Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1785239.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1785239.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1785239.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } 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 { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.11, per 1000 atoms: 0.33 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 124.8 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.70 - 0.94: 678 0.94 - 1.18: 991 1.18 - 1.42: 612 1.42 - 1.66: 824 1.66 - 1.91: 48 Bond restraints: 3153 Sorted by residual: bond pdb=" C LEU A 58 " pdb=" N GLU A 59 " ideal model delta sigma weight residual 1.335 1.112 0.223 1.25e-02 6.40e+03 3.18e+02 bond pdb=" C ASP A 131 " pdb=" O ASP A 131 " ideal model delta sigma weight residual 1.236 1.048 0.188 1.15e-02 7.56e+03 2.67e+02 bond pdb=" C ALA A 178 " pdb=" O ALA A 178 " ideal model delta sigma weight residual 1.236 1.047 0.189 1.16e-02 7.43e+03 2.66e+02 bond pdb=" C LYS A 148 " pdb=" O LYS A 148 " ideal model delta sigma weight residual 1.235 1.052 0.183 1.13e-02 7.83e+03 2.62e+02 bond pdb=" C BASN A 76 " pdb=" O BASN A 76 " ideal model delta sigma weight residual 1.236 1.422 -0.185 1.15e-02 7.56e+03 2.60e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.01 - 4.47: 3047 4.47 - 8.94: 1843 8.94 - 13.40: 705 13.40 - 17.87: 149 17.87 - 22.34: 33 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH2 ARG A 5 " ideal model delta sigma weight residual 119.20 107.03 12.17 9.00e-01 1.23e+00 1.83e+02 angle pdb=" O VAL A 51 " pdb=" C VAL A 51 " pdb=" N ILE A 52 " ideal model delta sigma weight residual 123.10 108.05 15.05 1.17e+00 7.31e-01 1.65e+02 angle pdb=" CA VAL A 181 " pdb=" C VAL A 181 " pdb=" N LYS A 182 " ideal model delta sigma weight residual 117.15 103.15 14.00 1.14e+00 7.69e-01 1.51e+02 angle pdb=" O SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " ideal model delta sigma weight residual 123.26 111.16 12.10 1.05e+00 9.07e-01 1.33e+02 angle pdb=" O ALA A 79 " pdb=" C ALA A 79 " pdb=" N BGLN A 80 " ideal model delta sigma weight residual 122.07 133.82 -11.75 1.03e+00 9.43e-01 1.30e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.42: 1306 17.42 - 34.83: 122 34.83 - 52.24: 39 52.24 - 69.65: 11 69.65 - 87.06: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ASP A 49 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual -122.60 -144.90 22.30 0 2.50e+00 1.60e-01 7.96e+01 dihedral pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual 122.80 142.89 -20.09 0 2.50e+00 1.60e-01 6.45e+01 dihedral pdb=" C ALYS A 99 " pdb=" N ALYS A 99 " pdb=" CA ALYS A 99 " pdb=" CB ALYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -141.75 19.15 0 2.50e+00 1.60e-01 5.87e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.006 - 0.245: 107 0.245 - 0.483: 77 0.483 - 0.722: 46 0.722 - 0.960: 12 0.960 - 1.199: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 177 " pdb=" CA VAL A 177 " pdb=" CG1 VAL A 177 " pdb=" CG2 VAL A 177 " both_signs ideal model delta sigma weight residual False -2.63 -3.83 1.20 2.00e-01 2.50e+01 3.59e+01 chirality pdb=" CA BPRO A 66 " pdb=" N BPRO A 66 " pdb=" C BPRO A 66 " pdb=" CB BPRO A 66 " both_signs ideal model delta sigma weight residual False 2.72 3.66 -0.94 2.00e-01 2.50e+01 2.22e+01 chirality pdb=" CA ATYR A 67 " pdb=" N ATYR A 67 " pdb=" C ATYR A 67 " pdb=" CB ATYR A 67 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.21e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.104 2.00e-02 2.50e+03 6.84e-02 1.40e+02 pdb=" CG PHE A 119 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.077 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.075 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.048 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.099 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.043 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.098 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " 0.022 2.00e-02 2.50e+03 6.74e-02 1.36e+02 pdb=" CG