Starting phenix.real_space_refine on Mon Nov 17 15:04:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6a6b_6988/11_2025/6a6b_6988.cif Found real_map, /net/cci-nas-00/data/ceres_data/6a6b_6988/11_2025/6a6b_6988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6a6b_6988/11_2025/6a6b_6988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6a6b_6988/11_2025/6a6b_6988.map" model { file = "/net/cci-nas-00/data/ceres_data/6a6b_6988/11_2025/6a6b_6988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6a6b_6988/11_2025/6a6b_6988.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.008 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: 3 Type Number sf(0) Gaussians C 3288 2.51 5 N 912 2.21 5 O 1056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5256 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 0.84, per 1000 atoms: 0.16 Number of scatterers: 5256 At special positions: 0 Unit cell: (101.64, 120.12, 46.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1056 8.00 N 912 7.00 C 3288 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: 0.45 Conformation dependent library (CDL) restraints added in 220.0 milliseconds 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1296 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 58 removed outlier: 8.973A pdb=" N VAL A 49 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N VAL B 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY A 51 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N THR B 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA A 53 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ALA B 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL A 55 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LYS B 58 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLU A 57 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N VAL B 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N VAL C 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY B 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N THR C 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA B 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ALA C 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS C 58 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU B 57 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N HIS D 50 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY C 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N HIS E 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY D 51 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N VAL E 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N VAL F 52 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY E 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR F 54 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA E 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ALA F 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL E 55 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LYS F 58 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU E 57 " --> pdb=" O LYS F 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 63 removed outlier: 6.619A pdb=" N GLN A 62 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLN B 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLN C 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN D 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLN E 62 " --> pdb=" O VAL F 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 removed outlier: 6.792A pdb=" N VAL A 71 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL C 71 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL D 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL E 71 " --> pdb=" O THR F 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 80 through 82 removed outlier: 6.665A pdb=" N THR A 81 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR B 81 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR C 81 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR D 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR E 81 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 89 through 92 removed outlier: 6.491A pdb=" N ALA A 89 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N THR B 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA A 91 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA B 89 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR C 92 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA B 91 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA C 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N