Starting phenix.real_space_refine on Tue Aug 4 12:28:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zwj_60529/08_2026/8zwj_60529.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zwj_60529/08_2026/8zwj_60529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zwj_60529/08_2026/8zwj_60529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zwj_60529/08_2026/8zwj_60529.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zwj_60529/08_2026/8zwj_60529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zwj_60529/08_2026/8zwj_60529.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 P 6 5.49 5 C 1704 2.51 5 N 486 2.21 5 O 564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2760 Number of models: 1 Model: "" Number of chains: 2 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "Q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Restraints were copied for chains: C, D, E, A, B, F Time building chain proxies: 0.69, per 1000 atoms: 0.25 Number of scatterers: 2760 At special positions: 0 Unit cell: (83.83, 103.75, 31.54, 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) P 6 15.00 O 564 8.00 N 486 7.00 C 1704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 118.1 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 46.0% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 58 removed outlier: 7.446A pdb=" N GLY G 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N HIS C 50 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N VAL G 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N VAL C 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY G 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N THR C 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA G 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ALA C 56 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL G 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LYS C 58 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLU G 57 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N GLU G 46 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N VAL D 49 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 9.095A pdb=" N VAL G 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLY D 51 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N HIS G 50 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N ALA D 53 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL G 52 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL D 55 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR G 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N GLU D 57 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA G 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 62 through 66 removed outlier: 6.577A pdb=" N GLN G 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ASN C 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR G 64 " --> pdb=" O ASN C 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 69 through 82 removed outlier: 6.917A pdb=" N VAL C 74 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR G 75 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA C 76 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL G 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N GLY D 73 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N THR G 72 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N THR D 75 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N VAL G 74 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N VAL D 77 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA G 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N GLN D 79 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA G 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N THR D 81 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS G 80 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 46 through 58 removed outlier: 7.446A pdb=" N GLY E 47 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N HIS A 50 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N VAL E 49 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N VAL A 52 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY E 51 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N THR A 54 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA E 53 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ALA A 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL E 55 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LYS A 58 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLU