Starting phenix.real_space_refine on Wed Apr 30 18:45:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jag_36113/04_2025/8jag_36113.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jag_36113/04_2025/8jag_36113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jag_36113/04_2025/8jag_36113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jag_36113/04_2025/8jag_36113.map" model { file = "/net/cci-nas-00/data/ceres_data/8jag_36113/04_2025/8jag_36113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jag_36113/04_2025/8jag_36113.cif" } resolution = 3.55 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= 0.001 sd= 0.079 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 6243 2.51 5 N 1607 2.21 5 O 1872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 9772 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8037 Classifications: {'peptide': 1028} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 979} Chain breaks: 10 Chain: "H" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Chain: "L" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 856 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.12, per 1000 atoms: 0.63 Number of scatterers: 9772 At special positions: 0 Unit cell: (118.34, 90.21, 193.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1872 8.00 N 1607 7.00 C 6243 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 133 " distance=2.02 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.04 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.04 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.08 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.11 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.02 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.07 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.02 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.02 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 89 " distance=2.07 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 92 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 330 " " NAG A1302 " - " ASN A 227 " " NAG A1303 " - " ASN A 269 " " NAG A1304 " - " ASN A 783 " " NAG A1305 " - " ASN A 65 " Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.1 seconds 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 20 sheets defined 21.6% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.825A pdb=" N TRP A 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.557A pdb=" N TYR A 356 " --> pdb=" O TYR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 377 removed outlier: 4.500A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 395 removed outlier: 4.333A pdb=" N ARG A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 395' Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 602 through 612 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.514A pdb=" N GLU A 755 " --> pdb=" O GLY A 751 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A 756 " --> pdb=" O ILE A 752 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 808 Processing helix chain 'A' and resid 848 through 867 removed outlier: 3.632A pdb=" N THR A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY A 867 " --> pdb=" O THR A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 895 through 901 removed outlier: 4.316A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 Processing helix chain 'A' and resid 927 through 947 Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 959 through 964 Processing helix chain 'A' and resid 967 through 1015 Processing helix chain 'A' and resid 1122 through 1127 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.193A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 59 removed outlier: 3.662A pdb=" N THR A 51 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N THR A 261 " --> pdb=" O ASP A 277 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ASP A 277 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N MET A 263 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA A 275 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LYS A 265 " --> pdb=" O THR A 273 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 removed outlier: 5.774A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL A 123 " --> pdb=" O SER A 165 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 137 removed outlier: 10.608A pdb=" N ASN A 135 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N PHE A 153 " --> pdb=" O ASN A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 