Starting phenix.real_space_refine on Sun Apr 27 09:19:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6a6b_6988/04_2025/6a6b_6988.cif Found real_map, /net/cci-nas-00/data/ceres_data/6a6b_6988/04_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_6988/04_2025/6a6b_6988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6a6b_6988/04_2025/6a6b_6988.map" model { file = "/net/cci-nas-00/data/ceres_data/6a6b_6988/04_2025/6a6b_6988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6a6b_6988/04_2025/6a6b_6988.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 3.24, per 1000 atoms: 0.62 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: 1.16 Conformation dependent library (CDL) restraints added in 695.3 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: 0.72 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: 1.31 Time building geometry restraints manager: 1.39 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' 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: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.260 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.720 ------------------------------------------------------------------------------- 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 : 7.15 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (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 HIS 0.009 0.006 HIS B 50 PHE 0.006 0.002 PHE K 94 TYR 0.007 0.002 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.12174 ( 76) hydrogen bonds : angle 6.83784 ( 228) covalent geometry : bond 0.00577 ( 5280) covalent geometry : angle 1.06789 ( 7140) *********************** 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 : 0.474 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: 0.7862 (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: 0.8011 (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: 0.8085 (m) REVERT: J 46 GLU cc_start: 0.6201 (pt0) cc_final: 0.5867 (pt0) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2245 time to fit residues: 52.2413 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 : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- 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** ** H 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 = 0.4609 r_free = 0.4609 target = 0.169398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.141517 restraints weight = 8963.250| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 4.35 r_work: 0.4163 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 5280 Z= 0.374 Angle : 0.714 5.512 7140 Z= 0.410 Chirality : 0.052 0.135 936 Planarity : 0.003 0.013 888 Dihedral : 6.343 21.682 756 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 8.70 % Allowed : 13.15 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.26), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.005 HIS G 50 PHE 0.008 0.002 PHE F 94 TYR 0.013 0.002 TYR K 39 Details of bonding type rmsd hydrogen bonds : bond 0.02402 ( 76) hydrogen bonds : angle 5.25661 ( 228) covalent geometry : bond 0.00838 ( 5280) covalent geometry : angle 0.71429 ( 7140) *********************** 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 169 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 122 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 43 LYS cc_start: 0.7342 (mtmm) cc_final: 0.6953 (mptt) REVERT: B 39 TYR cc_start: 0.6958 (m-80) cc_final: 0.6715 (m-80) REVERT: D 43 LYS cc_start: 0.6992 (mptt) cc_final: 0.6711 (mptt) REVERT: D 97 LYS cc_start: 0.8297 (tppt) cc_final: 0.7800 (mmmm) REVERT: F 57 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7788 (pm20) REVERT: F 58 LYS cc_start: 0.8958 (mttt) cc_final: 0.7982 (mmmt) REVERT: F 96 LYS cc_start: 0.6984 (mmtp) cc_final: 0.6307 (pptt) REVERT: G 43 LYS cc_start: 0.8417 (tttm) cc_final: 0.7907 (pptt) REVERT: G 58 LYS cc_start: 0.8689 (mttt) cc_final: 0.8065 (mmtt) REVERT: H 61 GLU cc_start: 0.8198 (tt0) cc_final: 0.7927 (tt0) REVERT: H 97 LYS cc_start: 0.8035 (mtpt) cc_final: 0.7744 (mtmt) outliers start: 47 outliers final: 32 residues processed: 148 average time/residue: 0.2250 time to fit residues: 41.7443 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 : 1.565 ------------------------------------------------------------------------------- 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 37 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 58 LYS Chi-restraints excluded: chain D residue 74 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 74 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 88 ILE 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 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 88 ILE 