E 57 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N GLU E 46 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N VAL B 49 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N VAL E 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLY B 51 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N HIS E 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N ALA B 53 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL E 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL B 55 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR E 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N GLU B 57 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA E 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 62 through 66 removed outlier: 6.577A pdb=" N GLN E 62 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ASN A 65 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR E 64 " --> pdb=" O ASN A 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 82 removed outlier: 6.917A pdb=" N VAL A 74 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR E 75 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA A 76 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL E 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N GLY B 73 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N THR E 72 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N THR B 75 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N VAL E 74 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N VAL B 77 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA E 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N GLN B 79 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA E 78 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N THR B 81 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS E 80 " --> pdb=" O THR B 81 " (cutoff:3.500A) 28 hydrogen bonds defined for protein. 84 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 0.37 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.30: 462 1.30 - 1.38: 503 1.38 - 1.46: 317 1.46 - 1.53: 1397 1.53 - 1.61: 109 Bond restraints: 2788 Sorted by residual: bond pdb=" C THR B 92 " pdb=" N GLY B 93 " ideal model delta sigma weight residual 1.329 1.309 0.020 1.62e-02 3.81e+03 1.53e+00 bond pdb=" C THR D 92 " pdb=" N GLY D 93 " ideal model delta sigma weight residual 1.329 1.309 0.020 1.62e-02 3.81e+03 1.47e+00 bond pdb=" C THR G 92 " pdb=" N GLY G 93 " ideal model delta sigma weight residual 1.329 1.309 0.019 1.62e-02 3.81e+03 1.45e+00 bond pdb=" C THR E 92 " pdb=" N GLY E 93 " ideal model delta sigma weight residual 1.329 1.309 0.019 1.62e-02 3.81e+03 1.40e+00 bond pdb=" C THR A 92 " pdb=" N GLY A 93 " ideal model delta sigma weight residual 1.329 1.310 0.019 1.62e-02 3.81e+03 1.39e+00 ... (remaining 2783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.82: 3166 0.82 - 1.65: 435 1.65 - 2.47: 125 2.47 - 3.29: 33 3.29 - 4.12: 37 Bond angle restraints: 3796 Sorted by residual: angle pdb=" O5' A F 14 " pdb=" C5' A F 14 " pdb=" C4' A F 14 " ideal model delta sigma weight residual 109.40 111.86 -2.46 8.00e-01 1.56e+00 9.44e+00 angle pdb=" O5' A Q 14 " pdb=" C5' A Q 14 " pdb=" C4' A Q 14 " ideal model delta sigma weight residual 109.40 111.85 -2.45 8.00e-01 1.56e+00 9.39e+00 angle pdb=" O5' A Q 12 " pdb=" C5' A Q 12 " pdb=" C4' A Q 12 " ideal model delta sigma weight residual 109.40 111.74 -2.34 8.00e-01 1.56e+00 8.56e+00 angle pdb=" O5' A Q 13 " pdb=" C5' A Q 13 " pdb=" C4' A Q 13 " ideal model delta sigma weight residual 109.40 111.74 -2.34 8.00e-01 1.56e+00 8.53e+00 angle pdb=" O5' A F 12 " pdb=" C5' A F 12 " pdb=" C4' A F 12 " ideal model delta sigma weight residual 109.40 111.74 -2.34 8.00e-01 1.56e+00 8.52e+00 ... (remaining 3791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.39: 1514 24.39 - 48.77: 94 48.77 - 73.15: 0 73.15 - 97.53: 0 97.53 - 121.91: 6 Dihedral angle restraints: 1614 sinusoidal: 588 harmonic: 1026 Sorted by residual: dihedral pdb=" CA VAL G 40 " pdb=" C VAL G 40 " pdb=" N GLY G 41 " pdb=" CA GLY G 41 " ideal model delta harmonic sigma weight residual 180.00 162.06 17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA VAL E 40 " pdb=" C VAL E 40 " pdb=" N GLY E 41 " pdb=" CA GLY E 41 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA VAL A 40 " pdb=" C VAL A 40 " pdb=" N GLY A 41 " pdb=" CA GLY A 41 " ideal model delta harmonic sigma weight residual 180.00 162.09 17.91 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 