615 through 616 removed outlier: 6.891A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 312 through 314 removed outlier: 5.952A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER A 561 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 345 Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.435A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AB1, first strand: chain 'A' and resid 640 through 646 removed outlier: 6.440A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N VAL A 642 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 693 through 697 removed outlier: 3.747A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLN A1088 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N SER A1093 " --> pdb=" O GLN A1088 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 700 through 710 removed outlier: 6.062A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.570A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AB6, first strand: chain 'A' and resid 1102 through 1107 removed outlier: 4.876A pdb=" N ALA A1069 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.605A pdb=" N GLU H 10 " --> pdb=" O THR H 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'H' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AC2, first strand: chain 'L' and resid 57 through 58 removed outlier: 6.775A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1074 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: 4.14 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2137 1.32 - 1.46: 3459 1.46 - 1.60: 4321 1.60 - 1.74: 16 1.74 - 1.88: 66 Bond restraints: 9999 Sorted by residual: bond pdb=" CA THR A 332 " pdb=" C THR A 332 " ideal model delta sigma weight residual 1.524 1.405 0.119 1.29e-02 6.01e+03 8.44e+01 bond pdb=" NE ARG A 18 " pdb=" CZ ARG A 18 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.58e+01 bond pdb=" CG LEU A 898 " pdb=" CD2 LEU A 898 " ideal model delta sigma weight residual 1.521 1.341 0.180 3.30e-02 9.18e+02 2.98e+01 bond pdb=" NE1 TRP H 36 " pdb=" CE2 TRP H 36 " ideal model delta sigma weight residual 1.370 1.311 0.059 1.10e-02 8.26e+03 2.85e+01 bond pdb=" NE ARG H 38 " pdb=" CZ ARG H 38 " ideal model delta sigma weight residual 1.326 1.382 -0.056 1.10e-02 8.26e+03 2.61e+01 ... (remaining 9994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 11271 2.23 - 4.45: 1916 4.45 - 6.68: 324 6.68 - 8.91: 64 8.91 - 11.14: 17 Bond angle restraints: 13592 Sorted by residual: angle pdb=" N PHE A 360 " pdb=" CA PHE A 360 " pdb=" C PHE A 360 " ideal model delta sigma weight residual 114.56 103.42 11.14 1.27e+00 6.20e-01 7.69e+01 angle pdb=" N THR A 332 " pdb=" CA THR A 332 " pdb=" C THR A 332 " ideal model delta sigma weight residual 111.36 101.87 9.49 1.09e+00 8.42e-01 7.57e+01 angle pdb=" N GLN L 46 " pdb=" CA GLN L 46 " pdb=" C GLN L 46 " ideal model delta sigma weight residual 111.71 121.41 -9.70 1.15e+00 7.56e-01 7.12e+01 angle pdb=" N SER L 47 " pdb=" CA SER L 47 " pdb=" C SER L 47 " ideal model delta sigma weight residual 108.25 117.98 -9.73 1.16e+00 7.43e-01 7.04e+01 angle pdb=" C GLN L 16 " pdb=" N PRO L 17 " pdb=" CA PRO L 17 " ideal model delta sigma weight residual 120.03 127.84 -7.81 9.90e-01 1.02e+00 6.22e+01 ... (remaining 13587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.70: 5842 24.70 - 49.40: 84 49.40 - 74.10: 30 74.10 - 98.80: 14 98.80 - 123.50: 14 Dihedral angle restraints: 5984 sinusoidal: 2380 harmonic: 3604 Sorted by residual: dihedral pdb=" CA ILE H 51 " pdb=" C ILE H 51 " pdb=" N PRO H 52 " pdb=" CA PRO H 52 " ideal model delta harmonic sigma weight residual -180.00 -56.50 -123.50 0 5.00e+00 4.00e-02 6.10e+02 dihedral pdb=" CB CYS A 278 " pdb=" SG CYS A 278 " pdb=" SG CYS A 288 " pdb=" CB CYS A 288 " ideal model delta sinusoidal sigma weight residual 93.00 -177.34 -89.66 1 1.00e+01 1.00e-02 9.54e+01 dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 92 " pdb=" CB CYS L 92 " ideal model delta sinusoidal sigma weight residual 93.00 38.94 54.06 1 1.00e+01 1.00e-02 3.97e+01 ... (remaining 5981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.321: 1534 0.321 - 0.643: 8 0.643 - 0.964: 0 0.964 - 1.285: 1 1.285 - 1.606: 1 Chirality restraints: 1544 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 330 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -0.79 -1.61 2.00e-01 2.50e+01 6.45e+01 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 65 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.47e+01 chirality pdb=" CA TYR H 87 " pdb=" N