Starting phenix.real_space_refine on Wed Jul 1 21:23:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zwj_60529/07_2026/8zwj_60529.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zwj_60529/07_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_60529/07_2026/8zwj_60529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zwj_60529/07_2026/8zwj_60529.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zwj_60529/07_2026/8zwj_60529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zwj_60529/07_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-dev-6108/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: 0.66, per 1000 atoms: 0.24 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: 0.16 Conformation dependent library (CDL) restraints added in 68.7 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: 0.35 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: 0.38 Time building geometry restraints manager: 0.21 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: 3184 0.82 - 1.65: 435 1.65 - 2.47: 113 2.47 - 3.29: 27 3.29 - 4.12: 37 Bond angle restraints: 3796 Sorted by residual: angle pdb=" C VAL A 49 " pdb=" N HIS A 50 " pdb=" CA HIS A 50 " ideal model delta sigma weight residual 121.94 117.82 4.12 1.76e+00 3.23e-01 5.47e+00 angle pdb=" C VAL D 49 " pdb=" N HIS D 50 " pdb=" CA HIS D 50 " ideal model delta sigma weight residual 121.94 117.83 4.11 1.76e+00 3.23e-01 5.46e+00 angle pdb=" C VAL G 49 " pdb=" N HIS G 50 " pdb=" CA HIS G 50 " ideal model delta sigma weight residual 121.94 117.83 4.11 1.76e+00 3.23e-01 5.46e+00 angle pdb=" C VAL B 49 " pdb=" N HIS B 50 " pdb=" CA HIS B 50 " ideal model delta sigma weight residual 121.94 117.83 4.11 1.76e+00 3.23e-01 5.46e+00 angle pdb=" C VAL E 49 " pdb=" N HIS E 50 " pdb=" CA HIS E 50 " ideal model delta sigma weight residual 121.94 117.83 4.11 1.76e+00 3.23e-01 5.44e+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 - 0.028: 186 0.028 - 0.055: 190 0.055 - 0.083: 48 0.083 - 0.110: 44 0.110 - 0.138: 30 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA VAL E 49 " pdb=" N VAL E 49 " pdb=" C VAL E 49 " pdb=" CB VAL E 49 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA VAL B 49 " pdb=" N VAL B 49 " pdb=" C VAL B 49 " pdb=" CB VAL B 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.42e-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: 3.210 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.550 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.230 ------------------------------------------------------------------------------- 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= 0.288 Angle : 0.737 4.117 3796 Z= 0.414 Chirality : 0.054 0.138 498 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 0.00633 / 0.29 ( 2788) covalent geometry : angle 0.73689 / 0.41 ( 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 : 0.059 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: 0.1185 time to fit residues: 3.9745 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 : 0.117 ------------------------------------------------------------------------------- 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 = 0.4486 r_free = 0.4486 target = 0.197625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.148352 restraints weight = 2765.080| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.26 r_work: 0.3826 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2788 Z= 0.107 Angle : 0.539 3.864 3796 Z= 0.294 Chirality : 0.050 0.140 498 Planarity : 0.002 0.011 450 Dihedral : 15.921 116.481 444 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % 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: -3.53 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 39 PHE 0.005 0.001 PHE B 94 HIS 0.006 0.003 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 ( 2788) covalent geometry : angle 0.53929 / 0.29 ( 3796) hydrogen bonds : bond 0.02703 / 1.54 ( 28) hydrogen bonds : angle 6.34325 / 4.01 ( 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: 0.8256 (ttpt) cc_final: 0.7932 (tttt) REVERT: C 60 LYS cc_start: 0.8505 (ttmt) cc_final: 0.8290 (tttt) REVERT: C 62 GLN cc_start: 0.7693 (mt0) cc_final: 0.7493 (tt0) REVERT: C 83 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7783 (tm-30) REVERT: E 60 LYS cc_start: 0.8455 (ttmt) cc_final: 0.8247 (tttt) REVERT: A 62 GLN cc_start: 0.7660 (mt0) cc_final: 0.7200 (tt0) REVERT: A 83 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7864 (tm-30) REVERT: B 60 LYS cc_start: 0.8436 (ttpt) cc_final: 0.8065 (ttmm) outliers start: 8 outliers final: 6 residues processed: 29 average time/residue: 0.1061 time to fit residues: 3.5439 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 : 0.097 ------------------------------------------------------------------------------- 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: 10.0000 chunk 11 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 31 optimal weight: 0.0970 overall best weight: 3.8186 ------------------------------------------------------------------------------- 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 = 0.4485 r_free = 0.4485 target = 0.196610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.145459 restraints weight = 2805.908| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.33 r_work: 0.3779 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 2788 Z= 0.268 Angle : 0.648 3.974 3796 Z= 0.359 Chirality : 0.054 0.153 498 Planarity : 0.003 0.015 450 Dihedral : 15.489 112.285 444 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 5.19 % Allowed : 15.19 % Favored : 79.63 % 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: -3.16 (0.36), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR E 39 PHE 0.012 0.003 PHE C 94 HIS 0.008 0.004 HIS E 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.27 ( 2788) covalent geometry : angle 0.64807 / 0.36 ( 3796) hydrogen bonds : bond 0.03565 / 2.05 ( 28) hydrogen bonds : angle 5.73324 / 3.60 ( 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 42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 28 time to evaluate : 0.058 Fit side-chains REVERT: G 60 LYS cc_start: 0.8371 (ttpt) cc_final: 0.7900 (ttmm) REVERT: G 96 LYS cc_start: 0.6369 (mttt) cc_final: 0.6146 (mttm) REVERT: C 60 LYS cc_start: 0.8711 (ttmt) cc_final: 0.8294 (tttt) REVERT: C 83 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7760 (tm-30) REVERT: E 60 LYS cc_start: 0.8438 (ttmt) cc_final: 0.8152 (tttm) REVERT: E 83 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7473 (tm-30) REVERT: A 60 LYS cc_start: 0.8597 (ttmm) cc_final: 0.8394 (ttmm) REVERT: A 62 GLN cc_start: 0.7716 (mt0) cc_final: 0.7122 (tt0) REVERT: A 83 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7896 (tm-30) REVERT: B 60 LYS cc_start: 0.8502 (ttpt) cc_final: 0.8263 (ttmm) outliers start: 14 outliers final: 12 residues processed: 37 average time/residue: 0.0637 time to fit residues: 2.7039 Evaluate side-chains 39 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 27 time to evaluate : 0.058 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.4535 r_free = 0.4535 target = 0.200058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.148260 restraints weight = 2735.595| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.40 r_work: 0.3838 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1372 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= 0.140 Angle : 0.525 4.435 3796 Z= 0.288 Chirality : 0.051 0.136 498 Planarity : 0.002 0.018 450 Dihedral : 15.172 110.513 444 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 4.07 % Allowed : 19.26 % Favored : 76.67 % 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 : -2.27 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR C 39 PHE 0.007 0.002 PHE A 94 HIS 0.006 0.003 HIS E 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 2788) covalent geometry : angle 0.52502 / 0.29 ( 3796) hydrogen bonds : bond 0.02366 / 1.33 ( 28) hydrogen bonds : angle 5.57804 / 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 31 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 0.055 Fit side-chains REVERT: G 60 LYS cc_start: 0.8309 (ttpt) cc_final: 0.7926 (tttt) REVERT: G 62 GLN cc_start: 0.7426 (mt0) cc_final: 0.7214 (tt0) REVERT: G 96 LYS cc_start: 0.6318 (mttt) cc_final: 0.6116 (mttm) REVERT: C 60 LYS cc_start: 0.8555 (ttmt) cc_final: 0.8082 (tmtt) REVERT: C 83 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7781 (tm-30) REVERT: E 60 LYS cc_start: 0.8401 (ttmt) cc_final: 0.8159 (tttm) REVERT: A 62 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7144 (tt0) REVERT: A 83 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7881 (tm-30) REVERT: B 60 LYS cc_start: 0.8479 (ttpt) cc_final: 0.8057 (ttmm) outliers start: 11 outliers final: 10 residues processed: 27 average time/residue: 0.0668 time to fit residues: 2.0973 Evaluate side-chains 30 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 19 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 