Starting phenix.real_space_refine on Wed Mar 5 16:28:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zwj_60529/03_2025/8zwj_60529.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zwj_60529/03_2025/8zwj_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zwj_60529/03_2025/8zwj_60529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zwj_60529/03_2025/8zwj_60529.map" model { file = "/net/cci-nas-00/data/ceres_data/8zwj_60529/03_2025/8zwj_60529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zwj_60529/03_2025/8zwj_60529.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2760 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "F" 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: Q, C, B, E, D, G Time building chain proxies: 2.17, per 1000 atoms: 0.79 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: 0.66 Conformation dependent library (CDL) restraints added in 343.3 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: 0.89 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: 0.54 Time building geometry restraints manager: 0.79 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: 0.03 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' } 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.990 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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= 0.435 Angle : 0.737 4.117 3796 Z= 0.412 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.007 0.004 HIS G 50 PHE 0.013 0.004 PHE A 94 TYR 0.010 0.003 TYR C 39 *********************** 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 : 0.276 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: 0.2883 time to fit residues: 9.8409 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 : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.0050 chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4587 r_free = 0.4587 target = 0.205974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.156235 restraints weight = 2666.856| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.25 r_work: 0.3950 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3826 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2788 Z= 0.150 Angle : 0.483 3.184 3796 Z= 0.265 Chirality : 0.051 0.137 498 Planarity : 0.002 0.010 450 Dihedral : 14.653 107.639 444 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.74 % Allowed : 16.30 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS E 50 PHE 0.004 0.001 PHE C 94 TYR 0.002 0.001 TYR C 39 *********************** 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 30 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.280 Fit side-chains REVERT: G 60 LYS cc_start: 0.8216 (ttpt) cc_final: 0.7820 (ttmm) REVERT: G 62 GLN cc_start: 0.7346 (mt0) cc_final: 0.7136 (tt0) REVERT: C 60 LYS cc_start: 0.8461 (ttmt) cc_final: 0.8197 (tttt) REVERT: C 62 GLN cc_start: 0.7637 (mt0) cc_final: 0.7357 (tt0) REVERT: C 83 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7808 (tm-30) REVERT: E 62 GLN cc_start: 0.7307 (mt0) cc_final: 0.6964 (tt0) REVERT: E 83 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7508 (tm-30) REVERT: A 60 LYS cc_start: 0.8317 (ttpt) cc_final: 0.8073 (ttmm) REVERT: A 62 GLN cc_start: 0.7644 (mt0) cc_final: 0.7093 (tt0) REVERT: A 83 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7951 (tm-30) REVERT: A 87 SER cc_start: 0.8760 (m) cc_final: 0.8513 (p) REVERT: B 60 LYS cc_start: 0.8328 (ttpt) cc_final: 0.7945 (ttmm) outliers start: 2 outliers final: 2 residues processed: 28 average time/residue: 0.2352 time to fit residues: 7.6345 Evaluate side-chains 30 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 GLN 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 29 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4521 r_free = 0.4521 target = 0.200451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.149230 restraints weight = 2696.042| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.27 r_work: 0.3885 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1448 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= 0.266 Angle : 0.516 3.824 3796 Z= 0.288 Chirality : 0.050 0.135 498 Planarity : 0.002 0.008 450 Dihedral : 14.142 103.802 444 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 3.70 % Allowed : 14.81 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.006 0.003 HIS G 50 PHE 0.010 0.003 PHE A 94 TYR 0.008 0.002 TYR D 39 *********************** 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 29 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 19 time to evaluate : 0.342 Fit side-chains REVERT: G 60 LYS cc_start: 0.8300 (ttpt) cc_final: 0.7990 (ttmt) REVERT: G 62 GLN cc_start: 