TYR H 87 " pdb=" C TYR H 87 " pdb=" CB TYR H 87 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.39e+00 ... (remaining 1541 not shown) Planarity restraints: 1748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " -0.304 2.00e-02 2.50e+03 2.62e-01 8.55e+02 pdb=" C7 NAG A1301 " 0.066 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " -0.006 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " 0.450 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " -0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1305 " -0.279 2.00e-02 2.50e+03 2.36e-01 6.95e+02 pdb=" C7 NAG A1305 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG A1305 " -0.177 2.00e-02 2.50e+03 pdb=" N2 NAG A1305 " 0.404 2.00e-02 2.50e+03 pdb=" O7 NAG A1305 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " -0.252 2.00e-02 2.50e+03 2.16e-01 5.82e+02 pdb=" C7 NAG A1304 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " 0.024 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " 0.361 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " -0.189 2.00e-02 2.50e+03 ... (remaining 1745 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 2 2.29 - 2.94: 4790 2.94 - 3.60: 13241 3.60 - 4.25: 23009 4.25 - 4.90: 37001 Nonbonded interactions: 78043 Sorted by model distance: nonbonded pdb=" CA GLY A 368 " pdb=" CE1 PHE A 416 " model vdw 1.641 3.740 nonbonded pdb=" O TYR A 367 " pdb=" CZ PHE A 416 " model vdw 2.137 3.340 nonbonded pdb=" N GLY A 368 " pdb=" CE1 PHE A 416 " model vdw 2.361 3.420 nonbonded pdb=" O TYR A 367 " pdb=" CE1 PHE A 416 " model vdw 2.363 3.340 nonbonded pdb=" N TRP H 50 " pdb=" O TRP H 50 " model vdw 2.376 2.496 ... (remaining 78038 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.080 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: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.250 Find NCS groups from input model: 0.110 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 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 : 0.020 0.180 10019 Z= 1.034 Angle : 1.818 11.137 13637 Z= 1.222 Chirality : 0.108 1.606 1544 Planarity : 0.013 0.262 1743 Dihedral : 12.735 123.499 3623 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.29 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.23), residues: 1216 helix: 0.05 (0.32), residues: 220 sheet: 0.92 (0.30), residues: 290 loop : -0.05 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.007 TRP H 50 HIS 0.015 0.003 HIS A 661 PHE 0.037 0.006 PHE A 137 TYR 0.062 0.009 TYR A 442 ARG 0.006 0.001 ARG A 620 Details of bonding type rmsd link_NAG-ASN : bond 0.01155 ( 5) link_NAG-ASN : angle 5.46303 ( 15) hydrogen bonds : bond 0.17951 ( 399) hydrogen bonds : angle 7.89561 ( 1074) SS BOND : bond 0.02733 ( 15) SS BOND : angle 3.31994 ( 30) covalent geometry : bond 0.01953 ( 9999) covalent geometry : angle 1.80508 (13592) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.8818 (mm) cc_final: 0.8578 (tt) REVERT: A 411 LYS cc_start: 0.7639 (tptt) cc_final: 0.7348 (tppt) REVERT: A 427 ASN cc_start: 0.7791 (p0) cc_final: 0.6856 (t0) REVERT: A 559 THR cc_start: 0.8124 (m) cc_final: 0.7852 (m) REVERT: A 965 ARG cc_start: 0.6947 (ptt180) cc_final: 0.5144 (tpt90) REVERT: A 1084 TRP cc_start: 0.7361 (m100) cc_final: 0.7110 (m100) REVERT: H 62 VAL cc_start: 0.7190 (t) cc_final: 0.6619 (t) REVERT: L 34 GLN cc_start: 0.4953 (tp-100) cc_final: 0.4496 (pt0) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.2262 time to fit residues: 91.3171 Evaluate side-chains 160 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 0.0030 chunk 111 optimal weight: 0.9980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 401 GLN A 530 ASN A 630 GLN A 759 ASN A 901 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.184981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.158035 restraints weight = 15430.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.160856 restraints weight = 10277.