PHE A 164 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.103 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.050 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.052 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.097 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.064 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.071 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.016 2.00e-02 2.50e+03 6.11e-02 1.12e+02 pdb=" CG TYR A 139 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.097 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.098 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.069 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.064 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.098 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.038 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.33: 1110 2.33 - 2.90: 8216 2.90 - 3.47: 10433 3.47 - 4.03: 15222 4.03 - 4.60: 21585 Nonbonded interactions: 56566 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.767 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.794 2.100 nonbonded pdb="HH21 ARG A 145 " pdb=" OE1 GLU A 163 " model vdw 1.802 2.450 nonbonded pdb=" H LEU A 72 " pdb=" O ALA A 103 " model vdw 1.808 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.816 2.100 ... (remaining 56561 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: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 2 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 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 ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 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 = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 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 { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_1785239_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2796 r_free= 0.1799 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.414217 | | target function (ml) not normalized (work): 71700.133905 | | target function (ml) not normalized (free): 3250.495201 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3198 0.2119 7.6072 5.03| | 2: 3.63 - 2.88 1.00 2711 122 0.2654 0.1642 4.3245 4.3071| | 3: 2.88 - 2.52 1.00 2682 148 0.2571 0.1740 4.1746 4.1804| | 4: 2.52 - 2.29 1.00 2661 139 0.2586 0.1486 3.5208 3.5481| | 5: 2.29 - 2.13 1.00 2678 122 0.2654 0.1529 3.3922 3.397| | 6: 2.13 - 2.00 1.00 2692 117 0.2720 0.1849 3.2995 3.4098| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 49.25 - 3.64 2819 159 0.88 17.34 0.77 0.23 1268.05| | 2: 3.63 - 2.88 2711 122 0.83 23.58 1.32 0.23 1268.05| | 3: 2.88 - 2.52 2682 148 0.74 32.50 1.28 0.23 1268.05| | 4: 2.52 - 2.29 2661 139 0.93 11.18 1.30 0.26 132.15| | 5: 2.29 - 2.13 2678 122 0.92 13.46 1.32 0.26 132.15| | 6: 2.13 - 2.00 2692 117 0.90 15.95 1.33 0.26 132.15| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 132.15 max = 1268.05 mean = 706.43| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.64 mean = 19.00| |phase err.(test): min = 0.00 max = 89.69 mean = 18.98| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.262 1557 Z= 5.552 Angle : 5.304 16.410 2118 Z= 3.719 Chirality : 0.393 1.199 243 Planarity : 0.031 0.096 284 Dihedral : 13.616 87.058 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 31.35 % Peptide Plane: Cis-proline : 18.18 % 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: -2.89 (0.48), residues: 224 helix: -2.45 (0.37), residues: 109 sheet: -1.32 (0.79), residues: 40 loop : -0.94 (0.66), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.074 0.019 ARG A 27 TYR 0.081 0.038 TYR A 139 PHE 0.111 0.046 PHE A 119 HIS 0.059 0.027 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2796 r_free= 0.1799 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.414217 | | target function (ml) not normalized (work): 71700.133905 | | target function (ml) not normalized (free): 3250.495201 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2925 percent. r_work = 0.2925 r_free = 0.1960 