Starting phenix.refine on Wed Apr 10 15:59:19 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 3NJW_complete.pdb Found miller_array, 3NJW.mtz Found phil, 3NJW.edits Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ 3NJW.edits Adding command-line PHIL: ------------------------- optimize_adp=true optimize_xyz=true hydrogens.refine=riding nproc=20 main.max_number_of_iterations=50 main.number_of_m=5 refine.adp.individual.aniso=not element H refine.adp.individual.iso=element H Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "3NJW_complete.pdb" } default_model = "3NJW_complete.pdb" miller_array { file = "3NJW.mtz" } default_miller_array = "3NJW.mtz" phil_files = "3NJW.edits" default_phil = "3NJW.edits" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { adp { individual { isotropic = element H anisotropic = not element H } } } main { number_of_macro_cycles = 5 max_number_of_iterations = 50 nproc = 20 } hydrogens { refine = individual *riding Auto } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 9 and name CG atom_selection_2 = chain A and resseq 1 and name N distance_ideal = 1.4 sigma = 0.02 } } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 343 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 268 Classifications: {'peptide': 19} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 13} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 75 Classifications: {'water': 25} Link IDs: {None: 24} Time building chain proxies: 0.14, per 1000 atoms: 0.41 Number of scatterers: 343 At special positions: 0 Unit cell: (19.465, 21.432, 29.523, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 2 16.00 O 49 8.00 N 23 7.00 C 95 6.00 H 174 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 19 " distance=2.03 Custom bonds: bond: atom 1: "ATOM 112 CG ASP A 9 .*. C " atom 2: "ATOM 1 N GLY A 1 .*. N " symmetry operation: x,y,z distance_model: 1.338 distance_ideal: 1.400 ideal - model: 0.062 slack: 0.000 delta_slack: 0.062 sigma: 0.0200 Total number of added/changed bonds: 1 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.13 Conformation dependent library (CDL) restraints added in 9.8 milliseconds Time building geometry restraints manager: 0.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.05: 72 1.05 - 1.24: 115 1.24 - 1.44: 64 1.44 - 1.63: 74 1.63 - 1.83: 2 Bond restraints: 327 Sorted by residual: bond pdb=" NE1 TRP A 17 " pdb=" HE1 TRP A 17 " ideal model delta sigma weight residual 0.860 1.020 -0.160 2.00e-02 2.50e+03 6.42e+01 bond pdb=" N ALA A 18 " pdb=" H ALA A 18 " ideal model delta sigma weight residual 0.860 1.020 -0.160 2.00e-02 2.50e+03 6.42e+01 bond pdb=" N GLY A 12 " pdb=" H GLY A 12 " ideal model delta sigma weight residual 0.860 1.020 -0.160 2.00e-02 2.50e+03 6.41e+01 bond pdb=" N ASN A 14 " pdb=" H ASN A 14 " ideal model delta sigma weight residual 0.860 1.020 -0.160 2.00e-02 2.50e+03 6.41e+01 bond pdb=" N SER A 8 " pdb=" H SER A 8 " ideal model delta sigma weight residual 0.860 1.020 -0.160 2.00e-02 2.50e+03 6.40e+01 ... (remaining 322 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.64: 57 106.64 - 113.82: 278 113.82 - 121.00: 104 121.00 - 128.18: 79 128.18 - 135.36: 9 Bond angle restraints: 527 Sorted by residual: angle pdb=" CA PRO A 7 " pdb=" C PRO A 7 " pdb=" N SER A 8 " ideal model delta sigma weight residual 115.50 120.90 -5.40 1.27e+00 6.20e-01 1.81e+01 angle pdb=" CA ASP A 9 " pdb=" CB ASP A 9 " pdb=" CG ASP A 9 " ideal model delta sigma weight residual 112.60 116.60 -4.00 1.00e+00 1.00e+00 1.60e+01 angle pdb=" C PRO A 7 " pdb=" N SER A 8 " pdb=" CA SER A 8 " ideal model delta sigma weight residual 121.70 128.59 -6.89 1.80e+00 3.09e-01 1.46e+01 angle pdb=" CA PRO A 7 " pdb=" C PRO A 7 " pdb=" O PRO A 7 " ideal model delta sigma weight residual 121.31 118.15 3.16 1.20e+00 6.94e-01 6.93e+00 angle pdb=" C TRP A 13 " pdb=" CA TRP A 13 " pdb=" CB TRP A 13 " ideal model delta sigma weight residual 110.42 115.57 -5.15 1.99e+00 2.53e-01 6.68e+00 ... (remaining 522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.64: 82 9.64 - 19.27: 17 19.27 - 28.91: 2 28.91 - 38.54: 3 38.54 - 48.18: 4 Dihedral angle restraints: 108 sinusoidal: 72 harmonic: 36 Sorted by residual: dihedral pdb=" CA SER A 8 " pdb=" C SER A 8 " pdb=" N ASP A 9 " pdb=" CA ASP A 9 " ideal model delta harmonic sigma weight residual 180.00 164.30 15.70 0 5.00e+00 4.00e-02 9.86e+00 dihedral pdb=" CA ASN A 14 " pdb=" C ASN A 14 " pdb=" N THR A 15 " pdb=" CA THR A 15 " ideal model delta harmonic sigma weight residual 180.00 167.42 12.58 0 5.00e+00 4.00e-02 6.33e+00 dihedral pdb=" CA GLY A 12 " pdb=" C GLY A 12 " pdb=" N TRP A 13 " pdb=" CA TRP A 13 " ideal model delta harmonic sigma weight residual 180.00 167.82 12.18 0 5.00e+00 4.00e-02 5.94e+00 ... (remaining 105 not shown) Histogram of chiral volume deviations from ideal: 0.021 - 0.067: 10 0.067 - 0.113: 4 0.113 - 0.159: 2 0.159 - 0.205: 2 0.205 - 0.250: 1 Chirality restraints: 19 Sorted by residual: chirality pdb=" CA ASP A 9 " pdb=" N ASP A 9 " pdb=" C ASP A 9 " pdb=" CB ASP