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.162243 restraints weight = 7237.846| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10019 Z= 0.156 Angle : 0.752 17.483 13637 Z= 0.383 Chirality : 0.052 0.593 1544 Planarity : 0.004 0.081 1743 Dihedral : 8.913 86.051 1436 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.78 % Favored : 95.89 % Rotamer: Outliers : 2.60 % Allowed : 10.23 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.23), residues: 1216 helix: 1.69 (0.35), residues: 213 sheet: 0.85 (0.30), residues: 276 loop : -0.37 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.009 0.001 HIS L 30 PHE 0.020 0.002 PHE L 75 TYR 0.016 0.002 TYR A 252 ARG 0.005 0.001 ARG L 58 Details of bonding type rmsd link_NAG-ASN : bond 0.01406 ( 5) link_NAG-ASN : angle 7.12719 ( 15) hydrogen bonds : bond 0.05744 ( 399) hydrogen bonds : angle 6.23192 ( 1074) SS BOND : bond 0.00967 ( 15) SS BOND : angle 1.87941 ( 30) covalent geometry : bond 0.00335 ( 9999) covalent geometry : angle 0.70967 (13592) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 ARG cc_start: 0.6807 (ttm-80) cc_final: 0.6308 (ttm-80) REVERT: A 296 ASP cc_start: 0.7789 (p0) cc_final: 0.7452 (m-30) REVERT: A 347 ASN cc_start: 0.8261 (m-40) cc_final: 0.7142 (t0) REVERT: A 411 LYS cc_start: 0.7731 (tptt) cc_final: 0.7241 (tppt) REVERT: A 427 ASN cc_start: 0.7599 (p0) cc_final: 0.6752 (t0) REVERT: A 509 THR cc_start: 0.7733 (OUTLIER) cc_final: 0.7202 (t) REVERT: A 530 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7663 (p0) REVERT: A 749 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7979 (mt) REVERT: A 837 PHE cc_start: 0.8237 (m-80) cc_final: 0.7820 (m-80) REVERT: A 965 ARG cc_start: 0.7077 (ptt180) cc_final: 0.4700 (tpt90) REVERT: A 1084 TRP cc_start: 0.7293 (m100) cc_final: 0.7070 (m100) REVERT: H 23 LYS cc_start: 0.8287 (mttt) cc_final: 0.7616 (mtmm) REVERT: H 73 TYR cc_start: 0.6425 (OUTLIER) cc_final: 0.5637 (m-80) outliers start: 28 outliers final: 17 residues processed: 217 average time/residue: 0.2255 time to fit residues: 68.7828 Evaluate side-chains 175 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain L residue 6 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 88 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 614 GLN A 661 HIS A 786 GLN A 901 ASN A 917 GLN A 987 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 HIS ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 94 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.183085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.156259 restraints weight = 15386.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.159211 restraints weight = 10113.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.160992 restraints weight = 7028.161| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10019 Z= 0.140 Angle : 0.675 18.598 13637 Z= 0.340 Chirality : 0.046 0.314 1544 Planarity : 0.004 0.046 1743 Dihedral : 6.247 62.324 1436 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.54 % Favored : 96.05 % Rotamer: Outliers : 3.26 % Allowed : 11.26 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.23), residues: 1216 helix: 1.93 (0.35), residues: 217 sheet: 0.57 (0.28), residues: 315 loop : -0.65 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 340 HIS 0.006 0.001 HIS L 30 PHE 0.019 0.002 PHE A 89 TYR 0.016 0.002 TYR A 252 ARG 0.004 0.000 ARG L 58 Details of bonding type rmsd link_NAG-ASN : bond 0.01456 ( 5) link_NAG-ASN : angle 6.78860 ( 15) hydrogen bonds : bond 0.04934 ( 399) hydrogen bonds : angle 5.93395 ( 1074) SS BOND : bond 0.00520 ( 15) SS BOND : angle 1.95627 ( 30) covalent geometry : bond 0.00309 ( 9999) covalent geometry : angle 0.63042 (13592) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 ASN cc_start: 0.6974 (p0) cc_final: 0.6520 (p0) REVERT: A 232 ARG cc_start: 0.6988 (ttm-80) cc_final: 0.6459 (ttm-80) REVERT: A 411 LYS cc_start: 0.7852 (tptt) cc_final: 0.7242 (tppt) REVERT: A 427 ASN cc_start: 0.7651 (p0) cc_final: 0.6892 (t0) REVERT: A 965 ARG cc_start: 0.7277 (ptt180) cc_final: 0.5143 (tpt90) REVERT: H 23 LYS cc_start: 0.8433 (mttt) cc_final: 0.7802 (mtmm) REVERT: H 73 TYR cc_start: 0.6617 (OUTLIER) cc_final: 0.5711 (m-80) REVERT: H 74 LEU cc_start: 0.7589 (tt) cc_final: 0.7370 (tp) REVERT: L 34 GLN cc_start: 0.4459 (tp-100) cc_final: 0.4084 (pt0) REVERT: L 37 PHE cc_start: 0.4077 (m-80) cc_final: 0.2769 (m-80) outliers start: 35 outliers final: 24 residues processed: 201 average time/residue: 0.2276 time to fit residues: 67.4421 Evaluate side-chains 177 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 30 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.179949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.152980 restraints weight = 15461.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.156168 restraints weight = 10034.