Starting phenix.refine on Sun Dec 29 09:24:42 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8960824.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_8960824.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8960824.pdb" 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" 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" } 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 4 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: 1.21, per 1000 atoms: 0.36 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: 0.28 Conformation dependent library (CDL) restraints added in 115.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 431 0.89 - 1.16: 1194 1.16 - 1.42: 654 1.42 - 1.68: 837 1.68 - 1.94: 37 Bond restraints: 3153 Sorted by residual: bond pdb=" N LEU A 112 " pdb=" CA LEU A 112 " ideal model delta sigma weight residual 1.459 1.687 -0.229 1.16e-02 7.43e+03 3.89e+02 bond pdb=" C LEU A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 1.335 1.593 -0.258 1.35e-02 5.49e+03 3.65e+02 bond pdb=" N LEU A 101 " pdb=" CA LEU A 101 " ideal model delta sigma weight residual 1.456 1.673 -0.217 1.22e-02 6.72e+03 3.17e+02 bond pdb=" N SER A 161 " pdb=" CA SER A 161 " ideal model delta sigma weight residual 1.459 1.661 -0.202 1.20e-02 6.94e+03 2.84e+02 bond pdb=" CA VAL A 35 " pdb=" C VAL A 35 " ideal model delta sigma weight residual 1.526 1.338 0.188 1.13e-02 7.83e+03 2.77e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 3126 4.69 - 9.38: 1925 9.38 - 14.07: 595 14.07 - 18.76: 114 18.76 - 23.44: 17 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.32 131.10 -11.78 7.40e-01 1.83e+00 2.53e+02 angle pdb=" CA MET A 133 " pdb=" C MET A 133 " pdb=" O MET A 133 " ideal model delta sigma weight residual 120.55 137.01 -16.46 1.06e+00 8.90e-01 2.41e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH1 ARG A 145 " ideal model delta sigma weight residual 121.50 135.28 -13.78 1.00e+00 1.00e+00 1.90e+02 angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH1 ARG A 27 " ideal model delta sigma weight residual 121.50 108.76 12.74 1.00e+00 1.00e+00 1.62e+02 angle pdb=" CA ALA A 107 " pdb=" C ALA A 107 " pdb=" O ALA A 107 " ideal model delta sigma weight residual 119.18 134.20 -15.02 1.19e+00 7.06e-01 1.59e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 19.06: 1320 19.06 - 38.11: 114 38.11 - 57.16: 39 57.16 - 76.20: 7 76.20 - 95.25: 1 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N GLU A 116 " pdb=" C GLU A 116 " pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " ideal model delta harmonic sigma weight residual 122.80 141.08 -18.28 0 2.50e+00 1.60e-01 5.34e+01 dihedral pdb=" C AGLU A 94 " pdb=" N AGLU A 94 " pdb=" CA AGLU A 94 " pdb=" CB AGLU A 94 " ideal model delta harmonic sigma weight residual -122.60 -140.50 17.90 0 2.50e+00 1.60e-01 5.13e+01 dihedral pdb=" N AGLU A 94 " pdb=" C AGLU A 94 " pdb=" CA AGLU A 94 " pdb=" CB AGLU A 94 " ideal model delta harmonic sigma weight residual 122.80 140.61 -17.81 0 2.50e+00 1.60e-01 5.08e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.182: 80 0.182 - 0.362: 69 0.362 - 0.543: 54 0.543 - 0.724: 21 0.724 - 0.905: 19 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ARG A 156 " pdb=" N ARG A 156 " pdb=" C ARG A 156 " pdb=" CB ARG A 156 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CB VAL A 169 " pdb=" CA VAL A 169 " pdb=" CG1 VAL A 169 " pdb=" CG2 VAL A 169 " both_signs ideal model delta sigma weight residual False -2.63 -3.53 0.90 2.00e-01 2.50e+01 2.03e+01 chirality pdb=" CA ARG A 98 " pdb=" N ARG A 98 " pdb=" C ARG A 98 " pdb=" CB ARG A 98 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.02e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.055 2.00e-02 2.50e+03 6.39e-02 1.22e+02 pdb=" CG TYR A 141 " -0.125 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.071 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.073 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.017 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.106 