A 9 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ILE A 10 " pdb=" N ILE A 10 " pdb=" C ILE A 10 " pdb=" CB ILE A 10 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA PRO A 11 " pdb=" N PRO A 11 " pdb=" C PRO A 11 " pdb=" CB PRO A 11 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.38e-01 ... (remaining 16 not shown) Planarity restraints: 41 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 17 " 0.041 2.00e-02 2.50e+03 4.78e-02 9.15e+01 pdb=" CG TRP A 17 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP A 17 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 17 " -0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP A 17 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 17 " -0.025 2.00e-02 2.50e+03 pdb=" CE3 TRP A 17 " -0.033 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 17 " -0.034 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 17 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 17 " 0.036 2.00e-02 2.50e+03 pdb=" HD1 TRP A 17 " 0.039 2.00e-02 2.50e+03 pdb=" HE1 TRP A 17 " 0.015 2.00e-02 2.50e+03 pdb=" HE3 TRP A 17 " -0.041 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 17 " -0.092 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 17 " 0.006 2.00e-02 2.50e+03 pdb=" HH2 TRP A 17 " 0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 4 " -0.012 2.00e-02 2.50e+03 3.81e-02 5.81e+01 pdb=" CG TRP A 4 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 4 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 4 " -0.077 2.00e-02 2.50e+03 pdb=" NE1 TRP A 4 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP A 4 " -0.043 2.00e-02 2.50e+03 pdb=" CE3 TRP A 4 " -0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 4 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 4 " 0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP A 4 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP A 4 " 0.096 2.00e-02 2.50e+03 pdb=" HE1 TRP A 4 " -0.013 2.00e-02 2.50e+03 pdb=" HE3 TRP A 4 " 0.003 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 4 " -0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 4 " 0.055 2.00e-02 2.50e+03 pdb=" HH2 TRP A 4 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 13 " -0.039 2.00e-02 2.50e+03 3.36e-02 4.51e+01 pdb=" CG TRP A 13 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP A 13 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 13 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP A 13 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TRP A 13 " -0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP A 13 " 0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 13 " -0.016 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 13 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP A 13 " -0.023 2.00e-02 2.50e+03 pdb=" HD1 TRP A 13 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 TRP A 13 " 0.082 2.00e-02 2.50e+03 pdb=" HE3 TRP A 13 " 0.032 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 13 " -0.014 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 13 " 0.035 2.00e-02 2.50e+03 pdb=" HH2 TRP A 13 " -0.057 2.00e-02 2.50e+03 ... (remaining 38 not shown) Histogram of nonbonded interaction distances: 0.83 - 1.58: 17 1.58 - 2.34: 200 2.34 - 3.09: 1280 3.09 - 3.85: 2284 3.85 - 4.60: 3817 Warning: very small nonbonded interaction distances. Nonbonded interactions: 7598 Sorted by model distance: nonbonded pdb=" O HOH A1006 " pdb=" O HOH A1106 " model vdw 0.827 2.200 nonbonded pdb=" O HOH A1012 " pdb=" O HOH A1112 " model vdw 0.831 2.200 nonbonded pdb=" O HOH A1007 " pdb=" O HOH A1016 " model vdw 1.287 2.200 nonbonded pdb=" O HOH A1013 " pdb=" O HOH A1112 " model vdw 1.406 2.200 nonbonded pdb=" O HOH A1009 " pdb=" O HOH A1118 " model vdw 1.456 2.200 ... (remaining 7593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 2 15.96 3 O 49 7.98 3 N 23 6.98 3 C 95 5.99 3 H 174 1.00 3 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== n_use = 343 n_use_u_iso = 190 n_use_u_aniso = 153 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 343 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (343 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 174 aniso = 169) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (16 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { adp { individual { isotropic = element H anisotropic = not element H } } } main { number_of_macro_cycles = 5 max_number_of_iterations = 50 nproc = 20 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 9 and name CG atom_selection_2 = chain A and resseq 1 and name N distance_ideal = 1.4 sigma = 0.02 } } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "3NJW_complete_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 174 occupancy sum: 174.00 (% of total atoms 51.94) Rotatable: count: 20 occupancy sum: 20.00 (% of total atoms 5.97) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.86 - 8.94 A, n_refl.