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 A residue 62 GLN 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: 3.9990 chunk 16 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 62 GLN ** B 62 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 = 0.4505 r_free = 0.4505 target = 0.197532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.144976 restraints weight = 2689.686| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.38 r_work: 0.3785 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 2788 Z= 0.288 Angle : 0.648 3.923 3796 Z= 0.359 Chirality : 0.054 0.147 498 Planarity : 0.003 0.010 450 Dihedral : 14.966 107.725 444 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 5.56 % Allowed : 18.15 % Favored : 76.30 % 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: -2.87 (0.37), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR E 39 PHE 0.014 0.004 PHE A 94 HIS 0.007 0.004 HIS E 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.29 ( 2788) covalent geometry : angle 0.64840 / 0.36 ( 3796) hydrogen bonds : bond 0.03023 / 1.75 ( 28) hydrogen bonds : angle 5.58695 / 3.53 ( 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 45 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 0.116 Fit side-chains REVERT: G 37 VAL cc_start: 0.3421 (OUTLIER) cc_final: 0.3203 (m) REVERT: G 60 LYS cc_start: 0.8431 (ttpt) cc_final: 0.7948 (ttmm) REVERT: C 60 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8289 (tttm) REVERT: C 83 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7814 (tm-30) REVERT: E 60 LYS cc_start: 0.8459 (ttmt) cc_final: 0.8204 (tttm) REVERT: E 83 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7495 (tm-30) REVERT: A 62 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7299 (tt0) REVERT: A 83 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7951 (tm-30) REVERT: B 60 LYS cc_start: 0.8467 (ttpt) cc_final: 0.8209 (ttmm) outliers start: 15 outliers final: 12 residues processed: 38 average time/residue: 0.0983 time to fit residues: 4.2787 Evaluate side-chains 44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 0.089 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 = 0.4549 r_free = 0.4549 target = 0.201066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.149651 restraints weight = 2704.067| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.30 r_work: 0.3854 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3729 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1723 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= 0.145 Angle : 0.509 4.118 3796 Z= 0.280 Chirality : 0.051 0.134 498 Planarity : 0.002 0.007 450 Dihedral : 14.576 105.492 444 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 5.93 % Allowed : 18.52 % 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: -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 0.006 0.002 TYR G 39 PHE 0.006 0.002 PHE E 94 HIS 0.006 0.003 HIS E 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 2788) covalent geometry : angle 0.50947 / 0.28 ( 3796) hydrogen bonds : bond 0.02196 / 1.21 ( 28) hydrogen bonds : angle 5.49277 / 3.48 ( 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 39 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 23 time to evaluate : 0.099 Fit side-chains REVERT: G 60 LYS cc_start: 0.8357 (ttpt) cc_final: 0.7916 (ttmm) REVERT: G 62 GLN cc_start: 0.7456 (mt0) cc_final: 0.7194 (tt0) REVERT: C 60 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8219 (tttm) REVERT: C 83 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7822 (tm-30) REVERT: E 60 LYS cc_start: 0.8408 (ttmt) cc_final: 0.8140 (tttm) REVERT: E 83 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7437 (tm-30) REVERT: A 62 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7217 (mt0) REVERT: A 83 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7905 (tm-30) REVERT: B 60 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8086 (ttmm) outliers start: 16 outliers final: 12 residues processed: 35 average time/residue: 0.0868 time to fit residues: 3.5550 Evaluate side-chains 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 22 time to evaluate : 0.099 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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 = 0.4541 r_free = 0.4541 target = 0.200519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.149048 restraints weight = 2667.526| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.32 r_work: 0.3842 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2788 