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 6 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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** ** 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** ** H 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 = 0.4661 r_free = 0.4661 target = 0.172639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.145364 restraints weight = 8895.657| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 4.37 r_work: 0.4217 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5280 Z= 0.221 Angle : 0.580 4.686 7140 Z= 0.333 Chirality : 0.049 0.125 936 Planarity : 0.002 0.012 888 Dihedral : 5.455 18.875 756 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 6.85 % Allowed : 17.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (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 HIS 0.007 0.003 HIS F 50 PHE 0.006 0.001 PHE G 94 TYR 0.010 0.002 TYR L 39 Details of bonding type rmsd hydrogen bonds : bond 0.01897 ( 76) hydrogen bonds : angle 4.69788 ( 228) covalent geometry : bond 0.00495 ( 5280) covalent geometry : angle 0.57996 ( 7140) *********************** 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 155 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 39 TYR cc_start: 0.6938 (m-80) cc_final: 0.6704 (m-80) REVERT: D 43 LYS cc_start: 0.6340 (mptt) cc_final: 0.5912 (mptt) REVERT: D 97 LYS cc_start: 0.8159 (tppt) cc_final: 0.7777 (mmmm) REVERT: E 43 LYS cc_start: 0.7799 (mtmm) cc_final: 0.7209 (mmtm) REVERT: F 43 LYS cc_start: 0.4505 (pptt) cc_final: 0.3760 (pttm) REVERT: F 57 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7701 (pm20) REVERT: F 58 LYS cc_start: 0.8929 (mttt) cc_final: 0.7879 (mmmt) REVERT: G 39 TYR cc_start: 0.7865 (m-80) cc_final: 0.7629 (m-80) REVERT: G 58 LYS cc_start: 0.8674 (mttt) cc_final: 0.7978 (mmmt) REVERT: H 61 GLU cc_start: 0.8219 (tt0) cc_final: 0.7864 (tt0) REVERT: H 97 LYS cc_start: 0.8019 (mtpt) cc_final: 0.7678 (mtmt) REVERT: K 61 GLU cc_start: 0.8031 (tt0) cc_final: 0.7788 (tt0) REVERT: L 39 TYR cc_start: 0.6286 (m-80) cc_final: 0.5842 (m-80) outliers start: 37 outliers final: 33 residues processed: 139 average time/residue: 0.1819 time to fit residues: 31.9219 Evaluate side-chains 142 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 44 THR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR 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 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 G residue 88 ILE 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 46 GLU Chi-restraints excluded: chain I residue 72 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 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 39 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.4680 r_free = 0.4680 target = 0.174124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.147165 restraints weight = 8947.764| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 4.33 r_work: 0.4275 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.4134 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= 0.205 Angle : 0.553 4.164 7140 Z= 0.320 Chirality : 0.049 0.125 936 Planarity : 0.002 0.011 888 Dihedral : 5.269 17.815 756 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 8.33 % Allowed : 16.48 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS G 50 PHE 0.006 0.001 PHE G 94 TYR 0.009 0.002 TYR L 39 Details of bonding type rmsd hydrogen bonds : bond 0.01773 ( 76) hydrogen bonds : angle 4.47867 ( 228) covalent geometry : bond 0.00452 ( 5280) covalent geometry : angle 0.55313 ( 7140) *********************** 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 158 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 113 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 39 TYR cc_start: 0.7012 (m-80) cc_final: 0.6693 (m-80) REVERT: D 43 LYS cc_start: 0.6592 (mptt) cc_final: 0.6372 (mptt) REVERT: D 97 LYS cc_start: 0.8271 (tppt) cc_final: 0.7656 (mmmm) REVERT: E 43 LYS cc_start: 0.7824 (mtmm) cc_final: 0.7573 (mptt) REVERT: F 39 TYR cc_start: 0.7998 (m-80) cc_final: 0.7739 (m-80) REVERT: F 57 GLU cc_start: 0.8527 (mt-10) cc_final: 0.7874 (pm20) REVERT: F 58 LYS cc_start: 0.9079 (mttt) cc_final: 0.8051 (mmmt) REVERT: G 39 TYR cc_start: 0.7934 (m-80) cc_final: 0.7633 (m-80) REVERT: G 58 LYS cc_start: 0.8633 (mttt) cc_final: 0.7958 (mmmt) REVERT: H 58 LYS cc_start: 0.9010 (mttm) cc_final: 0.8713 (mttm) REVERT: H 61 GLU cc_start: 0.8220 (tt0) cc_final: 0.7821 (tt0) REVERT: H 97 LYS cc_start: 0.8051 (mtpt) cc_final: 0.7664 (mtmt) REVERT: L 39 TYR cc_start: 0.6838 (m-80) cc_final: 0.6253 (m-80) outliers start: 45 outliers final: 39 residues processed: 142 average time/residue: 