=10638 (all), 10.00 % free)-------------| | | | r_work= 0.1162 r_free= 0.1161 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 1.074603 | | target function (ml) not normalized (work): 10288.245896 | | target function (ml) not normalized (free): 1108.329241 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 8.94 - 1.73 1.00 1296 144 0.1019 0.0992 2.287 2.1681| | 2: 1.73 - 1.37 1.00 1231 137 0.1005 0.1024 1.3943 1.41| | 3: 1.37 - 1.20 1.00 1223 136 0.1081 0.1094 0.9329 0.92256| | 4: 1.20 - 1.09 1.00 1192 132 0.1027 0.1074 0.91562 0.88561| | 5: 1.09 - 1.01 1.00 1195 133 0.1425 0.1455 0.8714 0.87602| | 6: 1.01 - 0.95 1.00 1209 134 0.1477 0.1348 0.76812 0.67827| | 7: 0.95 - 0.90 1.00 1170 131 0.1757 0.1811 0.65295 0.71981| | 8: 0.90 - 0.86 0.89 1058 117 0.2362 0.2412 0.60643 0.50331| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 8.94 - 1.73 1296 144 0.95 7.95 0.97 0.24 8.41| | 2: 1.73 - 1.37 1231 137 0.93 11.07 1.09 0.26 3.47| | 3: 1.37 - 1.20 1223 136 0.97 5.28 1.09 0.27 0.88| | 4: 1.20 - 1.09 1192 132 0.98 5.29 1.07 0.27 0.67| | 5: 1.09 - 1.01 1195 133 0.96 7.56 1.12 0.27 0.60| | 6: 1.01 - 0.95 1209 134 0.95 10.12 1.06 0.26 0.55| | 7: 0.95 - 0.90 1170 131 0.92 14.12 0.99 0.24 0.49| | 8: 0.90 - 0.86 1058 117 0.90 17.74 0.91 0.22 0.42| |alpha: min = 0.22 max = 0.27 mean = 0.25| |beta: min = 0.42 max = 8.41 mean = 2.03| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.83 mean = 9.74| |phase err.(test): min = 0.00 max = 89.32 mean = 9.97| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.069 153 Z= 1.093 Angle : 1.692 6.888 214 Z= 1.095 Chirality : 0.107 0.250 19 Planarity : 0.018 0.057 27 Dihedral : 10.041 36.838 49 Min Nonbonded Distance : 0.827 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 7.14 % 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: -3.35 (1.78), residues: 17 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (1.36), residues: 17 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.021 TRP A 4 Individual atomic B min max mean iso aniso Overall: 3.53 39.85 7.19 1.02 0 169 Protein: 3.53 11.03 5.68 1.02 0 144 Water: 6.92 39.85 15.87 N/A 0 25 Chain A: 3.53 39.85 7.19 N/A 0 169 Histogram: Values Number of atoms 3.53 - 7.16 124 7.16 - 10.79 25 10.79 - 14.42 6 14.42 - 18.06 5 18.06 - 21.69 5 21.69 - 25.32 3 25.32 - 28.95 0 28.95 - 32.59 0 32.59 - 36.22 0 36.22 - 39.85 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 0.86 - 8.94 A, n_refl.=10638 (all), 10.00 % free)-------------| | | | r_work= 0.1162 r_free= 0.1161 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 1.074603 | | target function (ml) not normalized (work): 10288.245896 | | target function (ml) not normalized (free): 1108.329241 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1162 0.1162 0.1161 n_refl.: 10638 re-set all scales: r(all,work,free)=0.1162 0.1162 0.1161 n_refl.: 10638 remove outliers: r(all,work,free)=0.1162 0.1162 0.1161 n_refl.: 10635 overall B=0.09 to atoms: r(all,work,free)=0.1188 0.1188 0.1184 n_refl.: 10635 bulk-solvent and scaling: r(all,work,free)=0.1007 0.1006 0.1018 n_refl.: 10635 remove outliers: r(all,work,free)=0.1006 0.1004 0.1018 n_refl.: 10633 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 8.943-4.242 99.02 90 11 0.1717 109.499 105.999 0.882 0.936 0.157 4.237-3.403 100.00 90 10 0.0782 116.471 115.849 0.913 0.940 0.130 3.400-2.732 100.00 159 17 0.0951 82.505 80.953 0.923 0.942 0.000 2.728-2.190 100.00 313 35 0.0882 68.359 68.000 0.938 0.945 0.000 2.188-1.756 100.00 585 64 0.0732 51.755 51.524 0.989 0.951 0.000 1.756-1.409 100.00 1103 123 0.0747 33.757 33.816 1.031 0.958 0.000 1.408-1.130 100.00 2106 235 0.0808 24.148 24.220 1.026 0.970 0.000 1.130-0.907 99.89 4002 445 0.1329 13.490 13.512 1.005 0.989 0.000 0.906-0.865 89.06 1121 124 0.2177 6.810 6.370 0.841 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=0.0092 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1004 r_free=0.1018 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1004 r_free=0.1018 ========================= Local real-space refinement ========================= Before: r_work=0.1004 r_free=0.1018 1 residues out of total 13 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.012 outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.2257 time to fit residues: 0.2413 After: r_work=0.1007 r_free=0.1023 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 12.929044 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 32.281908 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1139 0.1287 0.0148 0.005 1.1 3.7 0.0 0.0 0 6.465 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1139 r_free=0.1287 0 residues out of total 13 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.014 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0114 After: r_work=0.1139 r_free=0.1287 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.39 12.87 1.48 0.698 8.133 32.282 0.014 11.39 12.92 1.53 0.637 8.133 0.968 0.014 11.37 12.91 1.54 0.651 8.133 4.035 0.014 11.35 13.27 1.91 0.547 8.126 16.141 0.014 11.06 13.62 2.56 2.914 8.464 32.282 0.012 10.94 13.58 2.63 3.085 8.490 48.423 0.012 10.85 13.52 2.67 2.813 8.458 64.564 0.012 10.81 13.50 2.69 2.852 8.466 