THR D 92 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA C 91 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA D 89 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR E 92 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA D 91 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA E 89 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N THR F 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA E 91 " --> pdb=" O THR F 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 49 through 58 removed outlier: 6.897A pdb=" N HIS G 50 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY H 51 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N HIS H 50 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY I 51 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N HIS I 50 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY J 51 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N HIS J 50 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLY K 51 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N HIS K 50 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N ALA L 53 " --> pdb=" O HIS K 50 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL K 52 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL L 55 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR K 54 " --> pdb=" O VAL L 55 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU L 57 " --> pdb=" O THR K 54 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA K 56 " --> pdb=" O GLU L 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 61 through 63 Processing sheet with id=AA8, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'G' and resid 80 through 82 Processing sheet with id=AB1, first strand: chain 'G' and resid 89 through 92 Processing sheet with id=AB2, first strand: chain 'I' and resid 89 through 92 76 hydrogen bonds defined for protein. 228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.78 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 924 1.28 - 1.35: 816 1.35 - 1.42: 216 1.42 - 1.49: 918 1.49 - 1.56: 2406 Bond restraints: 5280 Sorted by residual: bond pdb=" CB ASN H 65 " pdb=" CG ASN H 65 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.30e+00 bond pdb=" CB ASN J 65 " pdb=" CG ASN J 65 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.30e+00 bond pdb=" CB ASN C 65 " pdb=" CG ASN C 65 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.28e+00 bond pdb=" CB ASN L 65 " pdb=" CG ASN L 65 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.28e+00 bond pdb=" CB ASN E 65 " pdb=" CG ASN E 65 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.28e+00 ... (remaining 5275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 6293 1.35 - 2.71: 607 2.71 - 4.06: 132 4.06 - 5.41: 83 5.41 - 6.77: 25 Bond angle restraints: 7140 Sorted by residual: angle pdb=" CA ASN C 65 " pdb=" CB ASN C 65 " pdb=" CG ASN C 65 " ideal model delta sigma weight residual 112.60 116.83 -4.23 1.00e+00 1.00e+00 1.79e+01 angle pdb=" CA ASN D 65 " pdb=" CB ASN D 65 " pdb=" CG ASN D 65 " ideal model delta sigma weight residual 112.60 116.82 -4.22 1.00e+00 1.00e+00 1.78e+01 angle pdb=" CA ASN K 65 " pdb=" CB ASN K 65 " pdb=" CG ASN K 65 " ideal model delta sigma weight residual 112.60 116.82 -4.22 1.00e+00 1.00e+00 1.78e+01 angle pdb=" CA ASN L 65 " pdb=" CB ASN L 65 " pdb=" CG ASN L 65 " ideal model delta sigma weight residual 112.60 116.81 -4.21 1.00e+00 1.00e+00 1.77e+01 angle pdb=" CA ASN F 65 " pdb=" CB ASN F 65 " pdb=" CG ASN F 65 " ideal model delta sigma weight residual 112.60 116.81 -4.21 1.00e+00 1.00e+00 1.77e+01 ... (remaining 7135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.13: 2448 6.13 - 12.25: 475 12.25 - 18.38: 125 18.38 - 24.51: 24 24.51 - 30.63: 24 Dihedral angle restraints: 3096 sinusoidal: 1044 harmonic: 2052 Sorted by residual: dihedral pdb=" CA THR I 72 " pdb=" C THR I 72 " pdb=" N GLY I 73 " pdb=" CA GLY I 73 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA THR E 72 " pdb=" C THR E 72 " pdb=" N GLY E 73 " pdb=" CA GLY E 73 " ideal model delta harmonic sigma weight residual 180.00 157.29 22.71 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA THR B 72 " pdb=" C THR B 72 " pdb=" N GLY B 73 " pdb=" CA GLY B 73 " ideal model delta harmonic sigma weight residual 180.00 157.29 22.71 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 3093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 679 0.065 - 0.131: 200 0.131 - 0.196: 45 0.196 - 0.261: 0 0.261 - 0.327: 12 Chirality restraints: 936 Sorted by residual: chirality pdb=" CB VAL E 66 " pdb=" CA VAL E 