 ASP cc_start: 0.8481 (m-30) cc_final: 0.8044 (p0) REVERT: C 92 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7468 (tm-30) outliers start: 25 outliers final: 14 residues processed: 130 average time/residue: 1.2468 time to fit residues: 174.9983 Evaluate side-chains 127 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 47 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 83 optimal weight: 0.0970 chunk 101 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.142649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.095789 restraints weight = 12429.791| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.45 r_work: 0.2916 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10344 Z= 0.214 Angle : 0.471 7.174 14009 Z= 0.244 Chirality : 0.042 0.150 1568 Planarity : 0.004 0.049 1812 Dihedral : 5.814 83.636 1408 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.30 % Allowed : 11.06 % 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: 1.63 (0.24), residues: 1273 helix: 1.84 (0.24), residues: 502 sheet: 0.95 (0.35), residues: 207 loop : 0.57 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS A 29 PHE 0.012 0.001 PHE A 360 TYR 0.008 0.001 TYR A 736 ARG 0.010 0.000 ARG C 5 *********************** 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 138 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7522 (mtp85) cc_final: 0.6792 (mtm-85) REVERT: A 184 MET cc_start: 0.8481 (mtp) cc_final: 0.8115 (mtt) REVERT: A 213 THR cc_start: 0.7383 (OUTLIER) cc_final: 0.6985 (t) REVERT: A 235 TYR cc_start: 0.8759 (m-80) cc_final: 0.8518 (m-80) REVERT: A 250 TYR cc_start: 0.7674 (m-80) cc_final: 0.7355 (m-80) REVERT: A 335 ASP cc_start: 0.7490 (m-30) cc_final: 0.7203 (p0) REVERT: A 353 ASP cc_start: 0.8233 (t0) cc_final: 0.7697 (m-30) REVERT: A 540 GLU cc_start: 0.8337 (tt0) cc_final: 0.7865 (mp0) REVERT: A 668 MET cc_start: 0.8096 (mmm) cc_final: 0.7696 (mpp) REVERT: A 723 ASP cc_start: 0.8122 (m-30) cc_final: 0.7883 (m-30) REVERT: A 762 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8486 (pttt) REVERT: A 879 LYS cc_start: 0.8775 (mmmm) cc_final: 0.8186 (mtmt) REVERT: A 937 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: A 983 GLU cc_start: 0.8324 (mp0) cc_final: 0.7761 (mp0) REVERT: B 39 ASP cc_start: 0.8508 (m-30) cc_final: 0.8061 (p0) REVERT: C 92 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7480 (tm-30) REVERT: D 27 LYS cc_start: 0.8792 (tppp) cc_final: 0.8543 (tppp) outliers start: 26 outliers final: 16 residues processed: 127 average time/residue: 1.2253 time to fit residues: 168.1047 Evaluate side-chains 130 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 14 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.141745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.094969 restraints weight = 12524.407| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.44 r_work: 0.2900 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10344 Z= 0.272 Angle : 0.486 7.405 14009 Z= 0.251 Chirality : 0.043 0.148 1568 Planarity : 0.004 0.045 1812 Dihedral : 5.905 83.684 1408 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.21 % Allowed : 11.59 % Favored : 86.19 % 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: 1.54 (0.24), residues: 1273 helix: 1.78 (0.24), residues: 502 sheet: 0.88 (0.35), residues: 207 loop : 0.52 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS C 125 PHE 0.013 0.001 PHE C 62 TYR 0.009 0.001 TYR A 81 ARG 0.009 0.000 ARG C 5 *********************** 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 145 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7556 (mtp85) cc_final: 0.6831 (mtm-85) REVERT: A 184 MET cc_start: 0.8628 (mtp) cc_final: 0.8276 (mtt) REVERT: A 213 THR cc_start: 0.7400 (OUTLIER) cc_final: 0.7005 (t) REVERT: A 235 TYR cc_start: 0.8767 (m-80) cc_final: 0.8520 (m-80) REVERT: A 250 TYR cc_start: 0.7709 (m-80) cc_final: 0.7391 (m-80) REVERT: A 335 ASP cc_start: 0.7504 (m-30) cc_final: 0.7223 (p0) REVERT: A 353 ASP cc_start: 0.8251 (t0) cc_final: 0.7711 (m-30) REVERT: A 540 GLU cc_start: 0.8352 (tt0) cc_final: 0.7865 (mp0) REVERT: A 668 MET cc_start: 0.8109 (mmm) cc_final: 0.7763 (mpp) REVERT: A 723 ASP cc_start: 0.8134 (m-30) cc_final: 0.7900 (m-30) REVERT: A 762 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8490 (pttt) REVERT: A 879 LYS cc_start: 0.8777 (mmmm) cc_final: 0.8186 (mtmt) REVERT: A 937 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: A 983 GLU cc_start: 0.8314 (mp0) cc_final: 0.7738 (mp0) REVERT: B 39 ASP cc_start: 