80.705 0.011 10.79 13.51 2.72 2.746 8.457 96.846 0.011 10.75 13.50 2.75 2.944 8.485 112.987 0.011 10.77 13.60 2.83 2.957 8.489 129.128 0.011 10.74 13.64 2.90 2.660 8.453 145.269 0.011 10.70 13.51 2.81 2.737 8.468 161.410 0.011 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 4.035 Accepted refinement result: 11.37 12.91 1.54 0.651 8.133 4.035 0.014 Individual atomic B min max mean iso aniso Overall: 3.66 39.94 7.27 0.95 0 169 Protein: 3.66 10.96 5.76 0.95 0 144 Water: 7.01 39.94 15.96 N/A 0 25 Chain A: 3.66 39.94 7.27 N/A 0 169 Histogram: Values Number of atoms 3.66 - 7.29 125 7.29 - 10.92 24 10.92 - 14.54 6 14.54 - 18.17 5 18.17 - 21.80 5 21.80 - 25.43 3 25.43 - 29.05 0 29.05 - 32.68 0 32.68 - 36.31 0 36.31 - 39.94 1 =========================== Idealize ADP of riding H ========================== r_work=0.1137 r_free=0.1291 r_work=0.1130 r_free=0.1282 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1130 r_free = 0.1282 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1113 r_free = 0.1267 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 0.86 - 8.94 A, n_refl.=10633 (all), 10.01 % free)-------------| | | | r_work= 0.1113 r_free= 0.1267 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ls_wunit_k1) (work): 0.012076 | | target function (ls_wunit_k1) not normalized (work): 115.552689 | | target function (ls_wunit_k1) not normalized (free): 18.859499 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1128 0.1113 0.1267 n_refl.: 10633 re-set all scales: r(all,work,free)=0.1296 0.1285 0.1395 n_refl.: 10633 remove outliers: r(all,work,free)=0.1296 0.1285 0.1395 n_refl.: 10633 overall B=-0.01 to atoms: r(all,work,free)=0.1293 0.1282 0.1392 n_refl.: 10633 bulk-solvent and scaling: r(all,work,free)=0.1125 0.1110 0.1262 n_refl.: 10633 remove outliers: r(all,work,free)=0.1125 0.1110 0.1262 n_refl.: 10633 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 8.943-4.242 99.02 90 11 0.1130 99.024 97.315 0.881 0.943 0.110 4.237-3.403 100.00 90 10 0.0684 105.329 105.132 0.912 0.945 0.096 3.400-2.732 100.00 159 17 0.0932 74.613 73.976 0.924 0.946 0.024 2.728-2.190 100.00 313 35 0.0952 61.819 61.606 0.944 0.947 0.000 2.188-1.756 100.00 585 64 0.0915 46.804 46.595 0.996 0.950 0.000 1.756-1.409 100.00 1103 123 0.0979 30.527 30.537 1.033 0.953 0.000 1.408-1.130 100.00 2106 235 0.1003 21.838 21.867 1.043 0.959 0.000 1.130-0.907 99.89 4002 445 0.1437 12.199 12.195 1.042 0.968 0.000 0.906-0.865 89.06 1121 124 0.2256 6.159 5.767 0.874 0.976 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.0354 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1110 r_free=0.1262 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1110 r_free=0.1262 ========================= Local real-space refinement ========================= Before: r_work=0.1110 r_free=0.1262 1 residues out of total 13 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.014 outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.2418 time to fit residues: 0.2603 After: r_work=0.1110 r_free=0.1262 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 11.557982 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 35.169796 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1650 0.1828 0.0178 0.003 0.8 3.7 0.0 0.0 0 0.125 0.1573 0.1751 0.0177 0.003 0.8 3.7 0.0 0.0 0 0.250 0.1395 0.1566 0.0171 0.003 0.8 3.7 0.0 0.0 0 0.500 0.1255 0.1414 0.0159 0.003 0.9 3.7 0.0 0.0 0 1.000 0.1176 0.1323 0.0147 0.003 0.9 3.7 0.0 0.0 0 2.000 0.1125 0.1255 0.0130 0.004 1.0 3.7 0.0 0.0 0 3.000 0.1102 0.1224 0.0122 0.004 1.0 3.7 0.0 0.0 0 4.000 0.1082 0.1203 0.0121 0.004 1.1 3.7 0.0 0.0 0 5.000 0.1070 0.1190 0.0119 0.005 1.1 3.7 0.0 0.0 0 6.000 0.1063 0.1186 0.0123 0.005 1.1 3.7 0.0 0.0 0 7.000 0.1057 0.1180 0.0124 0.005 1.1 3.7 0.0 0.0 0 8.000 0.1051 0.1174 0.0123 0.005 1.1 0.0 0.0 0.0 0 9.000 0.1049 0.1176 0.0128 0.005 1.1 0.0 0.0 0.0 0 10.000 0.1072 0.1196 0.0124 0.005 1.1 3.7 0.0 0.0 0 5.779 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1051 0.1174 0.0123 0.005 1.1 0.0 0.0 0.0 0 9.000 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1051 r_free=0.1174 1 residues out of total 13 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.012 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0104 After: r_work=0.1051 r_free=0.1174 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.51 11.74 1.23 1.706 9.026 35.170 0.011 10.51 11.74 1.24 1.705 9.026 1.055 0.011 10.50 11.74 1.23 1.706 9.026 4.396 0.011 10.51 12.08 1.56 1.675 9.025 17.585 0.011 10.20 12.51 2.31 1.805 9.274 35.170 0.009 10.08 12.47 2.39 1.868 9.295 52.755 0.009 10.03 12.38 2.36 1.958 9.323 70.340 0.009 9.99 12.39 2.40 1.941 9.323 87.924 0.009 9.94 12.36 2.42 1.895 9.321 105.509 0.009 9.92 12.35 2.43 1.935 9.332 123.094 0.009 9.90 12.31 2.41 1.928 9.335 140.679 0.009 9.87 12.33 2.45 1.837 9.321 158.264 0.009 9.85 12.36 2.51 1.764 9.304 175.849 0.009 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 4.396 Accepted refinement result: 10.50 11.74 1.23 1.706 9.026 4.396 0.011 Individual atomic B min max mean iso aniso Overall: 