66 " pdb=" CG1 VAL E 66 " pdb=" CG2 VAL E 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB VAL I 66 " pdb=" CA VAL I 66 " pdb=" CG1 VAL I 66 " pdb=" CG2 VAL I 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB VAL C 66 " pdb=" CA VAL C 66 " pdb=" CG1 VAL C 66 " pdb=" CG2 VAL C 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 933 not shown) Planarity restraints: 888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL K 66 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C VAL K 66 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL K 66 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY K 67 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 66 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.94e+00 pdb=" C VAL J 66 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL J 66 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY J 67 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 66 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.94e+00 pdb=" C VAL F 66 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL F 66 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY F 67 " -0.012 2.00e-02 2.50e+03 ... (remaining 885 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 929 2.79 - 3.32: 4519 3.32 - 3.85: 8698 3.85 - 4.37: 9679 4.37 - 4.90: 19868 Nonbonded interactions: 43693 Sorted by model distance: nonbonded pdb=" OE1 GLU D 46 " pdb=" NZ LYS E 80 " model vdw 2.263 3.120 nonbonded pdb=" N VAL K 37 " pdb=" O VAL L 37 " model vdw 2.267 3.120 nonbonded pdb=" NZ LYS K 80 " pdb=" OE1 GLU L 46 " model vdw 2.288 3.120 nonbonded pdb=" O VAL D 37 " pdb=" N VAL E 37 " model vdw 2.294 3.120 nonbonded pdb=" NZ LYS H 80 " pdb=" OE1 GLU I 46 " model vdw 2.317 3.120 ... (remaining 43688 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.010 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 6.650 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 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 0.038 5280 Z= 0.264 Angle : 1.068 6.767 7140 Z= 0.626 Chirality : 0.073 0.327 936 Planarity : 0.005 0.020 888 Dihedral : 7.612 30.635 1800 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.34 % Favored : 88.66 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.85 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR B 39 PHE 0.006 0.002 PHE K 94 HIS 0.009 0.006 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00577 ( 5280) covalent geometry : angle 1.06789 ( 7140) hydrogen bonds : bond 0.12174 ( 76) hydrogen bonds : angle 6.83784 ( 228) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 77 VAL cc_start: 0.8300 (t) cc_final: 0.8073 (m) REVERT: E 77 VAL cc_start: 0.8308 (t) cc_final: 0.8084 (t) REVERT: F 39 TYR cc_start: 0.7892 (m-80) cc_final: 0.5937 (p90) REVERT: F 43 LYS cc_start: 0.8083 (tttm) cc_final: 0.7850 (pptt) REVERT: F 57 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7287 (pm20) REVERT: F 58 LYS cc_start: 0.8866 (mttt) cc_final: 0.8062 (mmmt) REVERT: F 96 LYS cc_start: 0.6738 (mmtp) cc_final: 0.6491 (pttm) REVERT: G 39 TYR cc_start: 0.7672 (m-80) cc_final: 0.5514 (p90) REVERT: G 43 LYS cc_start: 0.8398 (tttm) cc_final: 0.8053 (pptt) REVERT: G 58 LYS cc_start: 0.8576 (mttt) cc_final: 0.8010 (mmmt) REVERT: H 58 LYS cc_start: 0.8666 (mttt) cc_final: 0.8419 (mttm) REVERT: H 77 VAL cc_start: 0.8311 (t) cc_final: 0.8084 (m) REVERT: J 46 GLU cc_start: 0.6201 (pt0) cc_final: 0.5866 (pt0) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.0899 time to fit residues: 21.3283 Evaluate side-chains 137 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.180212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.152651 restraints weight = 9034.878| |-----------------------------------------------------------------------------| r_work (start): 0.4450 rms_B_bonded: 4.43 r_work: 0.4326 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5280 Z= 0.155 Angle : 0.570 4.725 7140 Z= 0.320 Chirality : 0.049 0.131 936 Planarity : 0.002 0.013 888 Dihedral : 5.251 19.565 756 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 5.93 % Allowed : 14.