0.7424 (mt0) cc_final: 0.6941 (tt0) REVERT: C 60 LYS cc_start: 0.8600 (ttmt) cc_final: 0.8270 (tttt) REVERT: C 83 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7826 (tm-30) REVERT: D 60 LYS cc_start: 0.8600 (ttmm) cc_final: 0.8344 (tttm) REVERT: A 60 LYS cc_start: 0.8452 (ttpt) cc_final: 0.8229 (ttmm) REVERT: A 62 GLN cc_start: 0.7667 (mt0) cc_final: 0.7172 (tt0) REVERT: A 83 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7897 (tm-30) REVERT: B 60 LYS cc_start: 0.8435 (ttpt) cc_final: 0.8062 (ttmm) outliers start: 10 outliers final: 7 residues processed: 28 average time/residue: 0.2147 time to fit residues: 7.1801 Evaluate side-chains 26 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain C 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 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 7 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN D 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.188652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.137179 restraints weight = 2851.992| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.40 r_work: 0.3775 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2788 Z= 0.367 Angle : 0.598 3.716 3796 Z= 0.330 Chirality : 0.052 0.142 498 Planarity : 0.002 0.008 450 Dihedral : 13.673 100.241 444 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 4.44 % Allowed : 18.52 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.37), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS G 50 PHE 0.014 0.004 PHE A 94 TYR 0.011 0.003 TYR G 39 *********************** 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 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 23 time to evaluate : 0.285 Fit side-chains REVERT: G 60 LYS cc_start: 0.8353 (ttpt) cc_final: 0.7901 (tttt) REVERT: G 62 GLN cc_start: 0.7509 (mt0) cc_final: 0.7280 (tt0) REVERT: C 60 LYS cc_start: 0.8493 (ttmt) cc_final: 0.8227 (tttm) REVERT: C 83 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7792 (tm-30) REVERT: E 83 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7443 (tm-30) REVERT: A 60 LYS cc_start: 0.8518 (ttpt) cc_final: 0.8189 (ttmm) REVERT: A 62 GLN cc_start: 0.7726 (mt0) cc_final: 0.7257 (tt0) REVERT: A 83 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7910 (tm-30) REVERT: B 60 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8175 (ttmm) outliers start: 12 outliers final: 12 residues processed: 32 average time/residue: 0.2524 time to fit residues: 9.2813 Evaluate side-chains 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 23 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 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 37 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 59 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 24 optimal weight: 0.6980 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.195660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.145289 restraints weight = 2795.419| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.36 r_work: 0.3908 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2207 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= 0.137 Angle : 0.405 3.399 3796 Z= 0.228 Chirality : 0.050 0.132 498 Planarity : 0.001 0.005 450 Dihedral : 12.773 96.676 444 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 3.33 % Allowed : 20.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.003 0.001 PHE E 94 TYR 0.003 0.001 TYR B 39 *********************** 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 30 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.270 Fit side-chains REVERT: G 37 VAL cc_start: 0.3802 (OUTLIER) cc_final: 0.3540 (p) REVERT: G 60 LYS cc_start: 0.8275 (ttpt) cc_final: 0.7977 (ttmt) REVERT: G 62 GLN cc_start: 0.7519 (mt0) cc_final: 0.6963 (tt0) REVERT: C 60 LYS cc_start: 0.8444 (ttmt) cc_final: 0.8017 (tmtt) REVERT: C 83 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7874 (tm-30) REVERT: E 83 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7475 (tm-30) REVERT: A 60 LYS cc_start: 0.8382 (ttpt) cc_final: 0.8102 (ttmm) REVERT: A 62 GLN cc_start: 0.7699 (mt0) cc_final: 0.7245 (tt0) REVERT: A 83 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7942 (tm-30) REVERT: B 60 LYS cc_start: 0.8422 (ttpt) cc_final: 0.8147 (ttmm) outliers start: 9 outliers final: 6 residues processed: 27 average time/residue: 0.1786 time to fit residues: 5.8346 Evaluate side-chains 28 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.186710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.136328 restraints weight = 2947.872| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.32 r_work: 0.3740 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.043 2788 Z= 0.550 Angle : 0.722 5.713 3796 Z= 0.393 Chirality : 0.055 0.142 498 Planarity : 0.003 0.010 450 Dihedral : 12.253 94.191 444 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 4.44 % Allowed : 20.