0.8519 (m-30) cc_final: 0.8063 (p0) REVERT: C 92 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7485 (tm-30) REVERT: D 27 LYS cc_start: 0.8889 (tppp) cc_final: 0.8565 (tppp) outliers start: 25 outliers final: 18 residues processed: 136 average time/residue: 1.1927 time to fit residues: 175.4681 Evaluate side-chains 130 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 949 VAL 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 22 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.142228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.093877 restraints weight = 12693.275| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.47 r_work: 0.2891 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10344 Z= 0.274 Angle : 0.495 7.747 14009 Z= 0.257 Chirality : 0.043 0.178 1568 Planarity : 0.004 0.046 1812 Dihedral : 6.002 84.437 1408 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.21 % Allowed : 11.59 % Favored : 86.19 % 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: 1.49 (0.24), residues: 1273 helix: 1.73 (0.24), residues: 502 sheet: 0.85 (0.35), residues: 207 loop : 0.50 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS A 29 PHE 0.013 0.001 PHE A 360 TYR 0.013 0.001 TYR A 81 ARG 0.008 0.000 ARG C 143 *********************** 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 140 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7546 (mtp85) cc_final: 0.6891 (mtm-85) REVERT: A 80 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8610 (mm110) REVERT: A 184 MET cc_start: 0.8636 (mtp) cc_final: 0.8261 (mtt) REVERT: A 213 THR cc_start: 0.7405 (OUTLIER) cc_final: 0.7013 (t) REVERT: A 235 TYR cc_start: 0.8765 (m-80) cc_final: 0.8508 (m-80) REVERT: A 250 TYR cc_start: 0.7729 (m-80) cc_final: 0.7467 (m-80) REVERT: A 335 ASP cc_start: 0.7511 (m-30) cc_final: 0.7250 (p0) REVERT: A 353 ASP cc_start: 0.8290 (t0) cc_final: 0.7875 (t0) REVERT: A 540 GLU cc_start: 0.8346 (tt0) cc_final: 0.7863 (mp0) REVERT: A 668 MET cc_start: 0.8122 (mmm) cc_final: 0.7778 (mpp) REVERT: A 699 GLN cc_start: 0.8309 (mp10) cc_final: 0.8089 (mp10) REVERT: A 723 ASP cc_start: 0.8173 (m-30) cc_final: 0.7958 (m-30) REVERT: A 762 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8491 (pttt) REVERT: A 879 LYS cc_start: 0.8774 (mmmm) cc_final: 0.8180 (mtmt) REVERT: A 937 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: A 983 GLU cc_start: 0.8321 (mp0) cc_final: 0.7729 (mp0) REVERT: B 39 ASP cc_start: 0.8541 (m-30) cc_final: 0.8058 (p0) REVERT: C 92 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7484 (tm-30) outliers start: 25 outliers final: 18 residues processed: 131 average time/residue: 1.2615 time to fit residues: 178.7288 Evaluate side-chains 131 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 949 VAL 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 22 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 14 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 54 optimal weight: 0.3980 chunk 64 optimal weight: 0.3980 chunk 8 optimal weight: 0.0870 chunk 110 optimal weight: 0.6980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.143622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.095341 restraints weight = 12618.143| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.48 r_work: 0.2925 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10344 Z= 0.171 Angle : 0.476 7.785 14009 Z= 0.247 Chirality : 0.042 0.224 1568 Planarity : 0.004 0.049 1812 Dihedral : 5.827 84.711 1408 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.04 % Allowed : 12.04 % Favored : 85.93 % 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: 1.65 (0.24), residues: 1273 helix: 1.90 (0.24), residues: 502 sheet: 0.88 (0.35), residues: 207 loop : 0.57 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS C 125 PHE 0.012 0.001 PHE C 62 TYR 0.008 0.001 TYR A 736 ARG 0.008 0.000 ARG C 143 *********************** 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 134 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7502 (mtp85) cc_final: 0.6834 (mtm-85) REVERT: A 182 THR cc_start: 0.9071 (t) cc_final: 0.8797 (m) REVERT: A 184 MET cc_start: 0.8445 (mtp) cc_final: 0.8073 (mtt) REVERT: A 213 THR cc_start: 0.7387 (OUTLIER) cc_final: 0.6995 (t) REVERT: A 235 TYR cc_start: 0.8755 (m-80) cc_final: 0.8549 (m-80) REVERT: A 250 TYR cc_start: 0.7751 (m-80) cc_final: 0.7396 (m-80) REVERT: A 335 ASP cc_start: 0.7545 (m-30) cc_final: 0.7223 (p0) REVERT: A 353 ASP cc_start: 0.8264 (t0) cc_final: 0.7859 (t0) REVERT: A 540 