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.28), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR K 39 PHE 0.003 0.001 PHE F 94 HIS 0.005 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 5280) covalent geometry : angle 0.57018 ( 7140) hydrogen bonds : bond 0.01648 ( 76) hydrogen bonds : angle 4.94379 ( 228) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 VAL cc_start: 0.9167 (t) cc_final: 0.8891 (m) REVERT: B 39 TYR cc_start: 0.6925 (m-80) cc_final: 0.6593 (m-80) REVERT: C 97 LYS cc_start: 0.8266 (tppt) cc_final: 0.8052 (mmmt) REVERT: D 97 LYS cc_start: 0.8162 (tppt) cc_final: 0.7682 (mmmm) REVERT: F 39 TYR cc_start: 0.7821 (m-80) cc_final: 0.5612 (p90) REVERT: F 43 LYS cc_start: 0.8383 (tttm) cc_final: 0.7983 (pptt) REVERT: F 57 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7377 (pm20) REVERT: F 58 LYS cc_start: 0.9048 (mttt) cc_final: 0.8110 (mmmt) REVERT: G 43 LYS cc_start: 0.8448 (tttm) cc_final: 0.7997 (pptt) REVERT: G 58 LYS cc_start: 0.8763 (mttt) cc_final: 0.7894 (mmmt) REVERT: H 58 LYS cc_start: 0.8876 (mttt) cc_final: 0.8310 (mtpt) REVERT: H 61 GLU cc_start: 0.8122 (tt0) cc_final: 0.7197 (tt0) REVERT: K 97 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7711 (mtmm) outliers start: 32 outliers final: 17 residues processed: 148 average time/residue: 0.0837 time to fit residues: 15.5390 Evaluate side-chains 134 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 97 LYS Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 5 optimal weight: 0.0010 chunk 65 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 overall best weight: 6.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.170815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.142836 restraints weight = 8828.898| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 4.35 r_work: 0.4203 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 5280 Z= 0.278 Angle : 0.628 4.220 7140 Z= 0.361 Chirality : 0.049 0.138 936 Planarity : 0.003 0.012 888 Dihedral : 5.764 19.755 756 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 7.78 % Allowed : 13.33 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR F 39 PHE 0.007 0.002 PHE G 94 HIS 0.007 0.004 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00626 ( 5280) covalent geometry : angle 0.62777 ( 7140) hydrogen bonds : bond 0.01891 ( 76) hydrogen bonds : angle 4.85985 ( 228) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 39 TYR cc_start: 0.7020 (m-80) cc_final: 0.6726 (m-80) REVERT: C 97 LYS cc_start: 0.8320 (tppt) cc_final: 0.7987 (mppt) REVERT: D 43 LYS cc_start: 0.7117 (mptt) cc_final: 0.6885 (mptt) REVERT: E 43 LYS cc_start: 0.7237 (mppt) cc_final: 0.6993 (mppt) REVERT: F 39 TYR cc_start: 0.7939 (m-80) cc_final: 0.6007 (p90) REVERT: F 57 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7739 (pm20) REVERT: F 58 LYS cc_start: 0.9057 (mttt) cc_final: 0.7993 (mmmt) REVERT: G 39 TYR cc_start: 0.7944 (m-80) cc_final: 0.5800 (p90) REVERT: G 43 LYS cc_start: 0.8448 (tttm) cc_final: 0.7970 (pptt) REVERT: H 58 LYS cc_start: 0.8812 (mttt) cc_final: 0.8185 (mtpt) REVERT: H 61 GLU cc_start: 0.8093 (tt0) cc_final: 0.7357 (tt0) REVERT: H 97 LYS cc_start: 0.7995 (mtpt) cc_final: 0.7665 (mtmt) REVERT: K 61 GLU cc_start: 0.7963 (tt0) cc_final: 0.7738 (tt0) REVERT: L 39 TYR cc_start: 0.6603 (m-80) cc_final: 0.6101 (m-80) outliers start: 42 outliers final: 32 residues processed: 143 average time/residue: 0.0799 time to fit residues: 14.4868 Evaluate side-chains 146 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 31 optimal weight: 0.0470 chunk 3 optimal weight: 9.9990 overall best weight: 5.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.172893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.145216 restraints weight = 8782.790| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 4.31 r_work: 0.4259 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5280 Z= 0.225 Angle : 0.572 4.920 7140 Z= 0.330 Chirality : 0.049 0.139 936 Planarity : 0.002 0.011 888 Dihedral : 5.371 18.206 756 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 7.96 % Allowed : 14.81 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR E 39 PHE 0.005 0.001 PHE B 94 HIS 0.007 0.003 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 5280) covalent geometry : angle 0.57250 ( 7140) hydrogen bonds : bond 0.01831 ( 76) hydrogen bonds : angle 4.55892 ( 228) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 112 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: C 58 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8788 (mtpp) REVERT: C 97 LYS cc_start: 0.8264 (tppt) cc_final: 0.7782 (mmmm) REVERT: F 39 TYR cc_start: 0.7981 (m-80) cc_final: 0.5826 (p90) REVERT: F 57 GLU cc_start: 0.8426 (mt-10) cc_final: 0.7839 (pm20) REVERT: F 58 LYS cc_start: 0.9066 (mttt) cc_final: 0.8032 (mmmt) REVERT: F 97 LYS cc_start: 0.8691 (mmmt) cc_final: 0.8402 (mmmm) REVERT: G 39 TYR cc_start: 0.7980 (m-80) cc_final: 0.5794 (p90) REVERT: G 43 LYS cc_start: 0.8404 (tttm) cc_final: 0.7940 (pptt) REVERT: H 58 LYS cc_start: 0.8887 (mttt) cc_final: 0.8500 (mttt) REVERT: H 61 GLU cc_start: 0.8174 (tt0) cc_final: 0.7580 (tt0) REVERT: J 97 LYS cc_start: 0.8115 (mmmt) cc_final: 0.7865 (mmmt) REVERT: L 39 TYR cc_start: 0.6859 (m-80) cc_final: 0.6310 (m-80) outliers start: 43 outliers final: 39 residues processed: 142 average time/residue: 0.0812 time to fit residues: 14.5526 Evaluate side-chains 146 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 28 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 70 optimal weight: 0.4980 chunk 13 optimal weight: 9.