Z= 0.161 Angle : 0.530 3.982 3796 Z= 0.292 Chirality : 0.050 0.137 498 Planarity : 0.002 0.008 450 Dihedral : 14.401 104.553 444 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 5.56 % Allowed : 20.37 % 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: -2.58 (0.39), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR C 39 PHE 0.012 0.002 PHE B 94 HIS 0.005 0.003 HIS E 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 2788) covalent geometry : angle 0.53047 / 0.29 ( 3796) hydrogen bonds : bond 0.02204 / 1.25 ( 28) hydrogen bonds : angle 5.44997 / 3.45 ( 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 38 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 23 time to evaluate : 0.115 Fit side-chains REVERT: G 60 LYS cc_start: 0.8396 (ttpt) cc_final: 0.7919 (ttmm) REVERT: G 62 GLN cc_start: 0.7508 (mt0) cc_final: 0.7240 (tt0) REVERT: C 60 LYS cc_start: 0.8499 (ttmt) cc_final: 0.8224 (tttm) REVERT: C 83 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7799 (tm-30) REVERT: E 60 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8144 (tttm) REVERT: E 83 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7441 (tm-30) REVERT: A 83 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7896 (tm-30) REVERT: B 60 LYS cc_start: 0.8521 (ttpt) cc_final: 0.8125 (ttmm) REVERT: B 96 LYS cc_start: 0.6486 (mttm) cc_final: 0.5456 (mtmt) outliers start: 15 outliers final: 14 residues processed: 33 average time/residue: 0.0804 time to fit residues: 3.1268 Evaluate side-chains 37 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 23 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 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 87 SER 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: 1.9990 chunk 9 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 = 0.4517 r_free = 0.4517 target = 0.198285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.146069 restraints weight = 2743.014| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.32 r_work: 0.3805 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 2788 Z= 0.268 Angle : 0.616 4.062 3796 Z= 0.343 Chirality : 0.053 0.142 498 Planarity : 0.002 0.008 450 Dihedral : 14.297 103.264 444 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 6.30 % Allowed : 19.63 % 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: -2.59 (0.39), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.003 TYR G 39 PHE 0.013 0.003 PHE B 94 HIS 0.007 0.004 HIS E 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.27 ( 2788) covalent geometry : angle 0.61582 / 0.34 ( 3796) hydrogen bonds : bond 0.02733 / 1.55 ( 28) hydrogen bonds : angle 5.53899 / 3.51 ( 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 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 32 time to evaluate : 0.100 Fit side-chains REVERT: G 37 VAL cc_start: 0.3485 (OUTLIER) cc_final: 0.3258 (m) REVERT: G 60 LYS cc_start: 0.8421 (ttpt) cc_final: 0.7950 (ttmm) REVERT: G 62 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7186 (tt0) REVERT: C 60 LYS cc_start: 0.8526 (ttmt) cc_final: 0.8256 (tttm) REVERT: C 83 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7813 (tm-30) REVERT: E 60 LYS cc_start: 0.8422 (ttmt) cc_final: 0.8185 (tttm) REVERT: E 83 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7492 (tm-30) REVERT: A 83 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7884 (tm-30) REVERT: B 60 LYS cc_start: 0.8527 (ttpt) cc_final: 0.8274 (tttt) outliers start: 17 outliers final: 15 residues processed: 41 average time/residue: 0.0899 time to fit residues: 4.2753 Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 32 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 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 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 Chi-restraints excluded: chain B residue 81 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.4545 r_free = 0.4545 target = 0.201042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.149174 restraints weight = 2711.313| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.30 r_work: 0.3838 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1935 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= 0.147 Angle : 0.532 3.877 3796 Z= 0.294 Chirality : 0.051 0.136 498 Planarity : 0.002 0.008 450 Dihedral : 14.113 102.561 444 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 4.81 % Allowed : 21.85 % Favored : 73.33 % 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: -2.48 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR G 39 PHE 0.018 0.003 PHE G 94 HIS 0.006 0.003 HIS E 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 2788) covalent geometry : angle 0.53174 / 0.29 ( 3796) hydrogen bonds : bond 0.02230 / 1.25 ( 28) hydrogen bonds : angle 5.49055 / 3.48 ( 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 37 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.093 Fit side-chains REVERT: G 37 VAL cc_start: 0.3559 (OUTLIER) cc_final: 0.3334 (m) REVERT: G 60 LYS cc_start: 0.8380 (ttpt) cc_final: 0.7921 (ttmm) REVERT: G 62 GLN cc_start: 0.7470 (mt0) cc_final: 0.7239 (tt0) REVERT: C 60 LYS cc_start: 0.8504 (ttmt) cc_final: 0.8232 (tttm) REVERT: C 83 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7800 (tm-30) REVERT: E 60 LYS cc_start: 0.8385 (ttmt) cc_final: 0.8171 (tttm) REVERT: E 83 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7458 (tm-30) REVERT: A 83 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7892 (tm-30) REVERT: B 60 LYS cc_start: 0.8484 (ttpt) cc_final: 0.8244 (tttt) outliers start: 13 outliers final: 12 residues processed: 34 average time/residue: 0.0947 time to fit residues: 3.7490 Evaluate side-chains 37 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.093 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 2 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 6 optimal weight: 0.0070 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.7804 ------------------------------------------------------------------------------- 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 = 0.4554 r_free = 0.4554 target = 0.201522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.149951 restraints weight = 2716.637| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.28 r_work: 0.3851 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2788 Z= 0.140 Angle : 0.516 3.750 3796 Z= 0.286 Chirality : 0.050 0.136 498 Planarity : 0.002 0.008 450 Dihedral : 13.953 101.832 444 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 5.56 % Allowed : 21.48 % 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: -2.43 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR B 39 PHE 0.018 0.003 PHE D 94 HIS 0.005 0.003 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 2788) covalent geometry : angle 0.51619 / 0.29 ( 3796) hydrogen bonds : bond 0.02112 / 1.18 ( 28) hydrogen bonds : angle 5.43496 / 3.45 ( 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 37 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 22 time to evaluate : 0.115 Fit side-chains REVERT: G 60 LYS cc_start: 0.8393 (ttpt) cc_final: 0.7937 (ttmm) REVERT: G 62 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.7225 (tt0) REVERT: C 60 LYS cc_start: 0.8494 (ttmt) cc_final: 0.8221 (tttm) REVERT: C 83 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7780 (tm-30) REVERT: E 60 LYS cc_start: 0.8443 (ttmt) cc_final: 0.8177 (tttm) REVERT: E 83 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7498 (tm-30) REVERT: A 83 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7899 (tm-30) REVERT: B 60 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8257 (tttt) REVERT: B 62 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.6975 (tt0) REVERT: B 96 LYS cc_start: 0.6543 (mttm) cc_final: 0.5523 (mtmt) outliers start: 15 outliers final: 13 residues processed: 33 average time/residue: 0.0883 time to fit residues: 3.4291 Evaluate side-chains 37 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 22 time to evaluate : 0.095 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.201364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.149957 restraints weight = 2618.606| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.24 r_work: 0.3851 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2788 Z= 0.150 Angle : 0.516 3.677 3796 Z= 0.286 Chirality : 0.050 0.137 498 Planarity : 0.002 0.007 450 Dihedral : 13.800 101.059 444 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 5.56 % Allowed : 21.48 % 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: -2.41 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR B 39 PHE 0.015 0.003 PHE D 94 HIS 0.005 0.003 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 2788) covalent geometry : angle 0.51589 / 0.29 ( 3796) hydrogen bonds : bond 0.02175 / 1.21 ( 28) hydrogen bonds : angle 5.40529 / 3.43 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 887.63 seconds wall clock time: 15 minutes 54.86 seconds (954.86 seconds total)