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.023 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.063 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.024 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.058 2.00e-02 2.50e+03 6.29e-02 1.19e+02 pdb=" CG PHE A 164 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.106 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.105 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.078 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.088 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.018 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.055 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.037 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.042 2.00e-02 2.50e+03 6.06e-02 1.10e+02 pdb=" CG PHE A 119 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.141 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.037 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.044 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.037 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.023 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.086 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.054 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.047 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1020 2.32 - 2.89: 8040 2.89 - 3.46: 10588 3.46 - 4.03: 15216 4.03 - 4.60: 21742 Nonbonded interactions: 56606 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.749 2.100 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.812 2.450 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.831 2.270 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.832 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.839 2.450 ... (remaining 56601 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_8960824_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= 0.2788 r_free= 0.1872 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.387628 | | target function (ml) not normalized (work): 71268.244399 | | target function (ml) not normalized (free): 3273.258433 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3194 0.2265 7.4487 5.0458| | 2: 3.63 - 2.88 1.00 2711 122 0.2642 0.1703 4.3333 4.3433| | 3: 2.88 - 2.52 1.00 2682 148 0.2568 0.1711 4.1952 4.2115| | 4: 2.52 - 2.29 1.00 2661 139 0.2526 0.1709 3.4924 3.6372| | 5: 2.29 - 2.13 1.00 2678 122 0.2639 0.1463 3.3881 3.4307| | 6: 2.13 - 2.00 1.00 2692 117 0.2781 0.1799 3.3078 3.3647| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.79 0.77 0.23 1344.52| | 2: 3.63 - 2.88 2711 122 0.82 24.24 1.31 0.23 1344.52| | 3: 2.88 - 2.52 2682 148 0.73 33.27 1.29 0.23 1344.52| | 4: 2.52 - 2.29 2661 139 0.93 11.41 1.30 0.26 136.21| | 5: 2.29 - 2.13 2678 122 0.92 13.66 1.32 0.26 136.21| | 6: 2.13 - 2.00 2692 117 0.90 16.42 1.34 0.26 136.21| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 136.21 max = 1344.52 mean = 747.10| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 90.00 mean = 19.47| |phase err.(test): min = 0.00 max = 89.16 mean = 19.61| |-----------------------------------------------------------------------------| ----------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 0.267 1557 Z= 5.430 Angle : 5.342 16.459 2118 Z= 3.797 Chirality : 0.396 0.905 243 Planarity : 0.033 0.105 284 Dihedral : 14.246 95.252 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 32.43 % 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: -2.97 (0.45), residues: 224 helix: -3.06 (0.33), residues: 103 sheet: -1.10 (0.76), residues: 38 loop : -0.48 (0.58), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.012 ARG A 28 TYR 0.112 0.051 TYR A 141 PHE 0.123 0.054 PHE A 164 HIS 0.063 0.030 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= 0.2788 r_free= 0.1872 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.387628 | | target function (ml) not normalized (work): 71268.244399 | | target function (ml) not normalized (free): 3273.258433 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3112 