1611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 187 0.029 - 0.058: 191 0.058 - 0.087: 42 0.087 - 0.116: 56 0.116 - 0.144: 22 Chirality restraints: 498 Sorted by residual: chirality pdb=" C2' A Q 12 " pdb=" C3' A Q 12 " pdb=" O2' A Q 12 " pdb=" C1' A Q 12 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" C2' A F 12 " pdb=" C3' A F 12 " pdb=" O2' A F 12 " pdb=" C1' A F 12 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" C2' A Q 13 " pdb=" C3' A Q 13 " pdb=" O2' A Q 13 " pdb=" C1' A Q 13 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 495 not shown) Planarity restraints: 450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS G 50 " 0.010 2.00e-02 2.50e+03 8.45e-03 1.07e+00 pdb=" CG HIS G 50 " -0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS G 50 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS G 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS G 50 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS G 50 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 50 " -0.009 2.00e-02 2.50e+03 8.36e-03 1.05e+00 pdb=" CG HIS E 50 " 0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS E 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS E 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS E 50 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS E 50 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 50 " 0.009 2.00e-02 2.50e+03 8.24e-03 1.02e+00 pdb=" CG HIS D 50 " -0.017 2.00e-02 2.50e+03 pdb=" ND1 HIS D 50 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS D 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS D 50 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS D 50 " 0.004 2.00e-02 2.50e+03 ... (remaining 447 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 298 2.75 - 3.29: 2572 3.29 - 3.83: 4155 3.83 - 4.36: 4725 4.36 - 4.90: 9688 Nonbonded interactions: 21438 Sorted by model distance: nonbonded pdb=" OE2 GLU B 46 " pdb=" NZ LYS B 80 " model vdw 2.218 3.120 nonbonded pdb=" OE2 GLU A 46 " pdb=" NZ LYS A 80 " model vdw 2.218 3.120 nonbonded pdb=" OE2 GLU E 46 " pdb=" NZ LYS E 80 " model vdw 2.218 3.120 nonbonded pdb=" OE2 GLU D 46 " pdb=" NZ LYS D 80 " model vdw 2.219 3.120 nonbonded pdb=" OE2 GLU G 46 " pdb=" NZ LYS G 80 " model vdw 2.219 3.120 ... (remaining 21433 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: 0.01 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'Q' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.880 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.150 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 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 : 0.006 0.030 2788 Z= 0.290 Angle : 0.755 4.117 3796 Z= 0.434 Chirality : 0.056 0.144 498 Planarity : 0.002 0.009 450 Dihedral : 15.838 121.909 966 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 0.00 % Allowed : 17.78 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.10 (0.30), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.003 TYR C 39 PHE 0.013 0.004 PHE A 94 HIS 0.007 0.004 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.29 ( 2788) covalent geometry : angle 0.75548 / 0.43 ( 3796) hydrogen bonds : bond 0.19242 / 11.47 ( 28) hydrogen bonds : angle 8.54414 / 5.35 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.097 Fit side-chains REVERT: G 60 LYS cc_start: 0.8316 (ttpt) cc_final: 0.7928 (ttmm) REVERT: G 96 LYS cc_start: 0.6397 (mttt) cc_final: 0.6197 (mttm) REVERT: C 62 GLN cc_start: 0.7188 (mt0) cc_final: 0.6770 (tt0) REVERT: C 83 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7321 (tm-30) REVERT: E 62 GLN cc_start: 0.7018 (mt0) cc_final: 0.6599 (tt0) REVERT: E 83 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7314 (tm-30) REVERT: A 60 LYS cc_start: 0.8371 (ttpt) cc_final: 0.8102 (ttmm) REVERT: A 62 GLN cc_start: 0.7293 (mt0) cc_final: 0.6866 (tt0) REVERT: A 83 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7423 (tm-30) REVERT: B 60 LYS cc_start: 0.8311 (ttpt) cc_final: 0.8063 (ttmm) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1221 time to fit residues: 4.1358 Evaluate side-chains 29 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 62 GLN C 62 GLN D 62 GLN E 62 GLN A 62 GLN B 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.198258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.149330 restraints weight = 2774.252| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.25 r_work: 0.3843 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2788 Z= 0.110 Angle : 0.536 4.338 3796 Z= 0.293 