0.1871 time to fit residues: 33.6838 Evaluate side-chains 150 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 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 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 74 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 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 88 ILE 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 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 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 64 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 43 optimal weight: 0.0370 chunk 69 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 overall best weight: 5.4066 ------------------------------------------------------------------------------- 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** ** 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 = 0.4667 r_free = 0.4667 target = 0.173126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.146217 restraints weight = 8947.807| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 4.31 r_work: 0.4254 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5280 Z= 0.242 Angle : 0.582 5.257 7140 Z= 0.336 Chirality : 0.049 0.127 936 Planarity : 0.002 0.012 888 Dihedral : 5.411 17.668 756 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 10.19 % Allowed : 15.00 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS G 50 PHE 0.006 0.001 PHE J 94 TYR 0.009 0.002 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.01958 ( 76) hydrogen bonds : angle 4.51250 ( 228) covalent geometry : bond 0.00537 ( 5280) covalent geometry : angle 0.58249 ( 7140) *********************** 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 165 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 110 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 43 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.6877 (mptt) REVERT: B 97 LYS cc_start: 0.7974 (mtmt) cc_final: 0.7734 (mtmm) REVERT: E 43 LYS cc_start: 0.7732 (mtmm) cc_final: 0.7490 (mptt) REVERT: F 43 LYS cc_start: 0.3228 (pptt) cc_final: 0.2603 (pptt) REVERT: F 57 GLU cc_start: 0.8582 (mt-10) cc_final: 0.7874 (pm20) REVERT: F 58 LYS cc_start: 0.9076 (mttt) cc_final: 0.8018 (mmmt) REVERT: G 39 TYR cc_start: 0.8006 (m-80) cc_final: 0.7740 (m-80) REVERT: G 58 LYS cc_start: 0.8647 (mttt) cc_final: 0.8066 (mmtt) REVERT: G 97 LYS cc_start: 0.8724 (mmmm) cc_final: 0.8395 (mmmm) REVERT: H 58 LYS cc_start: 0.9034 (mttm) cc_final: 0.8741 (mttm) REVERT: H 61 GLU cc_start: 0.8255 (tt0) cc_final: 0.7819 (tt0) REVERT: J 39 TYR cc_start: 0.7130 (m-80) cc_final: 0.6755 (m-80) REVERT: J 43 LYS cc_start: 0.7334 (mtmm) cc_final: 0.7075 (mptt) REVERT: K 97 LYS cc_start: 0.7965 (mtmt) cc_final: 0.7742 (mtmm) REVERT: L 39 TYR cc_start: 0.7052 (m-80) cc_final: 0.6561 (m-80) outliers start: 55 outliers final: 45 residues processed: 148 average time/residue: 0.1836 time to fit residues: 34.1939 Evaluate side-chains 151 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 105 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS 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 37 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 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 74 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 G residue 88 ILE 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 46 GLU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 37 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 43 LYS 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 7 optimal weight: 10.0000 chunk 42 optimal weight: 30.0000 chunk 23 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.4687 r_free = 0.4687 target = 0.174292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.147766 restraints weight = 8957.977| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 4.21 r_work: 0.4285 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.4538 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= 0.218 Angle : 0.570 6.021 7140 Z= 0.327 Chirality : 0.050 0.128 936 Planarity : 0.002 0.011 888 Dihedral : 5.256 16.842 756 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 9.63 % Allowed : 17.22 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS F 50 PHE 0.005 0.001 PHE J 94 TYR 0.007 0.002 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.01914 ( 76) hydrogen bonds : angle 4.42469 ( 228) covalent geometry : bond 0.00484 ( 5280) covalent geometry : angle 0.56994 ( 7140) *********************** 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 162 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 110 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 43 