3.65 39.93 7.26 0.95 0 169 Protein: 3.65 10.94 5.75 0.95 0 144 Water: 7.00 39.93 15.95 N/A 0 25 Chain A: 3.65 39.93 7.26 N/A 0 169 Histogram: Values Number of atoms 3.65 - 7.28 125 7.28 - 10.91 24 10.91 - 14.53 6 14.53 - 18.16 5 18.16 - 21.79 5 21.79 - 25.42 3 25.42 - 29.04 0 29.04 - 32.67 0 32.67 - 36.30 0 36.30 - 39.93 1 =========================== Idealize ADP of riding H ========================== r_work=0.1050 r_free=0.1174 r_work=0.1050 r_free=0.1174 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1050 r_free = 0.1174 target_work(ls_wunit_k1) = 0.011 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1045 r_free = 0.1167 target_work(ls_wunit_k1) = 0.010 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 0.86 - 8.94 A, n_refl.=10633 (all), 10.01 % free)-------------| | | | r_work= 0.1045 r_free= 0.1167 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ls_wunit_k1) (work): 0.010418 | | target function (ls_wunit_k1) not normalized (work): 99.689233 | | target function (ls_wunit_k1) not normalized (free): 16.044843 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1057 0.1045 0.1167 n_refl.: 10633 re-set all scales: r(all,work,free)=0.1237 0.1227 0.1335 n_refl.: 10633 remove outliers: r(all,work,free)=0.1237 0.1227 0.1335 n_refl.: 10633 overall B=-0.01 to atoms: r(all,work,free)=0.1235 0.1225 0.1332 n_refl.: 10633 bulk-solvent and scaling: r(all,work,free)=0.1057 0.1045 0.1171 n_refl.: 10633 remove outliers: r(all,work,free)=0.1057 0.1045 0.1171 n_refl.: 10633 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 8.943-4.242 99.02 90 11 0.1134 99.024 97.560 0.881 0.947 0.126 4.237-3.403 100.00 90 10 0.0632 105.329 105.120 0.907 0.950 0.123 3.400-2.732 100.00 159 17 0.0849 74.613 74.121 0.918 0.950 0.010 2.728-2.190 100.00 313 35 0.0827 61.819 61.728 0.941 0.952 0.000 2.188-1.756 100.00 585 64 0.0820 46.804 46.683 0.989 0.954 0.000 1.756-1.409 100.00 1103 123 0.0889 30.527 30.583 1.028 0.958 0.000 1.408-1.130 100.00 2106 235 0.0940 21.838 21.853 1.037 0.964 0.000 1.130-0.907 99.89 4002 445 0.1408 12.199 12.203 1.035 0.973 0.000 0.906-0.865 89.06 1121 124 0.2228 6.159 5.773 0.867 0.981 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.0265 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1045 r_free=0.1171 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1045 r_free=0.1171 ========================= Local real-space refinement ========================= Before: r_work=0.1045 r_free=0.1171 1 residues out of total 13 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.013 outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.2480 time to fit residues: 0.2666 After: r_work=0.1045 r_free=0.1171 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.119596 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.809933 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1121 0.1229 0.0108 0.004 1.0 3.7 0.0 0.0 0 0.056 0.1052 0.1142 0.0090 0.004 1.2 0.0 0.0 0.0 0 0.168 0.1017 0.1106 0.0089 0.005 1.3 0.0 0.0 0.0 0 0.336 0.1004 0.1088 0.0084 0.006 1.3 0.0 0.0 0.0 0 0.504 0.0996 0.1079 0.0083 0.007 1.4 0.0 0.0 0.0 0 0.672 0.0991 0.1073 0.0082 0.007 1.4 0.0 0.0 0.0 0 0.840 0.0988 0.1071 0.0083 0.007 1.4 0.0 0.0 0.0 0 1.008 0.0985 0.1068 0.0083 0.008 1.5 0.0 0.0 0.0 0 1.176 0.1001 0.1083 0.0083 0.006 1.4 0.0 0.0 0.0 0 0.560 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0985 0.1068 0.0083 0.008 1.5 0.0 0.0 0.0 0 1.176 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.0985 r_free=0.1068 0 residues out of total 13 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.014 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0118 After: r_work=0.0985 r_free=0.1068 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.85 10.68 0.83 1.704 9.017 0.810 2.324 9.87 11.29 1.42 1.798 8.973 0.810 2.315 Individual atomic B min max mean iso aniso Overall: 3.66 40.04 7.16 0.65 0 169 Protein: 3.66 9.39 5.66 0.65 0 144 Water: 6.78 40.04 15.82 N/A 0 25 Chain A: 3.66 40.04 7.16 N/A 0 169 Histogram: Values Number of atoms 3.66 - 7.30 130 7.30 - 10.93 21 10.93 - 14.57 4 14.57 - 18.21 6 18.21 - 21.85 4 21.85 - 25.49 3 25.49 - 29.13 0 29.13 - 32.77 0 32.77 - 36.41 0 36.41 - 40.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.0987 r_free=0.1129 r_work=0.0987 r_free=0.1131 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0987 r_free = 0.1131 target_work(ml) = 2.314 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0985 r_free = 0.1126 target_work(ml) = 2.314 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 0.86 - 8.94 A, n_refl.