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.157324 restraints weight = 6838.209| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10019 Z= 0.163 Angle : 0.651 18.835 13637 Z= 0.336 Chirality : 0.047 0.271 1544 Planarity : 0.004 0.050 1743 Dihedral : 5.772 59.731 1436 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.87 % Favored : 95.72 % Rotamer: Outliers : 3.81 % Allowed : 13.12 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.23), residues: 1216 helix: 1.83 (0.35), residues: 225 sheet: 0.26 (0.28), residues: 333 loop : -0.83 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1084 HIS 0.021 0.002 HIS L 30 PHE 0.018 0.002 PHE A 89 TYR 0.017 0.002 TYR A 252 ARG 0.004 0.000 ARG L 58 Details of bonding type rmsd link_NAG-ASN : bond 0.01385 ( 5) link_NAG-ASN : angle 6.17210 ( 15) hydrogen bonds : bond 0.04874 ( 399) hydrogen bonds : angle 5.81909 ( 1074) SS BOND : bond 0.00380 ( 15) SS BOND : angle 2.00150 ( 30) covalent geometry : bond 0.00370 ( 9999) covalent geometry : angle 0.61138 (13592) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 ARG cc_start: 0.6947 (ttm-80) cc_final: 0.6436 (ttm-80) REVERT: A 308 VAL cc_start: 0.8612 (t) cc_final: 0.8334 (m) REVERT: A 411 LYS cc_start: 0.7960 (tptt) cc_final: 0.7468 (tppt) REVERT: A 427 ASN cc_start: 0.7704 (p0) cc_final: 0.6997 (t0) REVERT: A 611 HIS cc_start: 0.6601 (m-70) cc_final: 0.6054 (m-70) REVERT: A 931 GLN cc_start: 0.8430 (tp40) cc_final: 0.8006 (tt0) REVERT: A 965 ARG cc_start: 0.7338 (ptt180) cc_final: 0.5212 (tpt90) REVERT: H 23 LYS cc_start: 0.8406 (mttt) cc_final: 0.7763 (mtmm) REVERT: H 50 TRP cc_start: 0.4185 (t-100) cc_final: 0.3728 (t-100) REVERT: H 73 TYR cc_start: 0.6728 (OUTLIER) cc_final: 0.5771 (m-80) REVERT: H 74 LEU cc_start: 0.7593 (tt) cc_final: 0.7384 (tt) REVERT: H 75 GLN cc_start: 0.6978 (mp10) cc_final: 0.6762 (mp10) REVERT: L 49 GLN cc_start: 0.7054 (mm110) cc_final: 0.6844 (mm110) outliers start: 41 outliers final: 28 residues processed: 193 average time/residue: 0.2133 time to fit residues: 59.8593 Evaluate side-chains 176 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 87 TYR Chi-restraints excluded: chain L residue 6 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 34 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 49 optimal weight: 0.3980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A1030 HIS L 30 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.178036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.149227 restraints weight = 15375.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.152770 restraints weight = 9656.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.155168 restraints weight = 7039.214| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10019 Z= 0.161 Angle : 0.642 18.481 13637 Z= 0.330 Chirality : 0.047 0.267 1544 Planarity : 0.004 0.049 1743 Dihedral : 5.765 57.564 1436 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.19 % Favored : 95.39 % Rotamer: Outliers : 4.56 % Allowed : 13.21 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.23), residues: 1216 helix: 1.72 (0.34), residues: 231 sheet: 0.17 (0.28), residues: 330 loop : -1.04 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 340 HIS 0.004 0.001 HIS A1040 PHE 0.020 0.002 PHE A 89 TYR 0.017 0.002 TYR A 252 ARG 0.004 0.000 ARG L 58 Details of bonding type rmsd link_NAG-ASN : bond 0.01371 ( 5) link_NAG-ASN : angle 6.09450 ( 15) hydrogen bonds : bond 0.04770 ( 399) hydrogen bonds : angle 5.78103 ( 1074) SS BOND : bond 0.00427 ( 15) SS BOND : angle 1.84807 ( 30) covalent geometry : bond 0.00369 ( 9999) covalent geometry : angle 0.60433 (13592) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 166 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 ARG cc_start: 0.6799 (ttm-80) cc_final: 0.6318 (ttm-80) REVERT: A 411 LYS cc_start: 0.8144 (tptt) cc_final: 0.7543 (tppt) REVERT: A 427 ASN cc_start: 0.7793 (p0) cc_final: 0.6984 (t0) REVERT: A 965 ARG cc_start: 0.7379 (ptt180) cc_final: 0.5196 (tpt90) REVERT: H 23 LYS cc_start: 0.8518 (mttt) cc_final: 0.7770 (mtmm) REVERT: H 73 TYR cc_start: 0.6764 (OUTLIER) cc_final: 0.5796 (m-80) REVERT: H 74 LEU cc_start: 0.7594 (tt) cc_final: 0.7188 (tt) REVERT: H 75 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6957 (mp10) REVERT: L 34 GLN cc_start: 0.5006 (tp-100) cc_final: 0.4287 (pt0) outliers start: 49 outliers final: 29 residues processed: 200 average time/residue: 0.1996 time to fit residues: 57.2344 Evaluate side-chains 178 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 30 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 94 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 113 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN L 30 HIS ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.179883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.151599 restraints weight = 15363.