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6513 (mptt) REVERT: C 97 LYS cc_start: 0.8569 (mmmt) cc_final: 0.8245 (mmmt) REVERT: D 58 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8637 (mttm) REVERT: F 43 LYS cc_start: 0.3457 (pptt) cc_final: 0.2414 (pptt) REVERT: F 57 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7766 (pm20) REVERT: F 58 LYS cc_start: 0.9014 (mttt) cc_final: 0.7919 (mmmt) REVERT: G 39 TYR cc_start: 0.8014 (m-80) cc_final: 0.7719 (m-80) REVERT: G 58 LYS cc_start: 0.8610 (mttt) cc_final: 0.8091 (mmtt) REVERT: G 97 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8319 (mmmt) REVERT: H 58 LYS cc_start: 0.8989 (mttm) cc_final: 0.8694 (mttm) REVERT: H 61 GLU cc_start: 0.8305 (tt0) cc_final: 0.7884 (tt0) REVERT: H 97 LYS cc_start: 0.8006 (mmtm) cc_final: 0.7775 (mmmt) REVERT: J 43 LYS cc_start: 0.7341 (mtmm) cc_final: 0.7044 (mptt) REVERT: J 97 LYS cc_start: 0.8333 (mmmt) cc_final: 0.7910 (mmmt) REVERT: K 97 LYS cc_start: 0.8006 (mtmt) cc_final: 0.7708 (pttm) outliers start: 52 outliers final: 44 residues processed: 144 average time/residue: 0.1697 time to fit residues: 31.4301 Evaluate side-chains 153 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 107 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS 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 46 GLU Chi-restraints excluded: chain C residue 54 THR 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 58 LYS 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 88 ILE 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 46 GLU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 37 VAL 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 48 optimal weight: 30.0000 chunk 25 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** ** 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 = 0.4668 r_free = 0.4668 target = 0.171931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.145368 restraints weight = 8982.988| |-----------------------------------------------------------------------------| r_work (start): 0.4374 rms_B_bonded: 4.29 r_work: 0.4257 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.4692 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= 0.273 Angle : 0.614 7.475 7140 Z= 0.350 Chirality : 0.051 0.139 936 Planarity : 0.002 0.012 888 Dihedral : 5.527 17.127 756 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 10.00 % Allowed : 17.59 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (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 HIS 0.008 0.004 HIS G 50 PHE 0.005 0.002 PHE J 94 TYR 0.011 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.02107 ( 76) hydrogen bonds : angle 4.54260 ( 228) covalent geometry : bond 0.00604 ( 5280) covalent geometry : angle 0.61447 ( 7140) *********************** 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 160 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 106 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6815 (mptt) REVERT: C 39 TYR cc_start: 0.6499 (m-80) cc_final: 0.6181 (m-80) REVERT: C 97 LYS cc_start: 0.8574 (mmmt) cc_final: 0.8221 (mmmt) REVERT: E 43 LYS cc_start: 0.7822 (mtmm) cc_final: 0.7598 (mptt) REVERT: F 43 LYS cc_start: 0.4074 (pptt) cc_final: 0.3118 (pptt) REVERT: F 57 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7744 (pm20) REVERT: F 58 LYS cc_start: 0.9069 (mttt) cc_final: 0.8014 (mmmt) REVERT: H 58 LYS cc_start: 0.9008 (mttm) cc_final: 0.8743 (mttm) REVERT: H 61 GLU cc_start: 0.8347 (tt0) cc_final: 0.7944 (tt0) REVERT: J 39 TYR cc_start: 0.7114 (m-80) cc_final: 0.6646 (m-80) REVERT: J 43 LYS cc_start: 0.7422 (mtmm) cc_final: 0.7155 (mmtm) REVERT: J 97 LYS cc_start: 0.8192 (mmmt) cc_final: 0.7705 (mmmt) outliers start: 54 outliers final: 48 residues processed: 142 average time/residue: 0.1754 time to fit residues: 31.8166 Evaluate side-chains 153 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 104 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS 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 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 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 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 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 46 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain J residue 37 VAL 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 43 LYS 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 70 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 = 0.4733 r_free = 0.4733 target = 0.177326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.151382 restraints weight = 8960.183| |-----------------------------------------------------------------------------| r_work (start): 0.4446 rms_B_bonded: 4.24 r_work: 0.4333 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5280 Z= 0.159 Angle : 0.551 6.689 7140 Z= 0.310 Chirality : 0.050 0.129 936 Planarity : 0.002 0.011 888 Dihedral : 4.988 15.426 756 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 8.33 % Allowed : 18.52 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 50 PHE 0.004 0.001 PHE H 94 TYR 0.009 0.001 TYR L 39 Details of bonding type rmsd hydrogen bonds : bond 0.01825 ( 76) hydrogen bonds : angle 4.28064 ( 228) covalent geometry : bond 0.00353 ( 5280) covalent geometry : angle 0.55106 ( 7140) *********************** 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 157 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 112 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 43 LYS cc_start: 0.7040 (OUTLIER) cc_final: 0.6668 (mptt) REVERT: A 58 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8475 (mmtp) REVERT: C 46 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7442 (pt0) REVERT: E 43 LYS cc_start: 0.7727 (mtmm) cc_final: 0.7524 (mptt) REVERT: F 39 TYR cc_start: 0.8030 (m-80) cc_final: 0.5596 (p90) REVERT: F 43 LYS cc_start: 0.3905 (pptt) cc_final: 0.3187 (pptt) REVERT: F 57 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7771 (pm20) REVERT: F 58 LYS cc_start: 0.8918 (mttt) cc_final: 0.7824 (mmmt) REVERT: F 97 LYS cc_start: 0.8726 (mmmm) cc_final: 0.8271 (mmmt) REVERT: G 58 LYS cc_start: 0.8472 (mttm) cc_final: 0.7644 (mmmt) REVERT: H 58 LYS cc_start: 0.9048 (mttm) cc_final: 0.8837 (mttm) REVERT: J 39 TYR cc_start: 0.7162 (m-80) cc_final: 0.6672 (m-80) REVERT: J 43 LYS cc_start: 0.7413 (mtmm) cc_final: 0.7159 (mmtm) outliers start: 45 outliers final: 37 residues processed: 142 average time/residue: 0.1773 time to fit residues: 31.8109 Evaluate side-chains 148 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 58 LYS 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 46 GLU 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 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 H residue 37 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 46 GLU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 37 VAL 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 43 LYS 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 54 THR Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 18 optimal weight: 20.0000 chunk 27 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 overall best weight: 4.1386 ------------------------------------------------------------------------------- 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** ** 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 = 0.4719 r_free = 0.4719 target = 0.175306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.149193 restraints weight = 8952.478| |-----------------------------------------------------------------------------| r_work (start): 0.4429 rms_B_bonded: 4.21 r_work: 0.4318 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5280 Z= 0.197 Angle : 0.593 7.965 7140 Z= 0.331 Chirality : 0.050 0.127 936 Planarity : 0.002 0.012 888 Dihedral : 5.138 15.706 756 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 8.89 % Allowed : 18.89 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS G 50 PHE 0.005 0.001 PHE H 94 TYR 0.010 0.002 TYR A 39 Details of bonding type rmsd hydrogen bonds : bond 0.01854 ( 76) hydrogen bonds : angle 4.27455 ( 228) covalent geometry : bond 0.00438 ( 5280) covalent geometry : angle 0.59257 ( 7140) *********************** 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 159 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 111 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6692 (mptt) REVERT: A 58 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8292 (mmtp) REVERT: C 39 TYR cc_start: 0.7189 (m-80) cc_final: 0.6791 (m-80) REVERT: D 97 LYS cc_start: 0.8441 (mmmt) cc_final: 0.8007 (mmmt) REVERT: F 39 TYR cc_start: 0.8070 (m-80) cc_final: 0.5661 (p90) REVERT: F 43 LYS cc_start: 0.4010 (pptt) cc_final: 0.3160 (pptt) REVERT: F 57 GLU cc_start: 0.8483 (mt-10) cc_final: 0.7792 (pm20) REVERT: F 58 LYS cc_start: 0.8896 (mttt) cc_final: 0.7858 (mmmt) REVERT: F 97 LYS cc_start: 0.8768 (mmmm) cc_final: 0.8347 (mmmt) REVERT: G 58 LYS cc_start: 0.8493 (mttm) cc_final: 0.7604 (mmmt) REVERT: H 46 GLU cc_start: 0.7242 (pt0) cc_final: 0.6724 (pm20) REVERT: H 61 GLU cc_start: 0.8224 (tt0) cc_final: 0.7900 (tt0) REVERT: J 39 TYR cc_start: 0.7139 (m-80) cc_final: 0.6673 (m-80) REVERT: J 43 LYS cc_start: 0.7438 (mtmm) cc_final: 0.7179 (mmtm) outliers start: 48 outliers final: 44 residues processed: 145 average time/residue: 0.1921 time to fit