percent. r_work = 0.2919 r_free = 0.2034 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2866 0.2919 0.2034 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2866 0.2919 0.2034 n_refl.: 17050 remove outliers: r(all,work,free)=0.2155 0.2164 0.2034 n_refl.: 17045 overall B=-0.42 to atoms: r(all,work,free)=0.2127 0.2136 0.2015 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1609 0.1605 0.1685 n_refl.: 17045 remove outliers: r(all,work,free)=0.1607 0.1603 0.1685 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 0.3817 399.225 363.130 0.663 1.009 0.406 11.894-9.307 99.02 97 4 0.1827 634.063 612.628 0.931 1.011 0.390 9.237-7.194 100.00 213 7 0.2175 518.600 510.371 0.965 1.011 0.370 7.162-5.571 100.00 427 22 0.2334 389.210 376.019 0.919 1.010 0.298 5.546-4.326 100.00 867 58 0.1368 534.322 528.645 0.962 1.009 0.223 4.315-3.360 100.00 1859 96 0.1283 508.146 504.816 1.018 1.006 0.206 3.356-2.611 100.00 3867 181 0.1678 333.823 328.821 1.014 1.000 0.044 2.608-2.000 99.99 8818 434 0.1622 217.595 213.674 1.032 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.5160 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1603 r_free=0.1685 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1603 r_free=0.1685 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.277931 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.937266 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 0.1351 0.1650 0.0298 0.009 1.0 1.0 0.5 0.0 0 11.139 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.50 2.98 3.013 18.434 0.937 0.023 12.77 16.71 3.94 3.676 18.720 0.937 0.020 Individual atomic B min max mean iso aniso Overall: 6.17 113.87 20.00 4.12 1785 0 Protein: 6.17 113.03 17.25 4.13 1519 0 Water: 8.86 113.87 36.02 N/A 258 0 Other: 21.72 37.19 26.68 N/A 8 0 Chain A: 6.17 113.87 20.00 N/A 1785 0 Histogram: Values Number of atoms 6.17 - 16.94 1076 16.94 - 27.71 349 27.71 - 38.48 186 38.48 - 49.25 99 49.25 - 60.02 48 60.02 - 70.79 13 70.79 - 81.56 6 81.56 - 92.33 4 92.33 - 103.10 1 103.10 - 113.87 3 =========================== Idealize ADP of riding H ========================== r_work=0.1277 r_free=0.1671 r_work=0.1280 r_free=0.1677 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1280 r_free = 0.1677 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 = 0.1276 r_free = 0.1669 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.26 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= 0.1276 r_free= 0.1669 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019908 | | target function (ls_wunit_k1) not normalized (work): 323.226964 | | target function (ls_wunit_k1) not normalized (free): 27.751372 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1294 0.1276 0.1669 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1907 0.1906 0.1985 n_refl.: 17043 remove outliers: r(all,work,free)=0.1907 0.1906 0.1985 n_refl.: 17043 overall B=-0.40 to atoms: r(all,work,free)=0.1878 0.1876 0.1968 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1295 0.1277 0.1658 n_refl.: 17043 remove outliers: r(all,work,free)=0.1293 0.1275 0.1658 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 0.3424 306.873 281.794 0.632 1.009 0.370 11.894-9.307 99.02 97 4 0.1691 488.281 477.383 0.919 1.010 0.367 9.237-7.194 100.00 213 7 0.1833 399.364 396.208 0.961 1.009 0.351 7.162-5.571 100.00 427 22 0.1854 299.723 294.587 0.928 1.009 0.259 5.546-4.326 100.00 867 58 0.1040 411.472 409.350 0.959 1.007 0.205 4.315-3.360 100.00 1859 96 0.0926 391.314 391.041 1.018 1.004 0.191 3.356-2.611 100.00 3867 181 0.1302 257.071 255.821 1.016 1.000 0.081 2.608-2.000 99.99 8818 434 0.1352 167.566 166.079 1.025 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4330 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1658 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1658 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1658 | n_water=258 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.1284 r_free=0.1651 | n_water=252 | time (s): 19.600 (total