Chirality : 0.050 0.140 498 Planarity : 0.002 0.011 450 Dihedral : 15.712 113.397 444 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 2.96 % Allowed : 14.44 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 39 PHE 0.004 0.001 PHE B 94 HIS 0.006 0.003 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 2788) covalent geometry : angle 0.53556 / 0.29 ( 3796) hydrogen bonds : bond 0.02655 / 1.50 ( 28) hydrogen bonds : angle 6.23317 / 3.93 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.097 Fit side-chains REVERT: G 60 LYS cc_start: 0.8237 (ttpt) cc_final: 0.7891 (tttt) REVERT: G 62 GLN cc_start: 0.7365 (mt0) cc_final: 0.7140 (tt0) REVERT: C 60 LYS cc_start: 0.8511 (ttmt) cc_final: 0.8263 (tttt) REVERT: C 62 GLN cc_start: 0.7705 (mt0) cc_final: 0.7452 (tt0) REVERT: C 83 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7720 (tm-30) REVERT: E 60 LYS cc_start: 0.8435 (ttmt) cc_final: 0.8205 (tttt) REVERT: A 60 LYS cc_start: 0.8427 (ttpt) cc_final: 0.8200 (ttmm) REVERT: A 62 GLN cc_start: 0.7663 (mt0) cc_final: 0.7168 (tt0) REVERT: A 83 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7845 (tm-30) REVERT: B 60 LYS cc_start: 0.8402 (ttpt) cc_final: 0.7991 (ttmm) outliers start: 8 outliers final: 6 residues processed: 29 average time/residue: 0.1025 time to fit residues: 3.4242 Evaluate side-chains 27 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 62 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 31 optimal weight: 0.0030 overall best weight: 4.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 62 GLN B 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.194789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.143067 restraints weight = 2807.632| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.35 r_work: 0.3747 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 2788 Z= 0.346 Angle : 0.726 4.539 3796 Z= 0.403 Chirality : 0.055 0.154 498 Planarity : 0.003 0.012 450 Dihedral : 15.420 109.518 444 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 4.81 % Allowed : 17.04 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.36), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.004 TYR G 39 PHE 0.016 0.004 PHE C 94 HIS 0.008 0.005 HIS E 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00793 / 0.35 ( 2788) covalent geometry : angle 0.72626 / 0.40 ( 3796) hydrogen bonds : bond 0.04000 / 2.27 ( 28) hydrogen bonds : angle 5.76532 / 3.63 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.097 Fit side-chains REVERT: G 60 LYS cc_start: 0.8437 (ttpt) cc_final: 0.7971 (ttmm) REVERT: G 96 LYS cc_start: 0.6563 (mttt) cc_final: 0.6358 (mttm) REVERT: C 62 GLN cc_start: 0.7679 (mt0) cc_final: 0.7165 (tt0) REVERT: C 83 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7833 (tm-30) REVERT: E 60 LYS cc_start: 0.8484 (ttmt) cc_final: 0.8212 (tttm) REVERT: E 83 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7535 (tm-30) REVERT: A 60 LYS cc_start: 0.8515 (ttpt) cc_final: 0.8196 (ttmm) REVERT: A 62 GLN cc_start: 0.7757 (mt0) cc_final: 0.7299 (tt0) REVERT: A 83 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7948 (tm-30) REVERT: B 60 LYS cc_start: 0.8553 (ttpt) cc_final: 0.8314 (ttmm) outliers start: 13 outliers final: 11 residues processed: 40 average time/residue: 0.1009 time to fit residues: 4.6016 Evaluate side-chains 43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 59 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 62 GLN E 62 GLN B 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.199368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.148151 restraints weight = 2730.480| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.37 r_work: 0.3826 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2788 Z= 0.145 Angle : 0.536 4.322 3796 Z= 0.293 Chirality : 0.051 0.134 498 Planarity : 0.002 0.021 450 Dihedral : 15.048 107.427 444 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 4.07 % Allowed : 20.37 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.37), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR G 39 PHE 0.007 0.002 PHE D 94 HIS 0.006 0.003 HIS E 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 2788) covalent geometry : angle 0.53576 / 0.29 ( 3796) hydrogen bonds : bond 0.02535 / 1.40 ( 28) hydrogen bonds : angle 5.57048 / 3.52 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.098 Fit side-chains REVERT: G 60 LYS cc_start: 0.8350 (ttpt) cc_final: 0.7949 (tttt) REVERT: G 62 GLN cc_start: 0.7393 (mt0) cc_final: 0.7131 (tt0) REVERT: C 60 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8313 (tttt) REVERT: C 62 GLN cc_start: 0.7624 (mt0) cc_final: 0.7371 (tt0) REVERT: C 83 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7777 (tm-30) REVERT: E 60 LYS cc_start: 0.8403 (ttmt) cc_final: 0.8144 (tttm) REVERT: A 60 LYS cc_start: 0.8475 (ttpt) cc_final: 0.8223 (ttmm) REVERT: A 62 GLN cc_start: 0.7735 (mt0) cc_final: 0.7172 (tt0) REVERT: A 83 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7912 (tm-30) REVERT: B 60 LYS cc_start: 0.8478 (ttpt) cc_final: 0.8051 (ttmm) outliers start: 11 outliers final: 11 residues processed: 28 average time/residue: 0.1004 time to fit residues: 3.2701 Evaluate side-chains 31 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 0.3980 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 62 GLN B 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.197026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.145237 restraints weight = 2675.781| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.32 r_work: 0.3799 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2788 Z= 0.241 Angle : 0.600 3.902 3796 Z= 0.331 Chirality : 0.052 0.143 498 Planarity : 0.002 0.011 450 Dihedral : 14.793 104.958 444 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 6.30 % Allowed : 18.52 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR G 39 PHE 0.012 0.003 PHE E 94 HIS 0.007 0.004 HIS E 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.24 ( 2788) covalent geometry : angle 0.60012 / 0.33 ( 3796) hydrogen bonds : bond 0.02887 / 1.64 ( 28) hydrogen bonds : angle 5.53225 / 3.48 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 30 time to evaluate : 0.092 Fit side-chains REVERT: G 37 VAL cc_start: 0.3391 (OUTLIER) cc_final: 0.3169 (m) REVERT: G 60 LYS cc_start: 0.8437 (ttpt) cc_final: 0.7947 (ttmm) REVERT: G 96 LYS cc_start: 0.6485 (mttt) cc_final: 0.6273 (mttm) REVERT: C 60 LYS cc_start: 0.8625 (ttmt) cc_final: 0.8362 (tttt) REVERT: C 83 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7791 (tm-30) REVERT: E 60 LYS cc_start: 0.8434 (ttmt) cc_final: 0.8155 (tttm) REVERT: E 83 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7465 (tm-30) REVERT: A 60 LYS cc_start: 0.8496 (ttpt) cc_final: 0.8163 (ttmm) REVERT: A 62 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7223 (tt0) REVERT: A 83 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7918 (tm-30) REVERT: B 60 LYS cc_start: 0.8543 (ttpt) cc_final: 0.8108 (ttmm) outliers start: 17 outliers final: 12 residues processed: 39 average time/residue: 0.0926 time to fit residues: 4.1496 Evaluate side-chains 43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 62 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 62 GLN B 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.196935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.144710 restraints weight = 2721.928| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.37 r_work: 0.3795 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 2788 Z= 0.264 Angle : 0.624 3.661 3796 Z= 0.345 Chirality : 0.053 0.142 498 Planarity : 0.002 0.008 450 Dihedral : 14.615 103.495 444 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 7.41 % Allowed : 18.52 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR E 39 PHE 0.013 0.003 PHE C 94 HIS 0.007 0.004 HIS E 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.26 ( 2788) covalent geometry : angle 0.62443 / 0.35 ( 3796) hydrogen bonds : bond 0.02812 / 1.63 ( 28) hydrogen bonds : angle 5.57103 / 3.52 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 33 time to evaluate : 0.095 Fit side-chains REVERT: G 37 VAL cc_start: 0.3444 (OUTLIER) cc_final: 0.3218 (m) REVERT: G 60 LYS cc_start: 0.8468 (ttpt) cc_final: 0.7969 (ttmm) REVERT: G 62 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7259 (tt0) REVERT: C 60 LYS cc_start: 0.8565 (ttmt) cc_final: 0.8265 (tttm) REVERT: C 83 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7807 (tm-30) REVERT: E 60 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8168 (tttm) REVERT: E 83 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7459 (tm-30) REVERT: A 60 LYS cc_start: 0.8523 (ttpt) cc_final: 0.8187 (ttmm) REVERT: A 62 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7207 (tt0) REVERT: A 83 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7914 (tm-30) REVERT: B 60 LYS cc_start: 0.8459 (ttpt) cc_final: 0.8168 (tttt) outliers start: 20 outliers final: 14 residues processed: 43 average time/residue: 0.0621 