Starting phenix.real_space_refine on Sun Dec 29 04:24:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jag_36113/12_2024/8jag_36113.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jag_36113/12_2024/8jag_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_36113/12_2024/8jag_36113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jag_36113/12_2024/8jag_36113.map" model { file = "/net/cci-nas-00/data/ceres_data/8jag_36113/12_2024/8jag_36113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jag_36113/12_2024/8jag_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-5532/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: 5.96, per 1000 atoms: 0.61 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: 2.77 Conformation dependent library (CDL) restraints added in 1.6 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: 1.26 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: 4.06 Time building geometry restraints manager: 3.12 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.560 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.830 ------------------------------------------------------------------------------- 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 9999 Z= 1.271 Angle : 1.805 11.137 13592 Z= 1.220 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 : 0.08 % Allowed : 3.37 % 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 *********************** 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 : 1.073 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: 0.2293 time to fit residues: 91.9964 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 : 1.250 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 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 9999 Z= 0.217 Angle : 0.710 12.428 13592 Z= 0.374 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 *********************** 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 : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 ARG cc_start: 0.7207 (ttm-80) cc_final: 0.6855 (ttm-80) REVERT: A 347 ASN cc_start: 0.8260 (m-40) cc_final: 0.7254 (t0) REVERT: A 411 LYS cc_start: 0.7668 (tptt) cc_final: 0.7356 (tppt) REVERT: A 427 ASN cc_start: 0.7662 (p0) cc_final: 0.6992 (t0) REVERT: A 509 THR cc_start: 0.7862 (OUTLIER) cc_final: 0.7414 (t) REVERT: A 656 ILE cc_start: 0.8582 (tt) cc_final: 0.8328 (mt) REVERT: A 749 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8158 (mt) REVERT: A 837 PHE cc_start: 0.8365 (m-80) cc_final: 0.7991 (m-80) REVERT: A 965 ARG cc_start: 0.7023 (ptt180) cc_final: 0.4884 (tpt90) REVERT: H 23 LYS cc_start: 0.8471 (mttt) cc_final: 0.7977 (mtmm) REVERT: H 73 TYR cc_start: 0.6549 (OUTLIER) cc_final: 0.5814 (m-80) outliers start: 28 outliers final: 17 residues processed: 217 average time/residue: 0.2258 time to fit residues: 69.0801 Evaluate side-chains 175 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 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 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.0970 chunk 92 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 530 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9999 Z= 0.196 Angle : 0.629 12.541 13592 Z= 0.329 Chirality : 0.046 0.312 1544 Planarity : 0.004 0.045 1743 Dihedral : 6.252 62.461 1436 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.45 % Favored : 96.13 % Rotamer: Outliers : 3.07 % Allowed : 11.63 % Favored : 85.30 % 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: 0.20 (0.23), residues: 1216 helix: 1.93 (0.34), residues: 217 sheet: 0.55 (0.28), residues: 315 loop : -0.67 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1084 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 *********************** 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 208 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 ASN cc_start: 0.7076 (p0) cc_final: 0.6682 (p0) REVERT: A 232 ARG cc_start: 0.7423 (ttm-80) cc_final: 0.7099 (ttm-80) REVERT: A 411 LYS cc_start: 0.7849 (tptt) cc_final: 0.7434 (tppt) REVERT: A 427 ASN cc_start: 0.7754 (p0) cc_final: 0.7121 (t0) REVERT: A 961 ASP cc_start: 0.6669 (t0) cc_final: 0.6451 (t0) REVERT: A 965 ARG cc_start: 0.7181 (ptt180) cc_final: 0.5254 (tpt90) REVERT: H 23 LYS cc_start: 0.8593 (mttt) cc_final: 0.8150 (mtmm) REVERT: H 73 TYR cc_start: 0.6689 (OUTLIER) cc_final: 0.5926 (m-80) REVERT: L 34 GLN cc_start: 0.4669 (tp-100) cc_final: 0.4373 (pt0) REVERT: L 37 PHE cc_start: 0.4674 (m-80) cc_final: 0.3432 (m-80) outliers start: 33 outliers final: 21 residues processed: 200 average time/residue: 0.2003 time to fit residues: 57.4599 Evaluate side-chains 173 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 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 1012 SER 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 110 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 75 optimal weight: 0.6980 chunk 112 optimal weight: 0.0370 chunk 118 optimal weight: 0.0970 chunk 106 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN A 530 ASN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9999 Z= 0.150 Angle : 0.567 6.733 13592 Z= 0.300 Chirality : 0.045 0.257 1544 Planarity : 0.004 0.049 1743 Dihedral : 5.443 57.760 1436 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.37 % Favored : 96.22 % Rotamer: Outliers : 2.05 % Allowed : 14.23 % Favored : 83.72 % 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: 0.18 (0.23), residues: 1216 helix: 2.19 (0.35), residues: 217 sheet: 0.43 (0.28), residues: 316 loop : -0.72 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1084 HIS 0.018 0.001 HIS L 30 PHE 0.015 0.001 PHE A 89 TYR 0.016 0.001 TYR H 88 ARG 0.003 0.000 ARG L 58 *********************** 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 187 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 ARG cc_start: 0.7396 (ttm-80) cc_final: 0.6995 (ttm-80) REVERT: A 347 ASN cc_start: 0.8325 (m-40) cc_final: 0.8102 (m-40) REVERT: A 411 LYS cc_start: 0.7846 (tptt) cc_final: 0.7416 (tppt) REVERT: A 427 ASN cc_start: 0.7755 (p0) cc_final: 0.7143 (t0) REVERT: A 509 THR cc_start: 0.7796 (OUTLIER) cc_final: 0.7557 (t) REVERT: A 551 PHE cc_start: 0.7799 (p90) cc_final: 0.7496 (p90) REVERT: A 961 ASP cc_start: 0.6810 (t0) cc_final: 0.6586 (t0) REVERT: A 965 ARG cc_start: 0.7211 (ptt180) cc_final: 0.5211 (tpt90) REVERT: A 1092 PHE cc_start: 0.7850 (t80) cc_final: 0.7495 (t80) REVERT: H 23 LYS cc_start: 0.8569 (mttt) cc_final: 0.8094 (mtmm) REVERT: H 73 TYR cc_start: 0.6683 (OUTLIER) cc_final: 0.5837 (m-80) REVERT: H 75 GLN cc_start: 0.6885 (mp10) cc_final: 0.6589 (mp10) outliers start: 22 outliers final: 12 residues processed: 182 average time/residue: 0.2100 time to fit residues: 55.2985 Evaluate side-chains 167 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 509 THR Chi-restraints excluded: chain A residue 539 THR 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 959 LEU Chi-restraints excluded: chain A residue 985 SER 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN A 530 ASN A 786 GLN A 917 GLN A1030 HIS L 30 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9999 Z= 0.285 Angle : 0.641 8.070 13592 Z= 0.342 Chirality : 0.048 0.284 1544 Planarity : 0.004 0.053 1743 Dihedral : 5.961 64.091 1436 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.03 % Favored : 95.56 % Rotamer: Outliers : 4.74 % Allowed : 12.74 % Favored : 82.51 % 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: -0.20 (0.23), residues: 1216 helix: 1.70 (0.34), residues: 232 sheet: 0.14 (0.28), residues: 330 loop : -0.97 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 340 HIS 0.006 0.001 HIS L 30 PHE 0.023 0.002 PHE H 98 TYR 0.018 0.002 TYR A 252 ARG 0.004 0.001 ARG L 58 *********************** 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 213 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 162 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 ARG cc_start: 0.7418 (ttm-80) cc_final: 0.7030 (ttm-80) REVERT: A 411 LYS cc_start: 0.8210 (tptt) cc_final: 0.7794 (tppt) REVERT: A 427 ASN cc_start: 0.7882 (p0) cc_final: 0.7319 (t0) REVERT: A 965 ARG cc_start: 0.7340 (ptt180) cc_final: 0.5414 (tpt90) REVERT: A 1011 MET cc_start: 0.8332 (tpp) cc_final: 0.7835 (ttm) REVERT: H 23 LYS cc_start: 0.8759 (mttt) cc_final: 0.8216 (mtmm) REVERT: H 73 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.6038 (m-80) REVERT: L 53 TYR cc_start: 0.5923 (OUTLIER) cc_final: 0.5619 (p90) outliers start: 51 outliers final: 32 residues processed: 196 average time/residue: 0.2283 time to fit residues: 64.1389 Evaluate side-chains 178 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 322 LEU Chi-restraints excluded: chain A residue 401 GLN Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 537 VAL 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 610 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 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 12 VAL Chi-restraints excluded: chain L residue 30 HIS Chi-restraints excluded: chain L residue 53 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 8.9990 chunk 23 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.0470 chunk 119 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN L 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9999 Z= 0.163 Angle : 0.574 6.966 13592 Z= 0.303 Chirality : 0.046 0.233 1544 Planarity : 0.004 0.051 1743 Dihedral : 5.554 55.943 1436 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.54 % Favored : 96.13 % Rotamer: Outliers : 2.88 % Allowed : 15.44 % Favored : 81.67 % 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: -0.10 (0.23), residues: 1216 helix: 2.02 (0.35), residues: 227 sheet: 0.22 (0.29), residues: 305 loop : -0.95 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 340 HIS 0.013 0.001 HIS L 30 PHE 0.016 0.001 PHE A 89 TYR 0.020 0.001 TYR A 367 ARG 0.004 0.000 ARG A 449 *********************** 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 190 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 ARG cc_start: 0.7136 (ttm-80) cc_final: 0.6794 (ttt90) REVERT: A 411 LYS cc_start: 0.8117 (tptt) cc_final: 0.7694 (tppt) REVERT: A 427 ASN cc_start: 0.7794 (p0) cc_final: 0.7186 (t0) REVERT: A 965 ARG cc_start: 0.7192 (ptt180) cc_final: 0.5236 (tpt90) REVERT: A 1011 MET cc_start: 0.8274 (tpp) cc_final: 0.7802 (ttm) REVERT: H 23 LYS cc_start: 0.8736 (mttt) cc_final: 0.8179 (mtmm) REVERT: H 73 TYR cc_start: 0.6853 (OUTLIER) cc_final: 0.5948 (m-80) REVERT: L 53 TYR cc_start: 0.5828 (OUTLIER) cc_final: 0.5466 (p90) outliers start: 31 outliers final: 19 residues processed: 181 average time/residue: 0.2525 time to fit residues: 65.2631 Evaluate side-chains 164 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 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 863 THR Chi-restraints excluded: chain A residue 959 LEU 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 84 THR Chi-restraints excluded: chain H residue 87 TYR Chi-restraints excluded: chain L residue 53 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 54 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 0.0770 overall best weight: 1.2342 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9999 Z= 0.225 Angle : 0.596 7.309 13592 Z= 0.314 Chirality : 0.047 0.246 1544 Planarity : 0.004 0.050 1743 Dihedral : 5.674 56.238 1436 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.95 % Favored : 95.72 % Rotamer: Outliers : 2.98 % Allowed : 16.28 % Favored : 80.74 % 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 (0.24), residues: 1216 helix: 1.92 (0.35), residues: 233 sheet: 0.20 (0.28), residues: 320 loop : -1.12 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 340 HIS 0.008 0.001 HIS L 30 PHE 0.019 0.002 PHE A 89 TYR 0.017 0.002 TYR A 252 ARG 0.003 0.000 ARG A 449 *********************** 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 185 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 SER cc_start: 0.7739 (t) cc_final: 0.7447 (p) REVERT: A 232 ARG cc_start: 0.7288 (ttm-80) cc_final: 0.6975 (ttt90) REVERT: A 411 LYS cc_start: 0.8168 (tptt) cc_final: 0.7689 (tppt) REVERT: A 427 ASN cc_start: 0.7843 (p0) cc_final: 0.7252 (t0) REVERT: A 965 ARG cc_start: 0.7264 (ptt180) cc_final: 0.5296 (tpt90) REVERT: A 1011 MET cc_start: 0.8346 (tpp) cc_final: 0.7828 (ttm) REVERT: H 23 LYS cc_start: 0.8750 (mttt) cc_final: 0.8221 (mtmm) REVERT: H 73 TYR cc_start: 0.6926 (OUTLIER) cc_final: 0.6039 (m-80) REVERT: L 53 TYR cc_start: 0.5993 (OUTLIER) cc_final: 0.5644 (p90) outliers start: 32 outliers final: 27 residues processed: 175 average time/residue: 0.2226 time to fit residues: 55.2168 Evaluate side-chains 171 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 299 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 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 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 1009 THR 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 H residue 87 TYR Chi-restraints excluded: chain L residue 30 HIS Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 53 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 93 optimal weight: 0.0670 chunk 107 optimal weight: 0.9990 chunk 113 optimal weight: 0.1980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9999 Z= 0.161 Angle : 0.568 8.629 13592 Z= 0.297 Chirality : 0.045 0.215 1544 Planarity : 0.004 0.047 1743 Dihedral : 5.409 53.522 1436 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.29 % Favored : 96.38 % Rotamer: Outliers : 2.79 % Allowed : 17.21 % Favored : 80.00 % 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: -0.15 (0.24), residues: 1216 helix: 2.04 (0.35), residues: 234 sheet: 0.31 (0.30), residues: 293 loop : -1.08 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 340 HIS 0.009 0.001 HIS L 30 PHE 0.017 0.001 PHE A 130 TYR 0.015 0.001 TYR A 256 ARG 0.004 0.000 ARG A 449 *********************** 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: 30 poor density : 151 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 ARG cc_start: 0.7189 (ttm-80) cc_final: 0.6894 (ttt90) REVERT: A 411 LYS cc_start: 0.8101 (tptt) cc_final: 0.7622 (tppt) REVERT: A 427 ASN cc_start: 0.7799 (p0) cc_final: 0.7204 (t0) REVERT: A 965 ARG cc_start: 0.7176 (ptt180) cc_final: 0.5126 (tpt90) REVERT: A 1011 MET cc_start: 0.8319 (tpp) cc_final: 0.7798 (ttm) REVERT: H 23 LYS cc_start: 0.8730 (mttt) cc_final: 0.8213 (mtmm) REVERT: H 73 TYR cc_start: 0.6787 (OUTLIER) cc_final: 0.5909 (m-80) REVERT: L 53 TYR cc_start: 0.5938 (OUTLIER) cc_final: 0.5551 (p90) outliers start: 30 outliers final: 23 residues processed: 172 average time/residue: 0.2335 time to fit residues: 57.2802 Evaluate side-chains 165 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 2.125 ------------------------------------------------------------------------------- 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 299 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 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 959 LEU 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 Chi-restraints excluded: chain L residue 53 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 113 optimal weight: 0.0030 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9999 Z= 0.297 Angle : 0.646 8.163 13592 Z= 0.340 Chirality : 0.048 0.244 1544 Planarity : 0.004 0.048 1743 Dihedral : 5.835 55.671 1436 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.61 % Favored : 95.07 % Rotamer: Outliers : 3.07 % Allowed : 17.21 % Favored : 79.72 % 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: -0.40 (0.24), residues: 1216 helix: 1.84 (0.34), residues: 234 sheet: -0.08 (0.28), residues: 333 loop : -1.18 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 340 HIS 0.008 0.001 HIS L 30 PHE 0.022 0.002 PHE A 89 TYR 0.019 0.002 TYR A 252 ARG 0.005 0.000 ARG L 58 *********************** 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 179 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.6660 (m-10) cc_final: 0.6042 (t80) REVERT: A 232 ARG cc_start: 0.7356 (ttm-80) cc_final: 0.7038 (ttt90) REVERT: A 292 SER cc_start: 0.8720 (t) cc_final: 0.8046 (m) REVERT: A 411 LYS cc_start: 0.8228 (tptt) cc_final: 0.7815 (tppt) REVERT: A 427 ASN cc_start: 0.7874 (p0) cc_final: 0.7217 (t0) REVERT: A 802 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7680 (m-30) REVERT: A 965 ARG cc_start: 0.7361 (ptt180) cc_final: 0.5353 (tpt90) REVERT: A 1011 MET cc_start: 0.8411 (tpp) cc_final: 0.7863 (ttm) REVERT: H 23 LYS cc_start: 0.8801 (mttt) cc_final: 0.8231 (mtmm) REVERT: H 73 TYR cc_start: 0.6848 (OUTLIER) cc_final: 0.5983 (m-80) REVERT: L 53 TYR cc_start: 0.6123 (OUTLIER) cc_final: 0.5802 (p90) outliers start: 33 outliers final: 28 residues processed: 170 average time/residue: 0.2235 time to fit residues: 53.6482 Evaluate side-chains 166 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 299 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 551 PHE 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 802 ASP 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 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 37 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 Chi-restraints excluded: chain L residue 53 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 93 HIS L 30 HIS ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.5607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9999 Z= 0.198 Angle : 0.615 9.675 13592 Z= 0.320 Chirality : 0.046 0.220 1544 Planarity : 0.004 0.046 1743 Dihedral : 5.658 53.746 1436 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.44 % Favored : 95.23 % Rotamer: Outliers : 2.70 % Allowed : 18.42 % Favored : 78.88 % 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: -0.29 (0.24), residues: 1216 helix: 2.04 (0.34), residues: 233 sheet: -0.00 (0.28), residues: 322 loop : -1.14 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 340 HIS 0.005 0.001 HIS L 30 PHE 0.029 0.002 PHE A 909 TYR 0.022 0.002 TYR A 256 ARG 0.007 0.000 ARG A 426 ********************** 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 175 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.6635 (m-10) cc_final: 0.6008 (t80) REVERT: A 232 ARG cc_start: 0.7200 (ttm-80) cc_final: 0.6912 (ttt90) REVERT: A 411 LYS cc_start: 0.8233 (tptt) cc_final: 0.7816 (tppt) REVERT: A 504 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6406 (mp) REVERT: A 965 ARG cc_start: 0.7179 (ptt180) cc_final: 0.5113 (tpt90) REVERT: A 1011 MET cc_start: 0.8298 (tpp) cc_final: 0.7814 (ttm) REVERT: H 23 LYS cc_start: 0.8776 (mttt) cc_final: 0.8218 (mtmm) REVERT: H 73 TYR cc_start: 0.6767 (OUTLIER) cc_final: 0.5916 (m-80) REVERT: L 53 TYR cc_start: 0.6111 (OUTLIER) cc_final: 0.5759 (p90) outliers start: 29 outliers final: 24 residues processed: 167 average time/residue: 0.2265 time to fit residues: 53.4630 Evaluate side-chains 163 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 299 ILE Chi-restraints excluded: chain A residue 504 LEU 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 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 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 Chi-restraints excluded: chain L residue 53 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4037 r_free = 0.4037 target = 0.177591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.151383 restraints weight = 15335.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.154182 restraints weight = 10103.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.155982 restraints weight = 7011.872| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.5707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9999 Z= 0.223 Angle : 0.624 8.754 13592 Z= 0.326 Chirality : 0.047 0.220 1544 Planarity : 0.004 0.044 1743 Dihedral : 5.705 53.699 1436 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.02 % Favored : 94.65 % Rotamer: Outliers : 2.98 % Allowed : 18.70 % Favored : 78.33 % 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: -0.39 (0.23), residues: 1216 helix: 2.00 (0.34), residues: 233 sheet: -0.02 (0.28), residues: 314 loop : -1.24 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 340 HIS 0.014 0.001 HIS L 30 PHE 0.028 0.002 PHE A 909 TYR 0.021 0.002 TYR A 256 ARG 0.007 0.000 ARG A 426 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2365.35 seconds wall clock time: 44 minutes 3.44 seconds (2643.44 seconds total)