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2871 0.2925 0.1960 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2871 0.2925 0.1960 n_refl.: 17050 remove outliers: r(all,work,free)=0.2165 0.2177 0.1960 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2139 0.2151 0.1942 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1623 0.1621 0.1655 n_refl.: 17045 remove outliers: r(all,work,free)=0.1621 0.1619 0.1655 n_refl.: 17043 ======================== 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 32.574-12.150 98.94 88 5 0.3907 399.199 360.600 0.651 1.017 0.403 11.894-9.307 99.02 97 4 0.1833 634.022 615.717 0.923 1.018 0.390 9.237-7.194 100.00 213 7 0.2146 518.566 510.452 0.956 1.017 0.351 7.162-5.571 100.00 427 22 0.2289 389.185 375.037 0.916 1.015 0.290 5.546-4.326 100.00 867 58 0.1406 534.288 528.384 0.955 1.013 0.251 4.315-3.360 100.00 1859 96 0.1296 508.113 504.645 1.016 1.007 0.201 3.356-2.611 100.00 3867 181 0.1669 333.801 329.382 1.013 0.999 0.101 2.608-2.000 99.99 8818 434 0.1659 217.581 213.797 1.037 0.983 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4401 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1619 r_free=0.1655 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 80 GLN B A 173 ASN Total number of N/Q/H flips: 3 r_work=0.1625 r_free=0.1669 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.836998 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.942707 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1349 0.1643 0.0294 0.009 1.0 1.0 0.5 0.0 0 11.918 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.49 16.43 2.94 3.013 18.455 0.943 0.023 12.77 16.57 3.80 3.566 18.682 0.943 0.020 Individual atomic B min max mean iso aniso Overall: 6.14 113.89 19.91 4.09 1785 0 Protein: 6.14 113.48 17.14 4.09 1519 0 Water: 8.40 113.89 36.06 N/A 258 0 Other: 21.67 37.43 26.17 N/A 8 0 Chain A: 6.14 113.89 19.91 N/A 1785 0 Histogram: Values Number of atoms 6.14 - 16.91 1083 16.91 - 27.69 344 27.69 - 38.46 184 38.46 - 49.24 97 49.24 - 60.02 50 60.02 - 70.79 12 70.79 - 81.57 7 81.57 - 92.34 4 92.34 - 103.12 1 103.12 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1277 r_free=0.1657 r_work=0.1280 r_free=0.1664 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1280 r_free = 0.1664 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1278 r_free = 0.1677 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1278 r_free= 0.1677 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020028 | | target function (ls_wunit_k1) not normalized (work): 325.170143 | | target function (ls_wunit_k1) not normalized (free): 27.807511 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1297 0.1278 0.1677 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1906 0.1905 0.1987 n_refl.: 17043 remove outliers: r(all,work,free)=0.1906 0.1905 0.1987 n_refl.: 17043 overall B=-0.37 to atoms: r(all,work,free)=0.1879 0.1877 0.1972 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1295 0.1277 0.1660 n_refl.: 17043 remove outliers: r(all,work,free)=0.1294 0.1275 0.1660 n_refl.: 17041 ======================== 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 32.574-12.150 94.79 86 5 0.3537 306.695 280.875 0.624 1.006 0.368 11.894-9.307 99.02 97 4 0.1704 487.998 476.996 0.916 1.006 0.367 9.237-7.194 100.00 213 7 0.1818 399.133 395.760 0.960 1.006 0.340 7.162-5.571 100.00 427 22 0.1859 299.550 293.618 0.923 1.006 0.269 5.546-4.326 100.00 867 58 0.1061 411.233 407.916 0.957 1.005 0.215 4.315-3.360 100.00 1859 96 0.0928 391.087 390.581 1.017 1.003 0.191 3.356-2.611 100.00 3867 181 0.1296 256.922 255.668 1.013 1.001 0.101 2.608-2.000 99.99 8818 434 0.1348 167.469 166.146 1.017 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3368 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1660 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 80 GLN B A 173 ASN Total number of N/Q/H flips: 3 r_work=0.1277 r_free=0.1662 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1662 | n_water=258 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.1283 