=10633 (all), 10.01 % free)-------------| | | | r_work= 0.0985 r_free= 0.1126 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 2.313587 | | target function (ml) not normalized (work): 22138.717913 | | target function (ml) not normalized (free): 2562.030191 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0999 0.0985 0.1128 n_refl.: 10633 re-set all scales: r(all,work,free)=0.1220 0.1209 0.1325 n_refl.: 10633 remove outliers: r(all,work,free)=0.1220 0.1209 0.1325 n_refl.: 10633 overall B=-0.01 to atoms: r(all,work,free)=0.1215 0.1204 0.1320 n_refl.: 10633 bulk-solvent and scaling: r(all,work,free)=0.0997 0.0982 0.1133 n_refl.: 10633 remove outliers: r(all,work,free)=0.0997 0.0982 0.1133 n_refl.: 10633 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 8.943-4.242 99.02 90 11 0.1240 99.024 96.972 0.903 0.930 0.195 4.237-3.403 100.00 90 10 0.0632 105.329 104.909 0.919 0.932 0.190 3.400-2.732 100.00 159 17 0.0918 74.613 74.084 0.933 0.932 0.000 2.728-2.190 100.00 313 35 0.0893 61.819 61.565 0.956 0.933 0.000 2.188-1.756 100.00 585 64 0.0853 46.804 46.520 1.008 0.934 0.000 1.756-1.409 100.00 1103 123 0.0826 30.527 30.569 1.049 0.935 0.000 1.408-1.130 100.00 2106 235 0.0776 21.838 21.850 1.071 0.937 0.000 1.130-0.907 99.89 4002 445 0.1266 12.199 12.216 1.079 0.940 0.000 0.906-0.865 89.06 1121 124 0.2116 6.159 5.789 0.897 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.0390 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0982 r_free=0.1133 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0982 r_free=0.1133 ========================= Local real-space refinement ========================= Before: r_work=0.0982 r_free=0.1133 7 residues out of total 13 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.012 outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.1118 time to fit residues: 0.8143 After: r_work=0.1000 r_free=0.1156 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.157032 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.588705 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1105 0.1275 0.0170 0.004 1.0 3.7 0.0 0.0 0 0.058 0.1038 0.1203 0.0165 0.005 1.1 3.7 0.0 0.0 0 0.174 0.1010 0.1169 0.0159 0.005 1.2 0.0 0.0 0.0 0 0.347 0.0995 0.1151 0.0156 0.006 1.3 0.0 0.0 0.0 0 0.521 0.0990 0.1142 0.0153 0.006 1.3 0.0 0.0 0.0 0 0.694 0.0985 0.1137 0.0152 0.007 1.4 0.0 0.0 0.0 0 0.868 0.0980 0.1129 0.0148 0.007 1.4 0.0 0.0 0.0 0 1.041 0.0980 0.1129 0.0149 0.008 1.4 0.0 0.0 0.0 0 1.215 0.0993 0.1147 0.0154 0.006 1.3 0.0 0.0 0.0 0 0.579 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0980 0.1129 0.0148 0.007 1.4 0.0 0.0 0.0 0 1.041 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.0980 r_free=0.1129 7 residues out of total 13 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.014 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0117 After: r_work=0.0980 r_free=0.1129 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.80 11.29 1.48 1.614 8.847 0.589 2.314 9.80 11.29 1.48 1.614 8.847 0.018 2.314 9.80 11.29 1.48 1.614 8.847 0.074 2.314 9.80 11.29 1.48 1.614 8.847 0.294 2.314 9.80 11.29 1.48 1.614 8.847 0.589 2.314 9.81 11.30 1.49 1.611 8.852 0.883 2.315 9.76 11.31 1.56 1.604 8.861 1.177 2.310 9.72 11.30 1.58 1.606 8.862 1.472 2.307 9.69 11.30 1.60 1.607 8.864 1.766 2.305 9.68 11.29 1.61 1.607 8.865 2.060 2.303 9.66 11.28 1.62 1.607 8.866 2.355 2.302 9.57 11.24 1.67 1.601 8.879 2.649 2.296 9.64 11.30 1.66 1.608 8.869 2.944 2.301 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 2.649 Accepted refinement result: 9.57 11.24 1.67 1.601 8.879 2.649 2.296 Individual atomic B min max mean iso aniso Overall: 3.64 40.13 7.21 0.78 0 169 Protein: 3.64 9.93 5.71 0.78 0 144 Water: 6.73 40.13 15.84 N/A 0 25 Chain A: 3.64 40.13 7.21 N/A 0 169 Histogram: Values Number of atoms 3.64 - 7.29 127 7.29 - 10.94 24 10.94 - 14.59 4 14.59 - 18.24 6 18.24 - 21.89 4 21.89 - 25.54 3 25.54 - 29.18 0 29.18 - 32.83 0 32.83 - 36.48 0 36.48 - 40.13 1 =========================== Idealize ADP of riding H ========================== r_work=0.0957 r_free=0.1124 r_work=0.0957 r_free=0.1123 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0957 r_free = 0.1123 target_work(ml) = 2.296 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0958 r_free = 0.1123 target_work(ml) = 2.295 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 0.86 - 8.94 A, n_refl.=10633 (all), 10.01 % free)-------------| | | | r_work= 0.0958 r_free= 0.1123 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 2.295049 | | target function (ml) not normalized (work): 21961.325620 | | target function (ml) not normalized (free): 2560.057056 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0974 0.0958 0.1123 n_refl.: 10633 re-set all scales: r(all,work,free)=0.1206 0.1194 0.1312 n_refl.: 10633 remove outliers: r(all,work,free)=0.1206 0.1194 0.1312 n_refl.: 10633 overall B=-0.02 to atoms: r(all,work,free)=0.1199 0.1188 0.1306 n_refl.: 10633 bulk-solvent and scaling: r(all,work,free)=0.0988 0.0972 0.1136 n_refl.: 10633 remove outliers: r(all,work,free)=0.0988 0.0972 0.1136 n_refl.: 10633 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 8.943-4.242 99.02 90 11 0.1222 99.024 97.039 0.835 1.001 0.173 4.237-3.403 100.00 90 10 0.0644 105.329 105.073 0.854 1.002 0.143 3.400-2.732 100.00 159 17 0.0909 74.613 74.155 0.867 1.001 0.000 2.728-2.190 100.00 313 35 0.0891 61.819 61.662 0.890 1.000 0.000 2.188-1.756 100.00 585 64 0.0826 46.804 46.566 0.941 0.999 0.000 1.756-1.409 100.00 1103 123 0.0806 30.527 30.578 0.983 0.997 0.000 1.408-1.130 