Starting phenix.real_space_refine on Mon Jan 13 14:46:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zwj_60529/01_2025/8zwj_60529.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zwj_60529/01_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_60529/01_2025/8zwj_60529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zwj_60529/01_2025/8zwj_60529.map" model { file = "/net/cci-nas-00/data/ceres_data/8zwj_60529/01_2025/8zwj_60529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zwj_60529/01_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-5571/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: 2.10, per 1000 atoms: 0.76 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: 0.68 Conformation dependent library (CDL) restraints added in 342.0 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: 0.90 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: 0.52 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: 0.02 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: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.640 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: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.390 ------------------------------------------------------------------------------- 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 : 0.290 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: 0.2774 time to fit residues: 9.4806 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 : 0.283 ------------------------------------------------------------------------------- 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 = 0.4586 r_free = 0.4586 target = 0.205882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.155942 restraints weight = 2666.393| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 2.28 r_work: 0.3939 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3814 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.272 Fit side-chains REVERT: G 60 LYS cc_start: 0.8223 (ttpt) cc_final: 0.7830 (ttmm) REVERT: G 62 GLN cc_start: 0.7362 (mt0) cc_final: 0.7151 (tt0) REVERT: C 60 LYS cc_start: 0.8465 (ttmt) cc_final: 0.8202 (tttt) REVERT: C 62 GLN cc_start: 0.7652 (mt0) cc_final: 0.7372 (tt0) REVERT: C 83 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7824 (tm-30) REVERT: E 62 GLN cc_start: 0.7324 (mt0) cc_final: 0.6986 (tt0) REVERT: E 83 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7524 (tm-30) REVERT: A 60 LYS cc_start: 0.8320 (ttpt) cc_final: 0.8077 (ttmm) REVERT: A 62 GLN cc_start: 0.7660 (mt0) cc_final: 0.7110 (tt0) REVERT: A 83 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7958 (tm-30) REVERT: A 87 SER cc_start: 0.8769 (m) cc_final: 0.8523 (p) REVERT: B 60 LYS cc_start: 0.8338 (ttpt) cc_final: 0.7956 (ttmm) outliers start: 2 outliers final: 2 residues processed: 28 average time/residue: 0.2324 time to fit residues: 7.5503 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 : 0.269 ------------------------------------------------------------------------------- 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: 9.9990 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.4517 r_free = 0.4517 target = 0.200125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.149154 restraints weight = 2700.885| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.22 r_work: 0.3896 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2788 Z= 0.284 Angle : 0.530 3.804 3796 Z= 0.295 Chirality : 0.051 0.138 498 Planarity : 0.002 0.009 450 Dihedral : 14.182 103.843 444 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 4.07 % Allowed : 15.93 % Favored : 80.00 % 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: -3.16 (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 HIS 0.006 0.003 HIS G 50 PHE 0.010 0.003 PHE A 94 TYR 0.008 0.002 TYR E 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 31 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 0.345 Fit side-chains REVERT: G 60 LYS cc_start: 0.8301 (ttpt) cc_final: 0.7988 (ttmt) REVERT: G 62 GLN cc_start: 0.7412 (mt0) cc_final: 0.6882 (tt0) REVERT: C 60 LYS cc_start: 0.8614 (ttmt) cc_final: 0.8266 (tttt) REVERT: C 83 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7809 (tm-30) REVERT: D 60 LYS cc_start: 0.8596 (ttmm) cc_final: 0.8330 (tttm) REVERT: A 60 LYS cc_start: 0.8464 (ttpt) cc_final: 0.8232 (ttmm) REVERT: A 62 GLN cc_start: 0.7656 (mt0) cc_final: 0.7146 (tt0) REVERT: A 83 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7889 (tm-30) REVERT: B 60 LYS cc_start: 0.8435 (ttpt) cc_final: 0.8040 (ttmm) outliers start: 11 outliers final: 8 residues processed: 30 average time/residue: 0.2213 time to fit residues: 7.8037 Evaluate side-chains 28 