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.155142 restraints weight = 9516.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.157537 restraints weight = 6886.621| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10019 Z= 0.122 Angle : 0.616 18.557 13637 Z= 0.313 Chirality : 0.046 0.232 1544 Planarity : 0.004 0.047 1743 Dihedral : 5.594 54.893 1436 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.95 % Favored : 95.72 % Rotamer: Outliers : 3.07 % Allowed : 15.53 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.24), residues: 1216 helix: 2.06 (0.35), residues: 227 sheet: 0.26 (0.28), residues: 325 loop : -1.06 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 340 HIS 0.007 0.001 HIS L 30 PHE 0.024 0.001 PHE A 329 TYR 0.021 0.002 TYR A 367 ARG 0.003 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.01249 ( 5) link_NAG-ASN : angle 6.00524 ( 15) hydrogen bonds : bond 0.04350 ( 399) hydrogen bonds : angle 5.59483 ( 1074) SS BOND : bond 0.00355 ( 15) SS BOND : angle 1.91831 ( 30) covalent geometry : bond 0.00271 ( 9999) covalent geometry : angle 0.57667 (13592) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 ARG cc_start: 0.6651 (ttm-80) cc_final: 0.6131 (ttt90) REVERT: A 411 LYS cc_start: 0.8105 (tptt) cc_final: 0.7520 (tppt) REVERT: A 427 ASN cc_start: 0.7787 (p0) cc_final: 0.6872 (t0) REVERT: A 965 ARG cc_start: 0.7300 (ptt180) cc_final: 0.5125 (tpt90) REVERT: H 23 LYS cc_start: 0.8563 (mttt) cc_final: 0.7828 (mtmm) REVERT: H 50 TRP cc_start: 0.4289 (t-100) cc_final: 0.3880 (t-100) REVERT: H 73 TYR cc_start: 0.6770 (OUTLIER) cc_final: 0.6209 (m-80) REVERT: H 74 LEU cc_start: 0.7524 (tt) cc_final: 0.7242 (tt) REVERT: H 75 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6726 (mp10) REVERT: L 34 GLN cc_start: 0.4931 (tp-100) cc_final: 0.4298 (pt0) outliers start: 33 outliers final: 26 residues processed: 180 average time/residue: 0.2320 time to fit residues: 59.4804 Evaluate side-chains 177 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 87 TYR Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 30 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 86 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 110 optimal weight: 0.0770 chunk 88 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 90 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 30 HIS ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.180697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.153788 restraints weight = 15398.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.156526 restraints weight = 10597.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.157810 restraints weight = 7376.554| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10019 Z= 0.117 Angle : 0.604 18.348 13637 Z= 0.305 Chirality : 0.045 0.221 1544 Planarity : 0.004 0.043 1743 Dihedral : 5.445 53.260 1436 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.70 % Favored : 95.97 % Rotamer: Outliers : 3.07 % Allowed : 16.93 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.24), residues: 1216 helix: 1.99 (0.35), residues: 233 sheet: 0.44 (0.29), residues: 311 loop : -1.08 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 340 HIS 0.011 0.001 HIS L 30 PHE 0.019 0.001 PHE A 527 TYR 0.019 0.001 TYR H 87 ARG 0.004 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.01224 ( 5) link_NAG-ASN : angle 5.93979 ( 15) hydrogen bonds : bond 0.04176 ( 399) hydrogen bonds : angle 5.48387 ( 1074) SS BOND : bond 0.00274 ( 15) SS BOND : angle 1.61997 ( 30) covalent geometry : bond 0.00257 ( 9999) covalent geometry : angle 0.56667 (13592) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.6500 (t80) cc_final: 0.6151 (t80) REVERT: A 232 ARG cc_start: 0.6597 (ttm-80) cc_final: 0.6212 (ttt90) REVERT: A 411 LYS cc_start: 0.8087 (tptt) cc_final: 0.7515 (tppt) REVERT: A 427 ASN cc_start: 0.7739 (p0) cc_final: 0.6847 (t0) REVERT: A 965 ARG cc_start: 0.7323 (ptt180) cc_final: 0.5069 (tpt90) REVERT: H 23 LYS cc_start: 0.8563 (mttt) cc_final: 0.7828 (mtmm) REVERT: H 73 TYR cc_start: 0.6767 (OUTLIER) cc_final: 0.6261 (m-80) REVERT: H 74 LEU cc_start: 0.7616 (tt) cc_final: 0.7025 (tp) REVERT: H 75 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.6634 (mp10) REVERT: L 34 GLN cc_start: 0.4992 (tp-100) cc_final: 0.4360 (pt0) outliers start: 33 outliers final: 26 residues processed: 177 average time/residue: 0.2262 time to fit residues: 56.9587 Evaluate side-chains 168 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 87 TYR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain L residue 30 HIS Chi-restraints excluded: chain L residue 51 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 99 optimal weight: 0.4980 chunk 73 optimal weight: 5.9990 chunk 10 optimal weight: 0.0670 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 HIS L 30 HIS ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.181158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.154512 restraints weight = 15534.