time to fit residues: 3.0696 Evaluate side-chains 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 33 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 62 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 62 GLN B 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.198375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.146385 restraints weight = 2643.744| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.32 r_work: 0.3806 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2788 Z= 0.204 Angle : 0.569 3.598 3796 Z= 0.315 Chirality : 0.051 0.139 498 Planarity : 0.002 0.008 450 Dihedral : 14.272 101.415 444 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 6.67 % Allowed : 20.37 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.39), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR G 39 PHE 0.015 0.002 PHE G 94 HIS 0.006 0.004 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 ( 2788) covalent geometry : angle 0.56930 / 0.32 ( 3796) hydrogen bonds : bond 0.02503 / 1.43 ( 28) hydrogen bonds : angle 5.53478 / 3.50 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 28 time to evaluate : 0.106 Fit side-chains REVERT: G 37 VAL cc_start: 0.3499 (OUTLIER) cc_final: 0.3267 (m) REVERT: G 60 LYS cc_start: 0.8414 (ttpt) cc_final: 0.7908 (ttmm) REVERT: G 62 GLN cc_start: 0.7453 (mt0) cc_final: 0.7227 (tt0) REVERT: C 60 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8066 (tmtt) REVERT: C 83 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7768 (tm-30) REVERT: E 60 LYS cc_start: 0.8354 (ttmt) cc_final: 0.8086 (tttm) REVERT: E 83 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7415 (tm-30) REVERT: A 60 LYS cc_start: 0.8520 (ttpt) cc_final: 0.8173 (ttmm) REVERT: A 62 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7178 (tt0) REVERT: A 83 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7849 (tm-30) REVERT: B 60 LYS cc_start: 0.8559 (ttpt) cc_final: 0.8128 (ttmm) outliers start: 18 outliers final: 14 residues processed: 41 average time/residue: 0.0913 time to fit residues: 4.3175 Evaluate side-chains 44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 28 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 62 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 0.0470 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.200924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.149213 restraints weight = 2717.609| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.32 r_work: 0.3829 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2788 Z= 0.139 Angle : 0.514 3.762 3796 Z= 0.284 Chirality : 0.050 0.136 498 Planarity : 0.002 0.012 450 Dihedral : 14.009 100.369 444 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 5.56 % Allowed : 22.59 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR G 39 PHE 0.013 0.003 PHE G 94 HIS 0.006 0.003 HIS E 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 2788) covalent geometry : angle 0.51350 / 0.28 ( 3796) hydrogen bonds : bond 0.02233 / 1.26 ( 28) hydrogen bonds : angle 5.45265 / 3.45 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 27 time to evaluate : 0.099 Fit side-chains REVERT: G 60 LYS cc_start: 0.8405 (ttpt) cc_final: 0.7909 (ttmm) REVERT: G 62 GLN cc_start: 0.7441 (mt0) cc_final: 0.7214 (tt0) REVERT: C 60 LYS cc_start: 0.8550 (ttmt) cc_final: 0.8073 (tmtt) REVERT: C 83 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7793 (tm-30) REVERT: E 60 LYS cc_start: 0.8396 (ttmt) cc_final: 0.8089 (tttm) REVERT: E 83 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7418 (tm-30) REVERT: A 60 LYS cc_start: 0.8517 (ttpt) cc_final: 0.8254 (ttmm) REVERT: A 62 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7141 (tt0) REVERT: A 83 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7901 (tm-30) REVERT: B 60 LYS cc_start: 0.8410 (ttpt) cc_final: 0.8144 (tttt) outliers start: 15 outliers final: 13 residues processed: 37 average time/residue: 0.0921 time to fit residues: 3.9113 Evaluate side-chains 41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 27 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 62 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.0970 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.198785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.146504 restraints weight = 2754.587| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.34 r_work: 0.3841 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2788 Z= 0.140 Angle : 0.502 3.604 3796 Z= 0.279 Chirality : 0.050 0.136 498 