GLU cc_start: 0.8330 (tt0) cc_final: 0.7861 (mp0) REVERT: A 668 MET cc_start: 0.8083 (mmm) cc_final: 0.7692 (mpp) REVERT: A 699 GLN cc_start: 0.8218 (mp10) cc_final: 0.8006 (mp10) REVERT: A 723 ASP cc_start: 0.8163 (m-30) cc_final: 0.7929 (m-30) REVERT: A 762 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8472 (pttt) REVERT: A 879 LYS cc_start: 0.8756 (mmmm) cc_final: 0.8156 (mtmt) REVERT: A 937 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7933 (mp0) REVERT: A 983 GLU cc_start: 0.8299 (mp0) cc_final: 0.7696 (mp0) REVERT: B 39 ASP cc_start: 0.8507 (m-30) cc_final: 0.8037 (p0) REVERT: C 92 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7474 (tm-30) outliers start: 23 outliers final: 17 residues processed: 127 average time/residue: 1.2943 time to fit residues: 176.9197 Evaluate side-chains 130 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 949 VAL 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 22 THR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 17 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 chunk 117 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 64 optimal weight: 0.0270 chunk 34 optimal weight: 0.6980 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.144021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.095694 restraints weight = 12624.894| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.49 r_work: 0.2940 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10344 Z= 0.177 Angle : 0.472 7.853 14009 Z= 0.245 Chirality : 0.042 0.176 1568 Planarity : 0.004 0.052 1812 Dihedral : 5.671 84.156 1408 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.04 % Allowed : 12.12 % Favored : 85.84 % 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: 1.68 (0.24), residues: 1273 helix: 1.94 (0.24), residues: 502 sheet: 0.90 (0.35), residues: 207 loop : 0.58 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS C 125 PHE 0.013 0.001 PHE C 62 TYR 0.007 0.001 TYR A 736 ARG 0.005 0.000 ARG C 5 ********************** 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 137 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.7519 (mtp85) cc_final: 0.6850 (mtm-85) REVERT: A 182 THR cc_start: 0.9063 (t) cc_final: 0.8812 (m) REVERT: A 213 THR cc_start: 0.7423 (OUTLIER) cc_final: 0.7023 (t) REVERT: A 235 TYR cc_start: 0.8761 (m-80) cc_final: 0.8496 (m-80) REVERT: A 250 TYR cc_start: 0.7754 (m-80) cc_final: 0.7435 (m-80) REVERT: A 335 ASP cc_start: 0.7518 (m-30) cc_final: 0.7195 (p0) REVERT: A 353 ASP cc_start: 0.8254 (t0) cc_final: 0.7900 (t0) REVERT: A 540 GLU cc_start: 0.8335 (tt0) cc_final: 0.7859 (mp0) REVERT: A 668 MET cc_start: 0.8082 (mmm) cc_final: 0.7689 (mpp) REVERT: A 723 ASP cc_start: 0.8172 (m-30) cc_final: 0.7950 (m-30) REVERT: A 762 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8473 (pttt) REVERT: A 879 LYS cc_start: 0.8765 (mmmm) cc_final: 0.8168 (mtmt) REVERT: A 937 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: A 983 GLU cc_start: 0.8299 (mp0) cc_final: 0.7987 (mp0) REVERT: B 39 ASP cc_start: 0.8527 (m-30) cc_final: 0.8062 (p0) REVERT: C 92 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7471 (tm-30) outliers start: 23 outliers final: 16 residues processed: 129 average time/residue: 1.2931 time to fit residues: 179.3384 Evaluate side-chains 129 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 949 VAL 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 C residue 85 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 6 optimal weight: 0.0870 chunk 50 optimal weight: 0.0670 chunk 123 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 52 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.143993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.095760 restraints weight = 12579.517| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.48 r_work: 0.2931 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10344 Z= 0.191 Angle : 0.486 7.969 14009 Z= 0.250 Chirality : 0.042 0.170 1568 Planarity : 0.004 0.054 1812 Dihedral : 5.651 84.123 1408 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.04 % Allowed : 12.21 % Favored : 85.75 % 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: 1.91 (0.24), residues: 502 sheet: 0.89 (0.35), residues: 207 loop : 0.59 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS C 125 PHE 0.013 0.001 PHE C 62 TYR 0.007 0.001 TYR A 736 ARG 0.002 0.000 ARG C 5 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 7899.89 seconds wall clock time: 139 minutes 37.03 seconds (8377.03 seconds total)