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.172901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.145445 restraints weight = 9010.304| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 4.32 r_work: 0.4235 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 5280 Z= 0.223 Angle : 0.582 5.343 7140 Z= 0.333 Chirality : 0.049 0.138 936 Planarity : 0.002 0.012 888 Dihedral : 5.307 17.566 756 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 9.26 % Allowed : 13.52 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR A 39 PHE 0.006 0.001 PHE G 94 HIS 0.006 0.003 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 5280) covalent geometry : angle 0.58192 ( 7140) hydrogen bonds : bond 0.01865 ( 76) hydrogen bonds : angle 4.45101 ( 228) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 110 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 97 LYS cc_start: 0.8113 (tppt) cc_final: 0.7722 (mmmm) REVERT: F 39 TYR cc_start: 0.7915 (m-80) cc_final: 0.5862 (p90) REVERT: F 57 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7812 (pm20) REVERT: F 58 LYS cc_start: 0.8996 (mttt) cc_final: 0.7954 (mmmt) REVERT: G 39 TYR cc_start: 0.7928 (m-80) cc_final: 0.5832 (p90) REVERT: G 43 LYS cc_start: 0.8472 (tttm) cc_final: 0.7948 (pptt) REVERT: H 58 LYS cc_start: 0.8744 (mttt) cc_final: 0.8319 (mttt) REVERT: H 61 GLU cc_start: 0.8135 (tt0) cc_final: 0.7472 (tt0) REVERT: J 97 LYS cc_start: 0.8261 (mmmt) cc_final: 0.8010 (mmmt) outliers start: 50 outliers final: 45 residues processed: 143 average time/residue: 0.0780 time to fit residues: 14.2454 Evaluate side-chains 154 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 109 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 12 optimal weight: 30.0000 chunk 43 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 6 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.170932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.143510 restraints weight = 9018.228| |-----------------------------------------------------------------------------| r_work (start): 0.4337 rms_B_bonded: 4.30 r_work: 0.4210 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 5280 Z= 0.265 Angle : 0.622 7.380 7140 Z= 0.355 Chirality : 0.050 0.138 936 Planarity : 0.002 0.012 888 Dihedral : 5.511 17.697 756 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 10.56 % Allowed : 13.15 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR C 39 PHE 0.006 0.002 PHE B 94 HIS 0.007 0.004 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00589 ( 5280) covalent geometry : angle 0.62163 ( 7140) hydrogen bonds : bond 0.02091 ( 76) hydrogen bonds : angle 4.48365 ( 228) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 110 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 57 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7725 (pm20) REVERT: F 58 LYS cc_start: 0.9033 (mttt) cc_final: 0.7973 (mmmt) REVERT: G 43 LYS cc_start: 0.8463 (tttm) cc_final: 0.7949 (pptt) REVERT: G 97 LYS cc_start: 0.7566 (mmmt) cc_final: 0.7060 (mmmm) REVERT: H 58 LYS cc_start: 0.8747 (mttt) cc_final: 0.8129 (mttt) REVERT: H 61 GLU cc_start: 0.8196 (tt0) cc_final: 0.7460 (tt0) REVERT: J 97 LYS cc_start: 0.8354 (mmmt) cc_final: 0.7932 (mmmt) REVERT: L 39 TYR cc_start: 0.6486 (m-80) cc_final: 0.5988 (m-80) outliers start: 57 outliers final: 50 residues processed: 147 average time/residue: 0.0760 time to fit residues: 14.3027 Evaluate side-chains 158 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 108 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 56 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 24 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.172121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.144994 restraints weight = 9015.945| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 4.25 r_work: 0.4233 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 5280 Z= 0.234 Angle : 0.594 6.708 7140 Z= 0.340 Chirality : 0.050 0.138 936 Planarity : 0.002 0.011 888 Dihedral : 5.363 16.796 756 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 8.89 % Allowed : 15.56 