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 62 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 B 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.189037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.137688 restraints weight = 2863.752| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.40 r_work: 0.3776 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2788 Z= 0.360 Angle : 0.591 3.706 3796 Z= 0.327 Chirality : 0.052 0.142 498 Planarity : 0.002 0.008 450 Dihedral : 13.707 100.513 444 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % 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: -2.96 (0.37), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (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 : 0.297 Fit side-chains REVERT: G 60 LYS cc_start: 0.8358 (ttpt) cc_final: 0.7907 (tttt) REVERT: G 62 GLN cc_start: 0.7503 (mt0) cc_final: 0.7277 (tt0) REVERT: C 60 LYS cc_start: 0.8539 (ttmt) cc_final: 0.8228 (tttm) REVERT: C 83 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7805 (tm-30) REVERT: E 83 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7478 (tm-30) REVERT: A 60 LYS cc_start: 0.8519 (ttpt) cc_final: 0.8193 (ttmm) REVERT: A 62 GLN cc_start: 0.7737 (mt0) cc_final: 0.7266 (tt0) REVERT: A 83 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7935 (tm-30) REVERT: B 60 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8068 (ttmm) outliers start: 12 outliers final: 12 residues processed: 32 average time/residue: 0.2290 time to fit residues: 8.4863 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 : 0.271 ------------------------------------------------------------------------------- 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: 6.9990 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.190508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.139364 restraints weight = 2827.623| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.37 r_work: 0.3797 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 : 0.004 0.025 2788 Z= 0.254 Angle : 0.512 3.431 3796 Z= 0.285 Chirality : 0.051 0.139 498 Planarity : 0.002 0.007 450 Dihedral : 13.115 97.932 444 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 3.70 % Allowed : 20.00 % 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: -2.79 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS E 50 PHE 0.009 0.002 PHE C 94 TYR 0.007 0.002 TYR C 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 33 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.290 Fit side-chains REVERT: G 37 VAL cc_start: 0.3522 (OUTLIER) cc_final: 0.3270 (m) REVERT: G 60 LYS cc_start: 0.8318 (ttpt) cc_final: 0.7870 (tttt) REVERT: G 62 GLN cc_start: 0.7489 (mt0) cc_final: 0.7216 (tt0) REVERT: C 60 LYS cc_start: 0.8479 (ttmt) cc_final: 0.8185 (tttm) REVERT: C 83 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7815 (tm-30) REVERT: E 83 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7457 (tm-30) REVERT: A 60 LYS cc_start: 0.8471 (ttpt) cc_final: 0.8217 (ttmm) REVERT: A 62 GLN cc_start: 0.7701 (mt0) cc_final: 0.7179 (tt0) REVERT: A 83 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7913 (tm-30) REVERT: B 60 LYS cc_start: 0.8438 (ttpt) cc_final: 0.8053 (ttmm) REVERT: B 96 LYS cc_start: 0.6490 (mttm) cc_final: 0.5456 (mtmt) outliers start: 10 outliers final: 9 residues processed: 30 average time/residue: 0.2305 time to fit residues: 8.0303 Evaluate side-chains 33 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 D residue 62 GLN Chi-restraints excluded: chain E residue 37 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 31 optimal weight: 0.0470 chunk 11 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.188537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.137496 restraints weight = 2922.455| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.39 r_work: 0.3796 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2788 Z= 0.361 Angle : 0.588 4.198 3796 Z= 0.326 Chirality : 0.052 0.141 498 Planarity : 0.002 0.008 450 Dihedral : 12.523 95.954 444 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 4.81 % Allowed : 20.00 % 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: -2.68 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS G 50 PHE 0.012 0.003 PHE C 94 TYR 0.011 0.003 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 42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.288 Fit side-chains REVERT: G 60 LYS cc_start: 0.8395 (ttpt) cc_final: 0.7915 (ttmm) REVERT: G 62 GLN cc_start: 0.7525 (mt0) cc_final: 0.7324 (tt0) REVERT: C 60 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8202 (tttm) REVERT: C 83 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7883 (tm-30) REVERT: E 83 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7553 (tm-30) REVERT: A 60 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8217 (ttmm) REVERT: A 62 GLN cc_start: 0.7750 (mt0) cc_final: 0.7310 (tt0) REVERT: A 83 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7939 (tm-30) REVERT: B 60 LYS cc_start: 0.8498 (ttpt) cc_final: 0.8107 (ttmm) outliers start: 13 outliers final: 12 residues processed: 38 average time/residue: 0.2194 time to fit residues: 9.6801 Evaluate side-chains 41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 59 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4499 r_free = 0.4499 target = 0.194218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.143929 restraints weight = 2904.160| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.35 r_work: 0.3872 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2788 Z= 0.164 Angle : 0.445 3.439 3796 Z= 0.250 Chirality : 0.050 0.137 498 Planarity : 0.001 0.006 450 Dihedral : 11.824 92.504 444 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 4.81 % Allowed : 20.00 % 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: -2.51 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.008 0.002 PHE G 94 TYR 0.004 0.001 TYR B 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 38 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 0.288 Fit side-chains REVERT: G 37 VAL cc_start: 0.3877 (OUTLIER) cc_final: 0.3613 (p) REVERT: G 60 LYS cc_start: 0.8339 (ttpt) cc_final: 0.7950 (tttt) REVERT: G 62 GLN cc_start: 0.7507 (mt0) cc_final: 0.7198 (tt0) REVERT: C 60 LYS cc_start: 0.8424 (ttmt) cc_final: 0.8133 (tttm) REVERT: C 83 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7872 (tm-30) REVERT: D 60 LYS cc_start: 0.8597 (ttmm) cc_final: 0.8318 (ttmm) REVERT: D 96 LYS cc_start: 0.6547 (mtpp) cc_final: 0.5622 (mttp) REVERT: E 62 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7115 (tt0) REVERT: E 83 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7454 (tm-30) REVERT: A 60 LYS cc_start: 0.8432 (ttpt) cc_final: 0.8172 (ttmm) REVERT: A 62 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7135 (tt0) REVERT: A 83 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7928 (tm-30) REVERT: B 60 LYS cc_start: 0.8463 (ttpt) cc_final: 0.8064 (ttmm) outliers start: 13 outliers final: 10 residues processed: 32 average time/residue: 0.1873 time to fit residues: 7.1645 Evaluate side-chains 38 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain B residue 59 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 27 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4547 r_free = 0.4547 target = 0.197788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.148016 restraints weight = 2833.435| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.31 r_work: 0.3921 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3810 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2788 Z= 0.119 Angle : 0.396 3.337 3796 Z= 0.223 Chirality : 0.049 0.130 498 Planarity : 0.001 0.009 450 Dihedral : 11.212 89.359 444 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 3.70 % Allowed : 21.85 % 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: -2.32 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS E 50 PHE 0.006 0.001 PHE G 94 TYR 0.004 0.001 TYR B 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 37 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.286 Fit side-chains REVERT: G 60 LYS cc_start: 0.8348 (ttpt) cc_final: 0.8026 (ttmt) REVERT: G 62 GLN cc_start: 0.7524 (mt0) cc_final: 0.7025 (tt0) REVERT: C 60 LYS cc_start: 0.8381 (ttmt) cc_final: 0.8110 (tttm) REVERT: C 83 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7828 (tm-30) REVERT: E 62 GLN cc_start: 0.7417 (mt0) cc_final: 0.7214 (tt0) REVERT: E 83 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: A 60 LYS cc_start: 0.8389 (ttpt) cc_final: 0.8114 (ttmm) REVERT: A 62 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7233 (tt0) REVERT: A 83 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7918 (tm-30) REVERT: B 60 LYS cc_start: 0.8395 (ttpt) cc_final: 0.8023 (ttmm) outliers start: 10 outliers final: 6 residues processed: 34 average time/residue: 0.1931 time to fit residues: 7.7883 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 : 0.268 ------------------------------------------------------------------------------- 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 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A 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: 2.9990 chunk 21 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4560 r_free = 0.4560 target = 0.199032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.149850 