r_free=0.1653 | n_water=253 | time (s): 20.150 (total time: 20.760) Filter (q & B) r_work=0.1283 r_free=0.1652 | n_water=251 | time (s): 1.650 (total time: 22.410) Compute maps r_work=0.1283 r_free=0.1652 | n_water=251 | time (s): 0.520 (total time: 22.930) Filter (map) r_work=0.1315 r_free=0.1660 | n_water=216 | time (s): 1.760 (total time: 24.690) Find peaks r_work=0.1315 r_free=0.1660 | n_water=216 | time (s): 0.550 (total time: 25.240) Add new water r_work=0.1522 r_free=0.1873 | n_water=376 | time (s): 1.470 (total time: 26.710) Refine new water occ: r_work=0.1325 r_free=0.1611 adp: r_work=0.1271 r_free=0.1604 occ: r_work=0.1277 r_free=0.1586 adp: r_work=0.1245 r_free=0.1585 occ: r_work=0.1247 r_free=0.1570 adp: r_work=0.1235 r_free=0.1572 ADP+occupancy (water only), MIN, final r_work=0.1235 r_free=0.1572 r_work=0.1235 r_free=0.1572 | n_water=376 | time (s): 20.170 (total time: 46.880) Filter (q & B) r_work=0.1238 r_free=0.1579 | n_water=366 | time (s): 1.700 (total time: 48.580) Filter (dist only) r_work=0.1238 r_free=0.1581 | n_water=365 | time (s): 30.040 (total time: 78.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.882928 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.998838 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1212 0.1620 0.0408 0.008 0.9 2.9 0.5 0.0 0 12.441 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 16.20 4.08 4.171 21.007 0.999 0.018 11.97 16.36 4.39 4.201 21.358 0.999 0.018 Individual atomic B min max mean iso aniso Overall: 6.97 108.10 21.47 4.42 1892 0 Protein: 6.97 108.10 17.90 4.41 1519 0 Water: 8.43 68.58 36.18 N/A 365 0 Other: 22.63 38.50 28.61 N/A 8 0 Chain A: 6.97 108.10 19.67 N/A 1743 0 Chain S: 18.42 68.55 42.54 N/A 149 0 Histogram: Values Number of atoms 6.97 - 17.09 1048 17.09 - 27.20 358 27.20 - 37.31 219 37.31 - 47.43 162 47.43 - 57.54 65 57.54 - 67.65 27 67.65 - 77.77 5 77.77 - 87.88 4 87.88 - 97.99 2 97.99 - 108.10 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1636 r_work=0.1199 r_free=0.1639 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1639 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1637 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1193 r_free= 0.1637 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016925 | | target function (ls_wunit_k1) not normalized (work): 274.759592 | | target function (ls_wunit_k1) not normalized (free): 25.806270 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1193 0.1637 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1749 0.1740 0.1947 n_refl.: 17041 remove outliers: r(all,work,free)=0.1749 0.1740 0.1947 n_refl.: 17041 overall B=-0.38 to atoms: r(all,work,free)=0.1724 0.1715 0.1931 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1191 0.1631 n_refl.: 17041 remove outliers: r(all,work,free)=0.1212 0.1191 0.1631 n_refl.: 17041 ======================== 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 32.574-12.150 94.79 86 5 0.3216 306.695 289.552 0.601 1.005 0.350 11.894-9.307 99.02 97 4 0.1535 487.998 485.571 0.913 1.006 0.340 9.237-7.194 100.00 213 7 0.1640 399.133 399.806 0.971 1.006 0.310 7.162-5.571 100.00 427 22 0.1559 299.550 295.311 0.930 1.005 0.281 5.546-4.326 100.00 867 58 0.0886 411.233 408.070 0.958 1.005 0.211 4.315-3.360 100.00 1859 96 0.0819 391.087 390.436 1.016 1.003 0.201 3.356-2.611 100.00 3867 181 0.1204 256.922 256.280 1.013 1.001 0.058 2.608-2.000 99.99 8818 434 0.1333 167.469 166.458 1.018 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3611 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1631 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 97 ASN B Total number of N/Q/H flips: 2 r_work=0.1193 r_free=0.1636 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1636 | n_water=365 | time (s): 0.910 (total time: 0.910) Filter (dist) r_work=0.1193 r_free=0.1636 | n_water=365 | time (s): 29.190 (total time: 30.100) Filter (q & B) r_work=0.1193 r_free=0.1636 | n_water=365 | time (s): 0.920 (total time: 31.020) Compute maps r_work=0.1193 r_free=0.1636 | n_water=365 | time (s): 0.710 (total time: 31.730) Filter (map) r_work=0.1260 r_free=0.1654 | n_water=258 | time (s): 2.270 (total time: 34.000) Find peaks r_work=0.1260 r_free=0.1654 | n_water=258 | time (s): 0.610 (total time: 34.610) Add new water r_work=0.1456 r_free=0.1816 | n_water=413 | time (s): 1.510 (total time: 36.120) Refine new water occ: r_work=0.1255 r_free=0.1593 adp: r_work=0.1248 r_free=0.1592 occ: r_work=0.1229 r_free=0.1566 adp: r_work=0.1220 r_free=0.1567 occ: r_work=0.1210 r_free=0.1547 adp: r_work=0.1200 r_free=0.1545 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1545 r_work=0.1200 r_free=0.1545 | n_water=413 | time (s): 31.950 (total time: 68.070) Filter (q & B) r_work=0.1202 r_free=0.1548 | n_water=405 | time (s): 2.020 (total time: 70.090) Filter (dist only) r_work=0.1202 r_free=0.1548 | n_water=405 | time (s): 31.040 (total time: 101.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.958698 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.183396 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1182 0.1548 0.0366 0.009 1.0 4.8 0.5 0.0 0 0.979 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.82 15.48 3.66 4.438 21.694 0.183 4.994 11.59 15.43 3.84 5.016 21.623 0.183 4.969 Individual atomic B min max mean iso aniso Overall: 6.18 107.38 21.02 4.84 1932 0 Protein: 6.18 107.38 17.19 4.84 1519 0 Water: 8.91 64.67 35.30 N/A 405 0 Other: 19.53 38.49 26.17 N/A 8 0 Chain A: 6.18 107.38 18.96 N/A 1739 0 Chain S: 15.38 64.67 39.59 N/A 193 0 Histogram: Values Number of atoms 6.18 - 16.30 1066 16.30 - 26.42 356 26.42 - 36.54 219 36.54 - 46.66 183 46.66 - 56.78 71 56.78 - 66.90 24 66.90 - 77.02 5 77.02 - 87.14 4 87.14 - 97.26 2 97.26 - 107.38 2 =========================== Idealize ADP of riding H ========================== r_work=0.1159 r_free=0.1543 r_work=0.1159 r_free=0.1544 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1159 r_free = 0.1544 target_work(ml) = 4.969 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1148 r_free = 0.1539 target_work(ml) = 4.962 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1148 r_free= 0.1539 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.962371 | | target function (ml) not normalized (work): 80559.128295 | | target function (ml) not normalized (free): 4184.668071 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1167 0.1148 0.1539 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1671 0.1664 0.1861 n_refl.: 17041 remove outliers: r(all,work,free)=0.1671 0.1664 0.1861 n_refl.: 17041 overall B=-0.38 to atoms: r(all,work,free)=0.1645 0.1637 0.1847 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1164 0.1145 0.1536 n_refl.: 17041 remove outliers: r(all,work,free)=0.1163 0.1144 0.1536 n_refl.: 17040 ======================== 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 32.574-12.150 93.75 85 5 0.3643 303.202 280.855 0.561 1.005 0.340 11.894-9.307 99.02 97 4 0.1807 487.998 480.119 0.910 1.006 0.324 9.237-7.194 100.00 213 7 0.1781 399.133 399.374 0.979 1.007 0.275 7.162-5.571 100.00 427 22 0.1613 299.550 294.221 0.939 1.006 0.271 5.546-4.326 100.00 867 58 0.0947 411.233 407.772 0.961 1.005 0.211 4.315-3.360 100.00 1859 96 0.0887 391.087 388.621 1.013 1.004 0.201 3.356-2.611 100.00 3867 181 0.1290 256.922 254.600 1.013 1.001 0.131 2.608-2.000 99.99 8818 434 0.1078 167.469 166.079 1.019 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3679 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1144 r_free=0.1536 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1144 r_free=0.1536 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1144 r_free=0.1536 | n_water=405 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.1144 r_free=0.1536 | n_water=405 | time (s): 31.290 (total time: 31.930) Filter (q & B) r_work=0.1145 r_free=0.1538 | n_water=404 | time (s): 2.180 (total time: 34.110) Compute maps r_work=0.1145 r_free=0.1538 | n_water=404 | time (s): 0.630 (total time: 34.740) Filter (map) r_work=0.1200 r_free=0.1573 | n_water=314 | time (s): 2.080 (total