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR A 39 PHE 0.005 0.001 PHE J 94 HIS 0.007 0.003 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00520 ( 5280) covalent geometry : angle 0.59401 ( 7140) hydrogen bonds : bond 0.01989 ( 76) hydrogen bonds : angle 4.43684 ( 228) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 113 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 LYS cc_start: 0.8099 (mmmt) cc_final: 0.7255 (mtmm) REVERT: C 46 GLU cc_start: 0.7476 (pt0) cc_final: 0.6888 (pm20) REVERT: F 39 TYR cc_start: 0.7791 (m-80) cc_final: 0.5795 (p90) REVERT: F 57 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7715 (pm20) REVERT: F 58 LYS cc_start: 0.9052 (mttt) cc_final: 0.8007 (mmmt) REVERT: G 39 TYR cc_start: 0.7874 (m-80) cc_final: 0.5730 (p90) REVERT: G 43 LYS cc_start: 0.8459 (tttm) cc_final: 0.7957 (pptt) REVERT: H 46 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7269 (pt0) REVERT: H 58 LYS cc_start: 0.8763 (mttt) cc_final: 0.8127 (mttt) REVERT: H 61 GLU cc_start: 0.8188 (tt0) cc_final: 0.7451 (tt0) REVERT: L 39 TYR cc_start: 0.6630 (m-80) cc_final: 0.6124 (m-80) outliers start: 48 outliers final: 45 residues processed: 143 average time/residue: 0.0754 time to fit residues: 13.7879 Evaluate side-chains 156 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 110 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 44 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 24 optimal weight: 30.0000 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 30.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.177893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.151360 restraints weight = 8735.155| |-----------------------------------------------------------------------------| r_work (start): 0.4459 rms_B_bonded: 4.16 r_work: 0.4333 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5280 Z= 0.130 Angle : 0.560 11.313 7140 Z= 0.308 Chirality : 0.049 0.133 936 Planarity : 0.002 0.011 888 Dihedral : 4.739 15.112 756 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 7.22 % Allowed : 17.59 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR G 39 PHE 0.005 0.001 PHE H 94 HIS 0.004 0.002 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 5280) covalent geometry : angle 0.55985 ( 7140) hydrogen bonds : bond 0.01676 ( 76) hydrogen bonds : angle 4.13396 ( 228) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8496 (mttp) REVERT: B 97 LYS cc_start: 0.8091 (mmmt) cc_final: 0.7804 (mtmm) REVERT: C 46 GLU cc_start: 0.7454 (pt0) cc_final: 0.6605 (mp0) REVERT: C 97 LYS cc_start: 0.8030 (mmmm) cc_final: 0.7548 (mttt) REVERT: F 39 TYR cc_start: 0.7818 (m-80) cc_final: 0.5635 (p90) REVERT: F 57 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7795 (pm20) REVERT: F 58 LYS cc_start: 0.8918 (mttt) cc_final: 0.7835 (mmmt) REVERT: F 97 LYS cc_start: 0.8648 (mmmm) cc_final: 0.8132 (mmmt) REVERT: G 37 VAL cc_start: 0.3109 (OUTLIER) cc_final: 0.1998 (t) REVERT: G 39 TYR cc_start: 0.7911 (m-80) cc_final: 0.5771 (p90) REVERT: G 43 LYS cc_start: 0.8395 (tttm) cc_final: 0.7950 (pptt) REVERT: H 46 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7429 (pt0) REVERT: H 58 LYS cc_start: 0.8872 (mttt) cc_final: 0.8165 (mttt) REVERT: H 61 GLU cc_start: 0.8052 (tt0) cc_final: 0.7713 (tt0) REVERT: I 97 LYS cc_start: 0.8116 (mmmt) cc_final: 0.7889 (mmmt) REVERT: J 97 LYS cc_start: 0.7871 (mmmt) cc_final: 0.7558 (mmmt) REVERT: L 39 TYR cc_start: 0.6622 (m-80) cc_final: 0.6108 (m-80) outliers start: 39 outliers final: 32 residues processed: 139 average time/residue: 0.0784 time to fit residues: 13.8179 Evaluate side-chains 145 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 14 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.173406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.146891 restraints weight = 9017.235| |-----------------------------------------------------------------------------| r_work (start): 0.4392 rms_B_bonded: 4.17 r_work: 0.4274 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5280 Z= 0.207 Angle : 0.609 11.393 7140 Z= 0.339 Chirality : 0.050 0.138 936 Planarity : 0.002 0.012 888 Dihedral : 5.076 16.167 756 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 6.85 % Allowed : 18.89 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR A 39 PHE 0.005 0.001 PHE H 94 HIS 0.006 0.003 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 5280) covalent geometry : angle 0.60947 ( 7140) hydrogen bonds : bond 0.01839 ( 76) hydrogen bonds : angle 4.30670 ( 228) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8496 (mttp) REVERT: B 97 LYS