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.005 HIS G 50 PHE 0.017 0.004 PHE A 94 TYR 0.016 0.004 TYR G 39 *********************** 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 44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.297 Fit side-chains REVERT: G 60 LYS cc_start: 0.8428 (ttpt) cc_final: 0.7947 (ttmm) REVERT: G 62 GLN cc_start: 0.7510 (mt0) cc_final: 0.7260 (tt0) REVERT: C 60 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8169 (tttm) REVERT: C 83 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7816 (tm-30) REVERT: D 60 LYS cc_start: 0.8572 (ttmm) cc_final: 0.8353 (tttm) REVERT: E 83 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7526 (tm-30) REVERT: A 60 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8209 (ttmm) REVERT: A 62 GLN cc_start: 0.7756 (mt0) cc_final: 0.7301 (tt0) REVERT: A 83 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7891 (tm-30) REVERT: B 60 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8257 (ttmm) outliers start: 12 outliers final: 12 residues processed: 40 average time/residue: 0.2053 time to fit residues: 9.4697 Evaluate side-chains 44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A 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 6 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.0370 chunk 25 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.197434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.148061 restraints weight = 2890.383| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.35 r_work: 0.3927 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3812 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2788 Z= 0.110 Angle : 0.405 3.523 3796 Z= 0.228 Chirality : 0.050 0.134 498 Planarity : 0.001 0.006 450 Dihedral : 11.567 92.085 444 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.96 % Allowed : 22.59 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.005 0.001 PHE B 94 TYR 0.001 0.000 TYR D 39 *********************** 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 34 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.264 Fit side-chains REVERT: G 37 VAL cc_start: 0.3817 (OUTLIER) cc_final: 0.3615 (p) REVERT: G 60 LYS cc_start: 0.8299 (ttpt) cc_final: 0.7973 (ttmt) REVERT: G 62 GLN cc_start: 0.7428 (mt0) cc_final: 0.6916 (tt0) REVERT: C 60 LYS cc_start: 0.8380 (ttmt) cc_final: 0.8091 (tttm) REVERT: C 83 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7870 (tm-30) REVERT: E 83 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7439 (tm-30) REVERT: A 60 LYS cc_start: 0.8370 (ttpt) cc_final: 0.8079 (ttmm) REVERT: A 62 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: A 83 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7904 (tm-30) REVERT: B 60 LYS cc_start: 0.8384 (ttpt) cc_final: 0.7986 (ttmm) outliers start: 8 outliers final: 5 residues processed: 31 average time/residue: 0.1942 time to fit residues: 7.2406 Evaluate side-chains 31 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 E residue 59 THR Chi-restraints excluded: chain A residue 62 GLN 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 35 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 16 optimal weight: 0.4980 chunk 14 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.194203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.143378 restraints weight = 2826.071| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.36 r_work: 0.3867 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2647 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= 0.183 Angle : 0.456 3.927 3796 Z= 0.255 Chirality : 0.049 0.135 498 Planarity : 0.001 0.007 450 Dihedral : 11.233 88.627 444 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 2.96 % Allowed : 23.33 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 50 PHE 0.006 0.001 PHE B 94 TYR 0.006 0.001 TYR D 39 *********************** 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 33 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: G 60 LYS cc_start: 0.8347 (ttpt) cc_final: 0.7976 (tttt) REVERT: G 62 GLN cc_start: 0.7464 (mt0) cc_final: 0.7182 (tt0) REVERT: C 60 LYS cc_start: 0.8445 (ttmt) cc_final: 0.8167 (tttm) REVERT: C 83 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7852 (tm-30) REVERT: E 83 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7445 (tm-30) REVERT: A 60 LYS cc_start: 0.8426 (ttpt) cc_final: 0.8153 (ttmm) REVERT: A 62 GLN cc_start: 0.7700 (mt0) cc_final: 