time: 36.820) Find peaks r_work=0.1200 r_free=0.1573 | n_water=314 | time (s): 0.660 (total time: 37.480) Add new water r_work=0.1348 r_free=0.1685 | n_water=462 | time (s): 1.890 (total time: 39.370) Refine new water occ: r_work=0.1177 r_free=0.1496 adp: r_work=0.1169 r_free=0.1502 occ: r_work=0.1154 r_free=0.1478 adp: r_work=0.1146 r_free=0.1481 occ: r_work=0.1138 r_free=0.1467 adp: r_work=0.1132 r_free=0.1468 ADP+occupancy (water only), MIN, final r_work=0.1132 r_free=0.1468 r_work=0.1132 r_free=0.1468 | n_water=462 | time (s): 47.500 (total time: 86.870) Filter (q & B) r_work=0.1135 r_free=0.1474 | n_water=449 | time (s): 1.590 (total time: 88.460) Filter (dist only) r_work=0.1138 r_free=0.1479 | n_water=447 | time (s): 34.590 (total time: 123.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.881613 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.164359 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1125 0.1514 0.0389 0.009 1.0 3.8 0.5 0.0 0 0.941 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.25 15.14 3.89 4.606 21.279 0.164 4.949 11.13 15.27 4.14 4.743 21.340 0.164 4.943 Individual atomic B min max mean iso aniso Overall: 5.70 106.11 21.21 4.95 1974 0 Protein: 5.70 106.11 16.80 4.95 1519 0 Water: 8.72 65.32 36.13 N/A 447 0 Other: 17.45 34.43 23.77 N/A 8 0 Chain A: 5.70 106.11 18.51 N/A 1738 0 Chain S: 19.06 65.32 41.06 N/A 236 0 Histogram: Values Number of atoms 5.70 - 15.74 1051 15.74 - 25.78 368 25.78 - 35.82 231 35.82 - 45.86 185 45.86 - 55.90 98 55.90 - 65.95 27 65.95 - 75.99 6 75.99 - 86.03 4 86.03 - 96.07 2 96.07 - 106.11 2 =========================== Idealize ADP of riding H ========================== r_work=0.1113 r_free=0.1527 r_work=0.1113 r_free=0.1528 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1113 r_free = 0.1528 target_work(ml) = 4.944 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1106 r_free = 0.1527 target_work(ml) = 4.940 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1106 r_free= 0.1527 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.939778 | | target function (ml) not normalized (work): 80187.414081 | | target function (ml) not normalized (free): 4174.342265 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1126 0.1106 0.1527 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1603 0.1592 0.1859 n_refl.: 17040 remove outliers: r(all,work,free)=0.1603 0.1592 0.1859 n_refl.: 17040 overall B=-0.32 to atoms: r(all,work,free)=0.1582 0.1570 0.1847 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1123 0.1103 0.1524 n_refl.: 17040 remove outliers: r(all,work,free)=0.1123 0.1103 0.1524 n_refl.: 17040 ======================== 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 32.574-12.150 93.75 85 5 0.3605 303.202 280.022 0.549 1.000 0.330 11.894-9.307 99.02 97 4 0.1758 487.998 481.294 0.923 1.001 0.320 9.237-7.194 100.00 213 7 0.1732 399.133 400.546 0.983 1.002 0.240 7.162-5.571 100.00 427 22 0.1567 299.550 293.503 0.944 1.002 0.241 5.546-4.326 100.00 867 58 0.0905 411.233 407.603 0.966 1.002 0.196 4.315-3.360 100.00 1859 96 0.0855 391.087 388.608 1.011 1.002 0.191 3.356-2.611 100.00 3867 181 0.1235 256.922 254.464 1.008 1.001 0.141 2.608-2.000 99.99 8818 434 0.1042 167.469 166.279 1.006 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1238 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1103 r_free=0.1524 After: r_work=0.1105 r_free=0.1523 ================================== NQH flips ================================== r_work=0.1105 r_free=0.1523 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1105 r_free=0.1523 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1105 r_free=0.1523 | n_water=447 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.1105 r_free=0.1522 | n_water=446 | time (s): 37.230 (total time: 37.940) Filter (q & B) r_work=0.1105 r_free=0.1522 | n_water=446 | time (s): 0.900 (total time: 38.840) Compute maps r_work=0.1105 r_free=0.1522 | n_water=446 | time (s): 0.690 (total time: 39.530) Filter (map) r_work=0.1177 r_free=0.1569 | n_water=330 | time (s): 1.550 (total time: 41.080) Find peaks r_work=0.1177 r_free=0.1569 | n_water=330 | time (s): 0.430 (total time: 41.510) Add new water r_work=0.1304 r_free=0.1669 | n_water=473 | time (s): 1.850 (total time: 43.360) Refine new water occ: r_work=0.1140 r_free=0.1512 adp: r_work=0.1134 r_free=0.1518 occ: r_work=0.1121 r_free=0.1492 adp: r_work=0.1114 r_free=0.1498 occ: r_work=0.1107 r_free=0.1478 adp: r_work=0.1101 r_free=0.1483 ADP+occupancy (water only), MIN, final r_work=0.1101 r_free=0.1483 r_work=0.1101 r_free=0.1483 | n_water=473 | time (s): 34.640 (total time: 78.000) Filter (q & B) r_work=0.1106 r_free=0.1488 | n_water=462 | time (s): 1.720 (total time: 79.720) Filter (dist only) r_work=0.1106 r_free=0.1488 | n_water=462 | time (s): 34.980 (total time: 114.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.035009 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.145018 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1116 0.1522 0.0405 0.010 1.1 5.1 0.5 0.0 0 1.018 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.16 15.22 4.05 4.634 21.012 0.145 4.942 11.09 15.06 3.96 4.722 21.034 0.145 4.931 Individual atomic B min max mean iso aniso Overall: 5.35 103.42 21.01 4.98 1989 0 Protein: 5.35 103.42 16.45 4.99 1519 0 Water: 8.63 64.25 35.93 N/A 462 0 Other: 18.24 35.07 24.67 N/A 8 0 Chain A: 5.35 103.42 18.10 N/A 1737 0 Chain S: 19.18 64.25 41.04 N/A 252 0 Histogram: Values Number of atoms 5.35 - 15.15 1025 15.15 - 24.96 379 24.96 - 34.77 228 34.77 - 44.58 199 44.58 - 54.39 114 54.39 - 64.19 27 64.19 - 74.00 8 74.00 - 83.81 4 83.81 - 93.62 1 93.62 - 103.42 4 =========================== Idealize ADP of riding H ========================== r_work=0.1109 r_free=0.1506 r_work=0.1109 r_free=0.1506 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1109 r_free = 0.1506 target_work(ml) = 4.931 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1104 r_free = 0.1502 target_work(ml) = 4.926 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1104 r_free= 0.1502 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.926031 | | target function (ml) not normalized (work): 79964.268531 | | target function (ml) not normalized (free): 4156.416826 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1135 0.1370 5.4639 5.657| | 2: 3.63 - 2.88 1.00 2711 122 0.1092 0.1473 5.2174 5.3227| | 3: 2.88 - 2.52 1.00 2681 148 0.1339 0.1724 5.123 5.2115| | 4: 2.52 - 2.29 1.00 2661 139 0.0919 0.1501 4.6069 4.9298| | 5: 2.29 - 2.13 1.00 2678 122 0.0949 0.1482 4.561 4.8722| | 6: 2.13 - 2.00 1.00 2692 117 0.1100 0.1691 4.5534 4.7574| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 32.57 - 3.64 2810 159 0.95 9.04 1.00 0.96 6367.19| | 2: 3.63 - 2.88 2711 122 0.92 12.85 1.01 0.96 6367.19| | 3: 2.88 - 2.52 2681 148 0.87 19.04 0.99 0.96 6367.19| | 4: 2.52 - 2.29 2661 139 0.93 11.83 1.01 0.98 2025.74| | 5: 2.29 - 2.13 2678 122 0.92 13.75 1.00 0.98 2025.74| | 6: 2.13 - 2.00 2692 117 0.90 16.40 0.99 0.98 2025.74| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2025.74 max = 6367.19 mean = 4219.33| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.88 mean = 13.78| |phase err.(test): min = 0.00 max = 88.79 mean = 13.56| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1123 0.1104 0.1502 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1573 0.1561 0.1824 n_refl.: 17040 remove outliers: r(all,work,free)=0.1573 0.1561 0.1824 n_refl.: 17040 overall B=-0.28 to atoms: r(all,work,free)=0.1556 0.1544 0.1814 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1124 0.1105 0.1500 n_refl.: 17040 remove outliers: r(all,work,free)=0.1124 0.1105 0.1500 n_refl.: 17040 ======================== 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 32.574-12.150 93.75 85 5 0.3724 303.202 278.875 0.539 1.001 0.330 11.894-9.307 99.02 97 4 0.1756 487.998 480.673 0.922 1.002 0.330 9.237-7.194 100.00 213 7 0.1806 399.133 401.472 0.982 1.003 0.234 7.162-5.571 100.00 427 22 0.1646 299.550 293.061 0.938 1.002 0.210 5.546-4.326 100.00 867 58 0.0940 411.233 407.873 0.966 