100.00 2106 235 0.0759 21.838 21.840 1.007 0.994 0.000 1.130-0.907 99.89 4002 445 0.1277 12.199 12.235 1.026 0.989 0.000 0.906-0.865 89.06 1121 124 0.2084 6.159 5.770 0.843 0.987 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.0617 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0972 r_free=0.1136 After: r_work=0.0973 r_free=0.1137 ================================== NQH flips ================================== r_work=0.0973 r_free=0.1137 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0973 r_free=0.1137 ========================= Local real-space refinement ========================= Before: r_work=0.0973 r_free=0.1137 3 residues out of total 13 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.013 outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.1231 time to fit residues: 0.3927 After: r_work=0.0979 r_free=0.1143 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.118332 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.686973 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1072 0.1241 0.0169 0.007 1.0 3.7 0.0 0.0 0 0.056 0.1027 0.1196 0.0169 0.006 1.1 3.7 0.0 0.0 0 0.168 0.1005 0.1171 0.0166 0.006 1.2 3.7 0.0 0.0 0 0.335 0.0991 0.1155 0.0164 0.006 1.3 0.0 0.0 0.0 0 0.503 0.0982 0.1143 0.0161 0.007 1.3 0.0 0.0 0.0 0 0.671 0.0977 0.1137 0.0160 0.007 1.4 0.0 0.0 0.0 0 0.839 0.0974 0.1135 0.0161 0.007 1.4 0.0 0.0 0.0 0 1.006 0.0971 0.1133 0.0162 0.008 1.4 0.0 0.0 0.0 0 1.174 0.0988 0.1151 0.0163 0.006 1.3 0.0 0.0 0.0 0 0.559 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0971 0.1133 0.0162 0.008 1.4 0.0 0.0 0.0 0 1.174 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.0971 r_free=0.1133 3 residues out of total 13 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.013 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0112 After: r_work=0.0971 r_free=0.1133 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.71 11.33 1.62 1.648 8.917 0.687 2.305 9.71 11.33 1.62 1.648 8.917 0.021 2.305 9.71 11.33 1.62 1.648 8.917 0.086 2.305 9.71 11.33 1.62 1.648 8.917 0.343 2.305 9.71 11.33 1.62 1.648 8.917 0.687 2.305 9.71 11.33 1.61 1.646 8.919 1.030 2.306 9.71 11.33 1.62 1.646 8.920 1.374 2.306 9.71 11.33 1.62 1.645 8.921 1.717 2.305 9.71 11.32 1.61 1.643 8.923 2.061 2.305 9.71 11.33 1.63 1.639 8.927 2.404 2.305 9.66 11.34 1.68 1.623 8.928 2.748 2.304 9.60 11.35 1.74 1.617 8.944 3.091 2.299 9.59 11.33 1.74 1.615 8.946 3.435 2.298 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 2.061 Accepted refinement result: 9.71 11.32 1.61 1.643 8.923 2.061 2.305 Individual atomic B min max mean iso aniso Overall: 3.66 40.11 7.21 0.77 0 169 Protein: 3.66 9.90 5.71 0.77 0 144 Water: 6.74 40.11 15.83 N/A 0 25 Chain A: 3.66 40.11 7.21 N/A 0 169 Histogram: Values Number of atoms 3.66 - 7.31 127 7.31 - 10.95 24 10.95 - 14.60 4 14.60 - 18.24 6 18.24 - 21.89 4 21.89 - 25.53 3 25.53 - 29.18 0 29.18 - 32.82 0 32.82 - 36.47 0 36.47 - 40.11 1 =========================== Idealize ADP of riding H ========================== r_work=0.0971 r_free=0.1132 r_work=0.0971 r_free=0.1132 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0971 r_free = 0.1132 target_work(ml) = 2.305 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0970 r_free = 0.1132 target_work(ml) = 2.305 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.86 - 8.94 A, n_refl.=10633 (all), 10.01 % free)-------------| | | | r_work= 0.0970 r_free= 0.1132 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 2.305176 | | target function (ml) not normalized (work): 22058.231105 | | target function (ml) not normalized (free): 2571.418383 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 8.94 - 1.73 1.00 1296 144 0.0879 0.1065 3.3678 3.4516| | 2: 1.73 - 1.37 1.00 1231 137 0.0810 0.0818 2.6955 2.7464| | 3: 1.37 - 1.20 1.00 1223 136 0.0745 0.0979 2.2133 2.3712| | 4: 1.20 - 1.09 1.00 1192 132 0.0783 0.0959 2.1285 2.271| | 5: 1.09 - 1.01 1.00 1195 133 0.1084 0.1365 2.1038 2.2958| | 6: 1.01 - 0.95 1.00 1207 134 0.1309 0.1359 1.9907 2.028| | 7: 0.95 - 0.90 1.00 1169 131 0.1971 0.2334 1.9486 2.1791| | 8: 0.90 - 0.86 0.88 1056 117 0.2113 0.2188 1.834 1.8234| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 8.94 - 1.73 1296 144 0.95 7.64 1.00 0.99 109.53| | 2: 1.73 - 1.37 1231 137 0.93 11.47 1.00 1.00 47.86| | 3: 1.37 - 1.20 1223 136 0.96 6.67 1.01 1.00 14.81| | 4: 1.20 - 1.09 1192 132 0.97 6.45 1.00 1.02 11.14| | 5: 1.09 - 1.01 1195 133 0.96 8.72 1.06 1.00 9.58| | 6: 1.01 - 0.95 1207 134 0.95 11.14 0.98 0.97 8.38| | 7: 0.95 - 0.90 1169 131 0.93 14.12 0.90 0.93 7.18| | 8: 0.90 - 0.86 1056 117 0.89 18.99 1.01 0.94 6.08| |alpha: min = 0.93 max = 1.02 mean = 0.98| |beta: min = 6.08 max = 109.53 mean = 28.07| |figures of merit: min = 0.00 max = 1.00 mean = 0.94| |phase err.(work): min = 0.00 max = 89.75 mean = 10.48| |phase err.