0.7232 (tt0) REVERT: A 83 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7943 (tm-30) REVERT: B 60 LYS cc_start: 0.8469 (ttpt) cc_final: 0.8081 (ttmm) outliers start: 8 outliers final: 7 residues processed: 31 average time/residue: 0.2089 time to fit residues: 7.6554 Evaluate side-chains 30 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 59 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 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 28 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.195990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.146240 restraints weight = 2822.600| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.27 r_work: 0.3888 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3776 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2788 Z= 0.164 Angle : 0.447 5.223 3796 Z= 0.247 Chirality : 0.050 0.137 498 Planarity : 0.001 0.010 450 Dihedral : 10.787 86.392 444 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 3.33 % Allowed : 23.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS G 50 PHE 0.006 0.001 PHE B 94 TYR 0.005 0.001 TYR G 39 *********************** 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 30 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.236 Fit side-chains REVERT: G 60 LYS cc_start: 0.8347 (ttpt) cc_final: 0.7952 (tttt) REVERT: G 62 GLN cc_start: 0.7480 (mt0) cc_final: 0.7185 (tt0) REVERT: C 60 LYS cc_start: 0.8431 (ttmt) cc_final: 0.8134 (tttm) REVERT: C 83 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7793 (tm-30) REVERT: E 83 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7311 (tm-30) REVERT: A 60 LYS cc_start: 0.8411 (ttpt) cc_final: 0.8136 (ttmm) REVERT: A 62 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7221 (tt0) REVERT: A 83 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7845 (tm-30) REVERT: B 60 LYS cc_start: 0.8442 (ttpt) cc_final: 0.8023 (ttmm) outliers start: 9 outliers final: 6 residues processed: 26 average time/residue: 0.1737 time to fit residues: 5.4722 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 : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 62 GLN 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 31 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.194414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.143243 restraints weight = 2796.427| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.35 r_work: 0.3882 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2788 Z= 0.149 Angle : 0.429 3.565 3796 Z= 0.240 Chirality : 0.049 0.133 498 Planarity : 0.001 0.006 450 Dihedral : 10.464 83.326 444 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 2.59 % Allowed : 24.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 50 PHE 0.007 0.001 PHE B 94 TYR 0.005 0.001 TYR B 39 ********************** 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 30 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: G 60 LYS cc_start: 0.8325 (ttpt) cc_final: 0.7948 (tttt) REVERT: G 62 GLN cc_start: 0.7441 (mt0) cc_final: 0.7140 (tt0) REVERT: C 60 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8143 (tttm) REVERT: C 83 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7775 (tm-30) REVERT: E 83 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: A 60 LYS cc_start: 0.8427 (ttpt) cc_final: 0.8163 (ttmm) REVERT: A 62 GLN cc_start: 0.7726 (mt0) cc_final: 0.7242 (tt0) REVERT: A 83 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7846 (tm-30) REVERT: B 60 LYS cc_start: 0.8427 (ttpt) cc_final: 0.8010 (ttmm) outliers start: 7 outliers final: 6 residues processed: 26 average time/residue: 0.2024 time to fit residues: 6.3833 Evaluate side-chains 29 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain A 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 33 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 23 optimal weight: 9.9990 chunk 25 optimal weight: 0.0050 chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.200270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.151496 restraints weight = 2726.159| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.22 r_work: 0.3959 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3847 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2788 Z= 0.105 Angle : 0.378 3.228 3796 Z= 0.215 Chirality : 0.049 0.130 498 Planarity : 0.001 0.010 450 Dihedral : 10.158 81.620 444 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.59 % Allowed : 24.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 50 PHE 0.005 0.001 PHE G 94 TYR 0.003 0.001 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1923.20 seconds wall clock time: 33 minutes 51.43 seconds (2031.43 seconds total)