1.002 0.181 4.315-3.360 100.00 1859 96 0.0868 391.087 388.602 1.009 1.002 0.181 3.356-2.611 100.00 3867 181 0.1231 256.922 254.584 1.006 1.001 0.151 2.608-2.000 99.99 8818 434 0.1021 167.469 166.195 0.999 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9777 ================= 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_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2796 0.1799 0.082 5.304 8.8 119.3 19.9 258 0.000 1_bss: 0.1619 0.1655 0.082 5.304 8.4 118.9 19.5 258 0.000 1_settarget: 0.1619 0.1655 0.082 5.304 8.4 118.9 19.5 258 0.000 1_nqh: 0.1625 0.1669 0.082 5.304 8.4 118.9 19.5 258 0.010 1_weight: 0.1625 0.1669 0.082 5.304 8.4 118.9 19.5 258 0.010 1_xyzrec: 0.1349 0.1643 0.009 0.990 8.4 118.9 19.5 258 0.152 1_adp: 0.1277 0.1657 0.009 0.990 6.1 113.9 19.9 258 0.152 1_regHadp: 0.1280 0.1664 0.009 0.990 6.1 113.9 19.9 258 0.152 1_occ: 0.1278 0.1677 0.009 0.990 6.1 113.9 19.9 258 0.152 2_bss: 0.1275 0.1660 0.009 0.990 5.8 113.5 19.5 258 0.152 2_settarget: 0.1275 0.1660 0.009 0.990 5.8 113.5 19.5 258 0.152 2_updatecdl: 0.1275 0.1660 0.009 1.003 5.8 113.5 19.5 258 0.152 2_nqh: 0.1277 0.1662 0.009 1.003 5.8 113.5 19.5 258 0.144 2_sol: 0.1238 0.1581 0.009 1.003 5.8 113.1 20.8 365 n/a 2_weight: 0.1238 0.1581 0.009 1.003 5.8 113.1 20.8 365 n/a 2_xyzrec: 0.1212 0.1620 0.008 0.929 5.8 113.1 20.8 365 n/a 2_adp: 0.1197 0.1636 0.008 0.929 7.0 108.1 21.5 365 n/a 2_regHadp: 0.1199 0.1639 0.008 0.929 7.0 108.1 21.5 365 n/a 2_occ: 0.1193 0.1637 0.008 0.929 7.0 108.1 21.5 365 n/a 3_bss: 0.1191 0.1631 0.008 0.929 6.6 107.7 21.1 365 n/a 3_settarget: 0.1191 0.1631 0.008 0.929 6.6 107.7 21.1 365 n/a 3_updatecdl: 0.1191 0.1631 0.008 0.929 6.6 107.7 21.1 365 n/a 3_nqh: 0.1193 0.1636 0.008 0.929 6.6 107.7 21.1 365 n/a 3_sol: 0.1202 0.1548 0.008 0.929 6.6 107.7 21.2 405 n/a 3_weight: 0.1202 0.1548 0.008 0.929 6.6 107.7 21.2 405 n/a 3_xyzrec: 0.1182 0.1548 0.009 0.966 6.6 107.7 21.2 405 n/a 3_adp: 0.1159 0.1543 0.009 0.966 6.2 107.4 21.0 405 n/a 3_regHadp: 0.1159 0.1544 0.009 0.966 6.2 107.4 21.0 405 n/a 3_occ: 0.1148 0.1539 0.009 0.966 6.2 107.4 21.0 405 n/a 4_bss: 0.1144 0.1536 0.009 0.966 5.8 107.0 20.6 405 n/a 4_settarget: 0.1144 0.1536 0.009 0.966 5.8 107.0 20.6 405 n/a 4_updatecdl: 0.1144 0.1536 0.009 0.967 5.8 107.0 20.6 405 n/a 4_nqh: 0.1144 0.1536 0.009 0.967 5.8 107.0 20.6 405 n/a 4_sol: 0.1138 0.1479 0.009 0.967 5.8 107.0 21.1 447 n/a 4_weight: 0.1138 0.1479 0.009 0.967 5.8 107.0 21.1 447 n/a 4_xyzrec: 0.1125 0.1514 0.009 0.972 5.8 107.0 21.1 447 n/a 4_adp: 0.1113 0.1527 0.009 0.972 5.7 106.1 21.2 447 n/a 4_regHadp: 0.1113 0.1528 0.009 0.972 5.7 106.1 21.2 447 n/a 4_occ: 0.1106 0.1527 0.009 0.972 5.7 106.1 21.2 447 n/a 5_bss: 0.1103 0.1524 0.009 0.972 5.4 105.8 20.9 447 n/a 5_settarget: 0.1103 0.1524 0.009 0.972 5.4 105.8 20.9 447 n/a 5_updatecdl: 0.1103 0.1524 0.009 0.973 5.4 105.8 20.9 447 n/a 5_setrh: 0.1105 0.1523 0.009 0.973 5.4 105.8 20.9 447 n/a 5_nqh: 0.1105 0.1523 0.009 0.973 5.4 105.8 20.9 447 n/a 5_sol: 0.1106 0.1488 0.009 0.973 5.4 105.8 21.0 462 n/a 5_weight: 0.1106 0.1488 0.009 0.973 5.4 105.8 21.0 462 n/a 5_xyzrec: 0.1116 0.1522 0.010 1.066 5.4 105.8 21.0 462 n/a 5_adp: 0.1109 0.1506 0.010 1.066 5.3 103.4 21.0 462 n/a 5_regHadp: 0.1109 0.1506 0.010 1.066 5.3 103.4 21.0 462 n/a 5_occ: 0.1104 0.1502 0.010 1.066 5.3 103.4 21.0 462 n/a end: 0.1105 0.1500 0.010 1.066 5.1 103.1 20.7 462 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_1785239_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_1785239_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8300 Refinement macro-cycles (run) : 949.6800 Write final files (write_after_run_outputs) : 17.7400 Total : 971.2500 Total CPU time: 16.53 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:31 PST -0800 (1735494091.88 s) Start R-work = 0.1619, R-free = 0.1655 Final R-work = 0.1105, R-free = 0.1500 =============================================================================== Job complete usr+sys time: 1011.47 seconds wall clock time: 17 minutes 13.53 seconds (1033.53 seconds total)