cc_start: 0.8171 (mmmt) cc_final: 0.7859 (mtmm) REVERT: C 39 TYR cc_start: 0.6569 (m-80) cc_final: 0.6216 (m-80) REVERT: C 46 GLU cc_start: 0.7567 (pt0) cc_final: 0.6964 (pm20) REVERT: C 97 LYS cc_start: 0.8029 (mmmm) cc_final: 0.7625 (mttt) REVERT: F 39 TYR cc_start: 0.7887 (m-80) cc_final: 0.5637 (p90) REVERT: F 57 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7784 (pm20) REVERT: F 58 LYS cc_start: 0.9086 (mttt) cc_final: 0.8065 (mmmt) REVERT: F 97 LYS cc_start: 0.8607 (mmmm) cc_final: 0.8156 (mmmt) REVERT: G 37 VAL cc_start: 0.3239 (OUTLIER) cc_final: 0.2165 (t) REVERT: G 39 TYR cc_start: 0.7912 (m-80) cc_final: 0.5867 (p90) REVERT: G 43 LYS cc_start: 0.8407 (tttm) cc_final: 0.7943 (pptt) REVERT: H 46 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7280 (pt0) REVERT: H 58 LYS cc_start: 0.8820 (mttt) cc_final: 0.8131 (mttt) REVERT: H 61 GLU cc_start: 0.8166 (tt0) cc_final: 0.7655 (tt0) REVERT: J 97 LYS cc_start: 0.8299 (mmmt) cc_final: 0.8045 (mmmt) REVERT: K 97 LYS cc_start: 0.8134 (mmtp) cc_final: 0.7915 (mtmt) REVERT: L 39 TYR cc_start: 0.6932 (m-80) cc_final: 0.6383 (m-80) outliers start: 37 outliers final: 34 residues processed: 136 average time/residue: 0.0748 time to fit residues: 13.1643 Evaluate side-chains 148 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 66 optimal weight: 0.0870 chunk 35 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.173527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.146974 restraints weight = 9028.130| |-----------------------------------------------------------------------------| r_work (start): 0.4391 rms_B_bonded: 4.18 r_work: 0.4276 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5280 Z= 0.198 Angle : 0.599 10.879 7140 Z= 0.335 Chirality : 0.050 0.139 936 Planarity : 0.002 0.011 888 Dihedral : 5.037 15.941 756 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 7.41 % Allowed : 18.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR G 39 PHE 0.005 0.001 PHE H 94 HIS 0.006 0.003 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 5280) covalent geometry : angle 0.59915 ( 7140) hydrogen bonds : bond 0.01816 ( 76) hydrogen bonds : angle 4.30382 ( 228) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8519 (mttp) REVERT: C 39 TYR cc_start: 0.6626 (m-80) cc_final: 0.6257 (m-80) REVERT: C 46 GLU cc_start: 0.7587 (pt0) cc_final: 0.7022 (pm20) REVERT: C 97 LYS cc_start: 0.8052 (mmmm) cc_final: 0.7545 (mttp) REVERT: F 57 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7814 (pm20) REVERT: F 58 LYS cc_start: 0.9016 (mttt) cc_final: 0.7950 (mmmt) REVERT: F 97 LYS cc_start: 0.8656 (mmmm) cc_final: 0.8270 (mmmt) REVERT: G 37 VAL cc_start: 0.3235 (OUTLIER) cc_final: 0.2175 (t) REVERT: G 39 TYR cc_start: 0.7969 (m-80) cc_final: 0.5857 (p90) REVERT: G 43 LYS cc_start: 0.8381 (tttm) cc_final: 0.7936 (pptt) REVERT: H 46 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7313 (pt0) REVERT: H 58 LYS cc_start: 0.8839 (mttt) cc_final: 0.8186 (mttt) REVERT: H 61 GLU cc_start: 0.8182 (tt0) cc_final: 0.7691 (tt0) REVERT: J 97 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7807 (mmmt) REVERT: K 97 LYS cc_start: 0.8197 (mmtp) cc_final: 0.7955 (mtmm) REVERT: L 39 TYR cc_start: 0.6997 (m-80) cc_final: 0.6429 (m-80) outliers start: 40 outliers final: 34 residues processed: 138 average time/residue: 0.0746 time to fit residues: 13.2184 Evaluate side-chains 149 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 16 optimal weight: 0.7980 chunk 63 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 0.0970 chunk 70 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 overall best weight: 3.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.175390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.148620 restraints weight = 8969.230| |-----------------------------------------------------------------------------| r_work (start): 0.4416 rms_B_bonded: 4.21 r_work: 0.4291 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5280 Z= 0.161 Angle : 0.578 10.423 7140 Z= 0.321 Chirality : 0.049 0.138 936 Planarity : 0.002 0.011 888 Dihedral : 4.840 15.262 756 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 6.85 % Allowed : 18.89 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR A 39 PHE 0.004 0.001 PHE H 94 HIS 0.005 0.003 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5280) covalent geometry : angle 0.57814 ( 7140) hydrogen bonds : bond 0.01702 ( 76) hydrogen bonds : angle 4.22201 ( 228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1291.90 seconds wall clock time: 22 minutes 59.29 seconds (1379.29 seconds total)