restraints weight = 2802.984| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.25 r_work: 0.3928 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3815 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3002 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= 0.117 Angle : 0.409 4.121 3796 Z= 0.228 Chirality : 0.049 0.135 498 Planarity : 0.001 0.010 450 Dihedral : 10.828 86.026 444 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.96 % Allowed : 22.96 % 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 (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: -2.21 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS G 50 PHE 0.007 0.001 PHE G 94 TYR 0.004 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 34 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: G 60 LYS cc_start: 0.8289 (ttpt) cc_final: 0.7960 (ttmm) REVERT: G 62 GLN cc_start: 0.7465 (mt0) cc_final: 0.6973 (tt0) REVERT: C 37 VAL cc_start: 0.5387 (OUTLIER) cc_final: 0.5176 (m) REVERT: C 60 LYS cc_start: 0.8395 (ttmt) cc_final: 0.8120 (tttm) REVERT: C 83 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7774 (tm-30) REVERT: E 62 GLN cc_start: 0.7449 (mt0) cc_final: 0.7246 (tt0) REVERT: E 83 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: A 60 LYS cc_start: 0.8381 (ttpt) cc_final: 0.8137 (ttmm) REVERT: A 62 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7210 (tt0) REVERT: A 83 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7836 (tm-30) REVERT: B 60 LYS cc_start: 0.8341 (ttpt) cc_final: 0.7999 (ttmm) outliers start: 8 outliers final: 5 residues processed: 31 average time/residue: 0.1945 time to fit residues: 7.2146 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 : 0.291 ------------------------------------------------------------------------------- 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 D residue 62 GLN Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A 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: 3.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.4490 r_free = 0.4490 target = 0.191752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.140543 restraints weight = 2820.765| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.34 r_work: 0.3804 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2788 Z= 0.249 Angle : 0.502 4.151 3796 Z= 0.282 Chirality : 0.050 0.134 498 Planarity : 0.002 0.008 450 Dihedral : 10.641 82.908 444 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 4.07 % Allowed : 22.59 % 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: -2.21 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS G 50 PHE 0.014 0.002 PHE G 94 TYR 0.008 0.002 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 36 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: G 60 LYS cc_start: 0.8351 (ttpt) cc_final: 0.7957 (tttt) REVERT: G 62 GLN cc_start: 0.7500 (mt0) cc_final: 0.7180 (tt0) REVERT: C 60 LYS cc_start: 0.8456 (ttmt) cc_final: 0.8183 (tttm) REVERT: C 83 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7776 (tm-30) REVERT: E 62 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7111 (tt0) REVERT: E 83 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: A 60 LYS cc_start: 0.8468 (ttpt) cc_final: 0.8233 (ttmm) REVERT: A 62 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7194 (tt0) REVERT: A 83 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7906 (tm-30) REVERT: B 60 LYS cc_start: 0.8471 (ttpt) cc_final: 0.8070 (ttmm) outliers start: 11 outliers final: 7 residues processed: 31 average time/residue: 0.1893 time to fit residues: 7.1726 Evaluate side-chains 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 GLN 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 E residue 83 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain B residue 59 THR 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: 5.9990 chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.4520 r_free = 0.4520 target = 0.193710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.143718 restraints weight = 2720.194| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.29 r_work: 0.3857 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2788 Z= 0.194 Angle : 0.456 3.494 3796 Z= 0.257 Chirality : 0.050 0.136 498 Planarity : 0.002 0.007 450 Dihedral : 10.358 81.401 444 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.70 % Allowed : 23.70 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.17 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 50 PHE 0.011 0.002 PHE G 94 TYR 0.006 0.001 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1835.13 seconds wall clock time: 33 minutes 22.21 seconds (2002.21 seconds total)