Planarity : 0.002 0.006 450 Dihedral : 13.760 99.205 444 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 6.67 % Allowed : 22.59 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR B 39 PHE 0.013 0.002 PHE D 94 HIS 0.005 0.003 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 2788) covalent geometry : angle 0.50236 / 0.28 ( 3796) hydrogen bonds : bond 0.02122 / 1.20 ( 28) hydrogen bonds : angle 5.39494 / 3.41 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 28 time to evaluate : 0.094 Fit side-chains REVERT: G 60 LYS cc_start: 0.8419 (ttpt) cc_final: 0.7954 (ttmm) REVERT: G 62 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: C 60 LYS cc_start: 0.8475 (ttmt) cc_final: 0.8091 (tmtt) REVERT: C 83 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7760 (tm-30) REVERT: E 60 LYS cc_start: 0.8377 (ttmt) cc_final: 0.8092 (tttm) REVERT: E 83 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7464 (tm-30) REVERT: A 60 LYS cc_start: 0.8468 (ttpt) cc_final: 0.8224 (ttmm) REVERT: A 62 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7127 (tt0) REVERT: A 83 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7914 (tm-30) REVERT: B 60 LYS cc_start: 0.8508 (ttpt) cc_final: 0.8246 (tttt) outliers start: 18 outliers final: 16 residues processed: 40 average time/residue: 0.0644 time to fit residues: 3.0437 Evaluate side-chains 46 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 28 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 62 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 0.0070 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 0.0970 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.202869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.151428 restraints weight = 2712.307| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.25 r_work: 0.3860 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3738 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2788 Z= 0.129 Angle : 0.495 4.012 3796 Z= 0.273 Chirality : 0.050 0.136 498 Planarity : 0.002 0.009 450 Dihedral : 13.563 98.137 444 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 6.30 % Allowed : 22.96 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR B 39 PHE 0.012 0.002 PHE D 94 HIS 0.005 0.003 HIS E 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 2788) covalent geometry : angle 0.49453 / 0.27 ( 3796) hydrogen bonds : bond 0.02122 / 1.20 ( 28) hydrogen bonds : angle 5.37999 / 3.41 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 25 time to evaluate : 0.091 Fit side-chains REVERT: G 60 LYS cc_start: 0.8420 (ttpt) cc_final: 0.7956 (ttmm) REVERT: G 62 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.7230 (tt0) REVERT: G 96 LYS cc_start: 0.6475 (mttm) cc_final: 0.5543 (mtmt) REVERT: C 60 LYS cc_start: 0.8461 (ttmt) cc_final: 0.8072 (tmtt) REVERT: C 83 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7765 (tm-30) REVERT: E 60 LYS cc_start: 0.8376 (ttmt) cc_final: 0.8089 (tttm) REVERT: E 83 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7474 (tm-30) REVERT: A 60 LYS cc_start: 0.8440 (ttpt) cc_final: 0.8196 (ttmm) REVERT: A 62 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7127 (tt0) REVERT: A 83 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7880 (tm-30) REVERT: B 60 LYS cc_start: 0.8405 (ttpt) cc_final: 0.8169 (tttt) outliers start: 17 outliers final: 15 residues processed: 36 average time/residue: 0.0854 time to fit residues: 3.6058 Evaluate side-chains 41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 24 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 62 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.187918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.136271 restraints weight = 2757.234| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.36 r_work: 0.3780 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 2788 Z= 0.244 Angle : 0.595 3.954 3796 Z= 0.331 Chirality : 0.052 0.144 498 Planarity : 0.002 0.010 450 Dihedral : 13.427 97.145 444 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 7.41 % Allowed : 22.22 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.003 TYR B 39 PHE 0.012 0.003 PHE D 94 HIS 0.007 0.004 HIS E 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.24 ( 2788) covalent geometry : angle 0.59550 / 0.33 ( 3796) hydrogen bonds : bond 0.02575 / 1.49 ( 28) hydrogen bonds : angle 5.44064 / 3.44 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 992.30 seconds wall clock time: 17 minutes 41.01 seconds (1061.01 seconds total)