(test): min = 0.00 max = 88.45 mean = 10.77| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0986 0.0970 0.1132 n_refl.: 10633 re-set all scales: r(all,work,free)=0.1208 0.1197 0.1315 n_refl.: 10633 remove outliers: r(all,work,free)=0.1208 0.1197 0.1315 n_refl.: 10633 overall B=-0.02 to atoms: r(all,work,free)=0.1201 0.1190 0.1309 n_refl.: 10633 bulk-solvent and scaling: r(all,work,free)=0.0987 0.0971 0.1130 n_refl.: 10633 remove outliers: r(all,work,free)=0.0987 0.0971 0.1130 n_refl.: 10633 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 8.943-4.242 99.02 90 11 0.1232 99.024 97.009 0.833 1.000 0.159 4.237-3.403 100.00 90 10 0.0646 105.329 105.024 0.853 1.002 0.133 3.400-2.732 100.00 159 17 0.0917 74.613 74.130 0.866 1.001 0.000 2.728-2.190 100.00 313 35 0.0881 61.819 61.649 0.890 1.000 0.000 2.188-1.756 100.00 585 64 0.0827 46.804 46.590 0.941 1.000 0.000 1.756-1.409 100.00 1103 123 0.0802 30.527 30.577 0.983 0.998 0.000 1.408-1.130 100.00 2106 235 0.0757 21.838 21.851 1.008 0.995 0.000 1.130-0.907 99.89 4002 445 0.1275 12.199 12.237 1.026 0.991 0.000 0.906-0.865 89.06 1121 124 0.2093 6.159 5.772 0.844 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.0669 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.1162 0.1161 0.017 1.692 3.5 39.9 7.2 75 0.000 1_bss: 0.1004 0.1018 0.017 1.692 3.6 39.9 7.3 75 0.000 1_settarget: 0.1004 0.1018 0.017 1.692 3.6 39.9 7.3 75 0.000 1_nqh: 0.1004 0.1018 0.017 1.692 3.6 39.9 7.3 75 0.000 1_realsrl: 0.1007 0.1023 0.017 1.692 3.6 39.9 7.3 75 0.001 1_weight: 0.1007 0.1023 0.017 1.692 3.6 39.9 7.3 75 0.001 1_xyzrec: 0.1139 0.1287 0.005 1.095 3.6 39.9 7.3 75 0.100 1_realsrl2: 0.1139 0.1287 0.005 1.095 3.6 39.9 7.3 75 0.100 1_adp: 0.1137 0.1291 0.005 1.095 3.7 39.9 7.3 75 0.100 1_regHadp: 0.1130 0.1282 0.005 1.095 3.7 39.9 7.3 75 0.100 1_occ: 0.1113 0.1267 0.005 1.095 3.7 39.9 7.3 75 0.100 2_bss: 0.1110 0.1262 0.005 1.095 3.7 39.9 7.3 75 0.100 2_settarget: 0.1110 0.1262 0.005 1.095 3.7 39.9 7.3 75 0.100 2_updatecdl: 0.1110 0.1262 0.005 1.096 3.7 39.9 7.3 75 0.100 2_nqh: 0.1110 0.1262 0.005 1.096 3.7 39.9 7.3 75 0.100 2_realsrl: 0.1110 0.1262 0.005 1.096 3.7 39.9 7.3 75 0.100 2_weight: 0.1110 0.1262 0.005 1.096 3.7 39.9 7.3 75 0.100 2_xyzrec: 0.1051 0.1174 0.005 1.142 3.7 39.9 7.3 75 0.108 2_realsrl2: 0.1051 0.1174 0.005 1.142 3.7 39.9 7.3 75 0.108 2_adp: 0.1050 0.1174 0.005 1.142 3.7 39.9 7.3 75 0.108 2_regHadp: 0.1050 0.1174 0.005 1.142 3.7 39.9 7.3 75 0.108 2_occ: 0.1045 0.1167 0.005 1.142 3.7 39.9 7.3 75 0.108 3_bss: 0.1045 0.1171 0.005 1.142 3.6 39.9 7.3 75 0.108 3_settarget: 0.1045 0.1171 0.005 1.142 3.6 39.9 7.3 75 0.108 3_updatecdl: 0.1045 0.1171 0.005 1.209 3.6 39.9 7.3 75 0.108 3_nqh: 0.1045 0.1171 0.005 1.209 3.6 39.9 7.3 75 0.108 3_realsrl: 0.1045 0.1171 0.005 1.209 3.6 39.9 7.3 75 0.108 3_weight: 0.1045 0.1171 0.005 1.209 3.6 39.9 7.3 75 0.108 3_xyzrec: 0.0985 0.1068 0.008 1.464 3.6 39.9 7.3 75 0.104 3_realsrl2: 0.0985 0.1068 0.008 1.464 3.6 39.9 7.3 75 0.104 3_adp: 0.0987 0.1129 0.008 1.464 3.7 40.0 7.2 75 0.104 3_regHadp: 0.0987 0.1131 0.008 1.464 3.7 40.0 7.2 75 0.104 3_occ: 0.0985 0.1126 0.008 1.464 3.7 40.0 7.2 75 0.104 4_bss: 0.0982 0.1133 0.008 1.464 3.6 40.0 7.1 75 0.104 4_settarget: 0.0982 0.1133 0.008 1.464 3.6 40.0 7.1 75 0.104 4_updatecdl: 0.0982 0.1133 0.008 1.417 3.6 40.0 7.1 75 0.104 4_nqh: 0.0982 0.1133 0.008 1.417 3.6 40.0 7.1 75 0.104 4_realsrl: 0.1000 0.1156 0.008 1.417 3.6 40.0 7.1 75 0.113 4_weight: 0.1000 0.1156 0.008 1.417 3.6 40.0 7.1 75 0.113 4_xyzrec: 0.0980 0.1129 0.007 1.401 3.6 40.0 7.1 75 0.114 4_realsrl2: 0.0980 0.1129 0.007 1.401 3.6 40.0 7.1 75 0.114 4_adp: 0.0957 0.1124 0.007 1.401 3.6 40.1 7.2 75 0.114 4_regHadp: 0.0957 0.1123 0.007 1.401 3.6 40.1 7.2 75 0.114 4_occ: 0.0958 0.1123 0.007 1.401 3.6 40.1 7.2 75 0.114 5_bss: 0.0972 0.1136 0.007 1.401 3.6 40.1 7.2 75 0.114 5_settarget: 0.0972 0.1136 0.007 1.401 3.6 40.1 7.2 75 0.114 5_updatecdl: 0.0972 0.1136 0.007 1.401 3.6 40.1 7.2 75 0.114 5_setrh: 0.0973 0.1137 0.007 1.401 3.6 40.1 7.2 75 0.113 5_nqh: 0.0973 0.1137 0.007 1.401 3.6 40.1 7.2 75 0.113 5_realsrl: 0.0979 0.1143 0.007 1.401 3.6 40.1 7.2 75 0.113 5_weight: 0.0979 0.1143 0.007 1.401 3.6 40.1 7.2 75 0.113 5_xyzrec: 0.0971 0.1133 0.008 1.441 3.6 40.1 7.2 75 0.113 5_realsrl2: 0.0971 0.1133 0.008 1.441 3.6 40.1 7.2 75 0.113 5_adp: 0.0971 0.1132 0.008 1.441 3.7 40.1 7.2 75 0.113 5_regHadp: 0.0971 0.1132 0.008 1.441 3.7 40.1 7.2 75 0.113 5_occ: 0.0970 0.1132 0.008 1.441 3.7 40.1 7.2 75 0.113 end: 0.0971 0.1130 0.008 1.441 3.6 40.1 7.2 75 0.113 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/3NJW_complete_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/3NJW_complete_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 0.2600 Refinement macro-cycles (run) : 157.7600 Write final files (write_after_run_outputs) : 9.0500 Total : 167.0700 Total CPU time: 2.92 minutes =========================== phenix.refine: finished =========================== # Date 2024-04-10 Time 16:02:58 PDT -0700 (1712790178.15 s) Start R-work = 0.1004, R-free = 0.1018 Final R-work = 0.0971, R-free = 0.1130 =============================================================================== Job complete usr+sys time: 185.27 seconds wall clock time: 3 minutes 50.69 seconds (230.69 seconds total)