residues: 35.3323 Evaluate side-chains 154 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 108 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 58 LYS 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 61 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 37 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 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 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 46 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 37 VAL 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 43 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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** ** 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 = 0.4741 r_free = 0.4741 target = 0.177210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.151259 restraints weight = 8912.827| |-----------------------------------------------------------------------------| r_work (start): 0.4448 rms_B_bonded: 4.11 r_work: 0.4337 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.4958 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= 0.176 Angle : 0.594 9.478 7140 Z= 0.327 Chirality : 0.050 0.123 936 Planarity : 0.002 0.012 888 Dihedral : 5.034 15.406 756 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 8.15 % Allowed : 20.00 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.27), 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 HIS 0.005 0.003 HIS G 50 PHE 0.005 0.001 PHE H 94 TYR 0.014 0.002 TYR L 39 Details of bonding type rmsd hydrogen bonds : bond 0.01855 ( 76) hydrogen bonds : angle 4.26713 ( 228) covalent geometry : bond 0.00397 ( 5280) covalent geometry : angle 0.59433 ( 7140) ********************** 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 151 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 107 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 43 LYS cc_start: 0.7007 (OUTLIER) cc_final: 0.6633 (mptt) REVERT: A 58 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8483 (mmtp) REVERT: C 39 TYR cc_start: 0.7151 (m-80) cc_final: 0.6753 (m-80) REVERT: C 46 GLU cc_start: 0.7464 (pt0) cc_final: 0.7140 (pm20) REVERT: F 39 TYR cc_start: 0.8016 (m-80) cc_final: 0.5759 (p90) REVERT: F 43 LYS cc_start: 0.3776 (pptt) cc_final: 0.2876 (pptt) REVERT: F 57 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7751 (pm20) REVERT: F 58 LYS cc_start: 0.8948 (mttt) cc_final: 0.7891 (mmmt) REVERT: F 97 LYS cc_start: 0.8703 (mmmm) cc_final: 0.8279 (mmmt) REVERT: G 39 TYR cc_start: 0.7979 (m-80) cc_final: 0.5955 (p90) REVERT: H 46 GLU cc_start: 0.7223 (pt0) cc_final: 0.6663 (pm20) REVERT: H 61 GLU cc_start: 0.8214 (tt0) cc_final: 0.7861 (tt0) REVERT: J 43 LYS cc_start: 0.7389 (mtmm) cc_final: 0.7154 (mmtm) REVERT: J 97 LYS cc_start: 0.8178 (mmmt) cc_final: 0.7536 (mttp) outliers start: 44 outliers final: 42 residues processed: 139 average time/residue: 0.1724 time to fit residues: 30.6474 Evaluate side-chains 148 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 104 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 58 LYS 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 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 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 H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 72 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 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 37 VAL 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 43 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 6 optimal weight: 20.0000 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 30.0000 chunk 68 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- 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** ** 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 = 0.4678 r_free = 0.4678 target = 0.171325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.145191 restraints weight = 9006.290| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 4.21 r_work: 0.4265 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 5280 Z= 0.292 Angle : 0.683 11.251 7140 Z= 0.378 Chirality : 0.052 0.157 936 Planarity : 0.003 0.012 888 Dihedral : 5.618 16.448 756 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 9.26 % Allowed : 19.44 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS G 50 PHE 0.006 0.002 PHE J 94 TYR 0.016 0.002 TYR L 39 Details of bonding type rmsd hydrogen bonds : bond 0.02164 ( 76) hydrogen bonds : angle 4.50009 ( 228) covalent geometry : bond 0.00652 ( 5280) covalent geometry : angle 0.68298 ( 7140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2799.57 seconds wall clock time: 49 minutes 24.05 seconds (2964.05 seconds total)