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.156960 restraints weight = 10556.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.158203 restraints weight = 7564.578| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10019 Z= 0.115 Angle : 0.601 18.148 13637 Z= 0.304 Chirality : 0.045 0.215 1544 Planarity : 0.004 0.040 1743 Dihedral : 5.359 52.534 1436 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.87 % Favored : 95.81 % Rotamer: Outliers : 3.07 % Allowed : 17.30 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.24), residues: 1216 helix: 2.04 (0.34), residues: 234 sheet: 0.41 (0.29), residues: 313 loop : -1.05 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 340 HIS 0.009 0.001 HIS L 30 PHE 0.017 0.001 PHE A 329 TYR 0.019 0.001 TYR H 87 ARG 0.005 0.000 ARG L 58 Details of bonding type rmsd link_NAG-ASN : bond 0.01217 ( 5) link_NAG-ASN : angle 5.90192 ( 15) hydrogen bonds : bond 0.04082 ( 399) hydrogen bonds : angle 5.41525 ( 1074) SS BOND : bond 0.00245 ( 15) SS BOND : angle 1.84183 ( 30) covalent geometry : bond 0.00258 ( 9999) covalent geometry : angle 0.56279 (13592) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.6598 (t80) cc_final: 0.6151 (t80) REVERT: A 232 ARG cc_start: 0.6540 (ttm-80) cc_final: 0.6187 (ttt90) REVERT: A 411 LYS cc_start: 0.8083 (tptt) cc_final: 0.7461 (tppt) REVERT: A 427 ASN cc_start: 0.7731 (p0) cc_final: 0.7056 (t0) REVERT: A 965 ARG cc_start: 0.7320 (ptt180) cc_final: 0.5001 (tpt90) REVERT: H 23 LYS cc_start: 0.8592 (mttt) cc_final: 0.7798 (mtmm) REVERT: H 73 TYR cc_start: 0.6774 (OUTLIER) cc_final: 0.6106 (m-80) REVERT: H 74 LEU cc_start: 0.7604 (tt) cc_final: 0.7048 (tp) REVERT: H 75 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.6662 (mp10) outliers start: 33 outliers final: 25 residues processed: 173 average time/residue: 0.3421 time to fit residues: 84.6178 Evaluate side-chains 169 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 87 TYR Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 30 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 20 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 114 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 HIS ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.177040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.150294 restraints weight = 15439.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.152954 restraints weight = 9985.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.154660 restraints weight = 7123.426| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10019 Z= 0.173 Angle : 0.658 17.812 13637 Z= 0.334 Chirality : 0.047 0.237 1544 Planarity : 0.004 0.040 1743 Dihedral : 5.694 53.759 1436 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.77 % Favored : 94.90 % Rotamer: Outliers : 3.16 % Allowed : 17.12 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.24), residues: 1216 helix: 1.74 (0.34), residues: 240 sheet: 0.16 (0.28), residues: 334 loop : -1.19 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 340 HIS 0.007 0.001 HIS L 30 PHE 0.020 0.002 PHE A 89 TYR 0.018 0.002 TYR H 87 ARG 0.005 0.000 ARG L 58 Details of bonding type rmsd link_NAG-ASN : bond 0.01291 ( 5) link_NAG-ASN : angle 5.92288 ( 15) hydrogen bonds : bond 0.04723 ( 399) hydrogen bonds : angle 5.64113 ( 1074) SS BOND : bond 0.00337 ( 15) SS BOND : angle 2.07128 ( 30) covalent geometry : bond 0.00410 ( 9999) covalent geometry : angle 0.62174 (13592) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 SER cc_start: 0.7775 (t) cc_final: 0.7379 (p) REVERT: A 232 ARG cc_start: 0.6667 (ttm-80) cc_final: 0.6305 (ttt90) REVERT: A 411 LYS cc_start: 0.8141 (tptt) cc_final: 0.7543 (tppt) REVERT: A 427 ASN cc_start: 0.7739 (p0) cc_final: 0.6892 (t0) REVERT: A 802 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7284 (m-30) REVERT: A 837 PHE cc_start: 0.8672 (m-80) cc_final: 0.8392 (m-80) REVERT: A 965 ARG cc_start: 0.7408 (ptt180) cc_final: 0.5151 (tpt90) REVERT: H 23 LYS cc_start: 0.8626 (mttt) cc_final: 0.7823 (mtmm) REVERT: H 73 TYR cc_start: 0.6821 (OUTLIER) cc_final: 0.6383 (m-80) REVERT: H 74 LEU cc_start: 0.7805 (tt) cc_final: 0.7320 (tt) REVERT: H 75 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6601 (mp10) outliers start: 34 outliers final: 27 residues processed: 180 average time/residue: 0.2279 time to fit residues: 57.7432 Evaluate side-chains 178 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 87 TYR Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 30 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 0.0870 chunk 109 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 HIS ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.179249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.152574 restraints weight = 15486.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.154547 restraints weight = 10642.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.156058 restraints weight = 7550.469| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10019 Z= 0.128 Angle : 0.640 17.765 13637 Z= 0.321 Chirality : 0.046 0.217 1544 Planarity : 0.004 0.039 1743 Dihedral : 5.528 52.534 1436 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.28 % Favored : 95.39 % Rotamer: Outliers : 2.70 % Allowed : 18.14 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.24), residues: 1216 helix: 1.95 (0.34), residues: 235 sheet: 0.17 (0.29), residues: 317 loop : -1.04 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 340 HIS 0.007 0.001 HIS L 30 PHE 0.027 0.002 PHE A 909 TYR 0.023 0.002 TYR H 88 ARG 0.007 0.000 ARG A 426 Details of bonding type rmsd link_NAG-ASN : bond 0.01196 ( 5) link_NAG-ASN : angle 5.86881 ( 15) hydrogen bonds : bond 0.04292 ( 399) hydrogen bonds : angle 5.52769 ( 1074) SS BOND : bond 0.00293 ( 15) SS BOND : angle 2.05783 ( 30) covalent geometry : bond 0.00292 ( 9999) covalent geometry : angle 0.60255 (13592) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 SER cc_start: 0.7708 (t) cc_final: 0.7361 (p) REVERT: A 232 ARG cc_start: 0.6596 (ttm-80) cc_final: 0.6254 (ttt90) REVERT: A 411 LYS cc_start: 0.8149 (tptt) cc_final: 0.7553 (tppt) REVERT: A 802 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7310 (m-30) REVERT: A 965 ARG cc_start: 0.7343 (ptt180) cc_final: 0.5080 (tpt90) REVERT: H 23 LYS cc_start: 0.8613 (mttt) cc_final: 0.7828 (mtmm) REVERT: H 34 MET cc_start: 0.8615 (mpp) cc_final: 0.8123 (mmt) REVERT: H 73 TYR cc_start: 0.6794 (OUTLIER) cc_final: 0.6154 (m-80) REVERT: H 74 LEU cc_start: 0.7629 (tt) cc_final: 0.7154 (tt) REVERT: H 75 GLN cc_start: 0.6951 (OUTLIER) cc_final: 0.6585 (mp10) outliers start: 29 outliers final: 23 residues processed: 176 average time/residue: 0.2356 time to fit residues: 58.8536 Evaluate side-chains 170 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1012 SER Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 30 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 54 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 HIS ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.175458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.148309 restraints weight = 15419.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.151047 restraints weight = 10485.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.152490 restraints weight = 7357.490| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10019 Z= 0.208 Angle : 0.709 17.443 13637 Z= 0.362 Chirality : 0.049 0.241 1544 Planarity : 0.004 0.043 1743 Dihedral : 5.988 54.698 1436 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.43 % Favored : 94.24 % Rotamer: Outliers : 3.16 % Allowed : 18.42 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.24), residues: 1216 helix: 1.51 (0.34), residues: 242 sheet: -0.02 (0.28), residues: 345 loop : -1.32 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 340 HIS 0.009 0.002 HIS L 30 PHE 0.029 0.002 PHE A 909 TYR 0.030 0.002 TYR H 87 ARG 0.005 0.001 ARG L 58 Details of bonding type rmsd link_NAG-ASN : bond 0.01300 ( 5) link_NAG-ASN : angle 5.94203 ( 15) hydrogen bonds : bond 0.05020 ( 399) hydrogen bonds : angle 5.81480 ( 1074) SS BOND : bond 0.00398 ( 15) SS BOND : angle 2.37969 ( 30) covalent geometry : bond 0.00493 ( 9999) covalent geometry : angle 0.67344 (13592) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3825.43 seconds wall clock time: 68 minutes 36.16 seconds (4116.16 seconds total)