time: 20.320) Filter (q & B) r_work=0.1284 r_free=0.1651 | n_water=250 | time (s): 1.740 (total time: 22.060) Compute maps r_work=0.1284 r_free=0.1651 | n_water=250 | time (s): 0.540 (total time: 22.600) Filter (map) r_work=0.1320 r_free=0.1645 | n_water=211 | time (s): 1.600 (total time: 24.200) Find peaks r_work=0.1320 r_free=0.1645 | n_water=211 | time (s): 0.470 (total time: 24.670) Add new water r_work=0.1536 r_free=0.1873 | n_water=370 | time (s): 1.560 (total time: 26.230) Refine new water occ: r_work=0.1333 r_free=0.1558 adp: r_work=0.1276 r_free=0.1569 occ: r_work=0.1279 r_free=0.1528 adp: r_work=0.1248 r_free=0.1550 occ: r_work=0.1249 r_free=0.1530 adp: r_work=0.1238 r_free=0.1537 ADP+occupancy (water only), MIN, final r_work=0.1238 r_free=0.1537 r_work=0.1238 r_free=0.1537 | n_water=370 | time (s): 19.050 (total time: 45.280) Filter (q & B) r_work=0.1239 r_free=0.1541 | n_water=365 | time (s): 1.650 (total time: 46.930) Filter (dist only) r_work=0.1240 r_free=0.1544 | n_water=364 | time (s): 29.390 (total time: 76.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.072851 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.946280 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 0.1205 0.1586 0.0381 0.008 0.9 3.5 0.5 0.0 0 12.036 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 15.86 3.81 4.200 21.056 0.946 0.018 11.90 16.18 4.27 4.216 21.391 0.946 0.017 Individual atomic B min max mean iso aniso Overall: 6.63 107.63 21.43 4.32 1891 0 Protein: 6.63 107.63 17.87 4.31 1519 0 Water: 8.66 65.75 35.94 N/A 364 0 Other: 24.88 45.77 35.50 N/A 8 0 Chain A: 6.63 107.63 19.60 N/A 1738 0 Chain S: 17.23 62.36 42.16 N/A 153 0 Histogram: Values Number of atoms 6.63 - 16.73 1017 16.73 - 26.83 380 26.83 - 36.93 230 36.93 - 47.03 160 47.03 - 57.13 66 57.13 - 67.23 27 67.23 - 77.33 3 77.33 - 87.43 5 87.43 - 97.53 1 97.53 - 107.63 2 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1618 r_work=0.1192 r_free=0.1619 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1619 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1618 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.26 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= 0.1190 r_free= 0.1618 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.016870 | | target function (ls_wunit_k1) not normalized (work): 273.872728 | | target function (ls_wunit_k1) not normalized (free): 25.247825 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1190 0.1618 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1744 0.1734 0.1969 n_refl.: 17041 remove outliers: r(all,work,free)=0.1744 0.1734 0.1969 n_refl.: 17041 overall B=-0.39 to atoms: r(all,work,free)=0.1719 0.1709 0.1950 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1184 0.1613 n_refl.: 17041 remove outliers: r(all,work,free)=0.1204 0.1183 0.1613 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 0.3154 303.710 287.663 0.597 1.004 0.343 11.894-9.307 99.02 97 4 0.1481 488.281 487.403 0.915 1.005 0.338 9.237-7.194 100.00 213 7 0.1648 399.364 400.676 0.974 1.005 0.310 7.162-5.571 100.00 427 22 0.1517 299.723 296.422 0.932 1.004 0.230 5.546-4.326 100.00 867 58 0.0855 411.472 408.841 0.963 1.004 0.221 4.315-3.360 100.00 1859 96 0.0818 391.314 390.450 1.016 1.002 0.191 3.356-2.611 100.00 3867 181 0.1196 257.071 256.173 1.014 1.000 0.091 2.608-2.000 99.99 8818 434 0.1332 167.566 166.509 1.019 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3926 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1183 r_free=0.1613 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=0.1184 r_free=0.1615 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1184 r_free=0.1615 | n_water=364 | time (s): 0.860 (total time: 0.860) Filter (dist) r_work=0.1184 r_free=0.1615 | n_water=364 | time (s): 27.270 (total time: 28.130) Filter (q & B) r_work=0.1184 r_free=0.1615 | n_water=364 | time (s): 0.800 (total time: 28.930) Compute maps r_work=0.1184 r_free=0.1615 | n_water=364 | time (s): 0.590 (total time: 29.520) Filter (map) r_work=0.1256 r_free=0.1611 | n_water=271 | time (s): 1.470 (total time: 30.990) Find peaks r_work=0.1256 r_free=0.1611 | n_water=271 | time (s): 0.430 (total time: 31.420) Add new water r_work=0.1433 r_free=0.1802 | n_water=424 | time (s): 1.620 (total time: 33.040) Refine new water occ: r_work=0.1247 r_free=0.1579 adp: r_work=0.1240 r_free=0.1588 occ: r_work=0.1219 r_free=0.1541 adp: r_work=0.1210 r_free=0.1554 occ: r_work=0.1201 r_free=0.1527 adp: r_work=0.1191 r_free=0.1533 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1533 r_work=0.1191 r_free=0.1533 | n_water=424 | time (s): 53.580 (total time: 86.620) Filter (q & B) r_work=0.1194 r_free=0.1530 | n_water=413 | time (s): 2.010 (total time: 88.630) Filter (dist only) r_work=0.1193 r_free=0.1531 | n_water=412 | time (s): 32.660 (total time: 121.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.910348 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.168313 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 0.1165 0.1554 0.0389 0.009 1.0 3.5 0.5 0.0 0 0.955 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.65 15.54 3.89 4.380 21.745 0.168 4.995 11.43 15.56 4.13 4.970 21.626 0.168 4.969 Individual atomic B min max mean iso aniso Overall: 6.26 105.13 21.07 4.70 1939 0 Protein: 6.26 105.13 17.03 4.70 1519 0 Water: 8.71 65.00 35.69 N/A 412 0 Other: 27.28 47.58 35.76 N/A 8 0 Chain A: 6.26 105.13 18.80 N/A 1735 0 Chain S: 18.75 65.00 40.46 N/A 204 0 Histogram: Values Number of atoms 6.26 - 16.15 1058 16.15 - 26.03 351 26.03 - 35.92 230 35.92 - 45.81 174 45.81 - 55.70 83 55.70 - 65.58 30 65.58 - 75.47 5 75.47 - 85.36 3 85.36 - 95.25 3 95.25 - 105.13 2 =========================== Idealize ADP of riding H ========================== r_work=0.1143 r_free=0.1556 r_work=0.1143 r_free=0.1557 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1143 r_free = 0.1557 target_work(ml) = 4.968 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1134 r_free = 0.1544 target_work(ml) = 4.961 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1134 r_free= 0.1544 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.961056 | | target function (ml) not normalized (work): 80532.829660 | | target function (ml) not normalized (free): 4186.619206 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1154 0.1134 0.1544 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1666 0.1657 0.1878 n_refl.: 17040 remove outliers: r(all,work,free)=0.1666 0.1657 0.1878 n_refl.: 17040 overall B=-0.38 to atoms: r(all,work,free)=0.1640 0.1630 0.1864 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1153 0.1133 0.1547 n_refl.: 17040 remove outliers: r(all,work,free)=0.1153 0.1133 0.1547 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 0.3403 303.710 284.791 0.579 1.001 0.338 11.894-9.307 99.02 97 4 0.1726 488.281 483.734 0.913 1.003 0.330 9.237-7.194 100.00 213 7 0.1811 399.364 400.266 0.985 1.003 0.260 7.162-5.571 100.00 427 22 0.1625 299.723 293.981 0.941 1.003 0.235 5.546-4.326 100.00 867 58 0.0920 411.472 408.256 0.968 1.003 0.221 4.315-3.360 100.00 1859 96 0.0875 391.314 389.012 1.012 1.002 0.211 3.356-2.611 100.00 3867 181 0.1263 257.071 254.828 1.012 1.001 0.121 2.608-2.000 99.99 8818 434 0.1084 167.566 166.254 1.016 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3788 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1133 r_free=0.1547 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1133 r_free=0.1547 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1133 r_free=0.1547 | n_water=412 | time (s): 0.930 (total time: 0.930) Filter (dist) r_work=0.1133 r_free=0.1547 | n_water=412 | time (s): 31.210 (total time: 32.140) Filter (q & B) r_work=0.1133 r_free=0.1547 | n_water=412 | time (s): 1.280 (total time: 33.420) Compute maps r_work=0.1133 r_free=0.1547 | n_water=412 | time (s): 0.810 (total time: 34.230) Filter (map) r_work=0.1198 r_free=0.1565 | n_water=318 | time (s): 1.930 (total time: 36.160) Find peaks r_work=0.1198 r_free=0.1565 | n_water=318 | time (s): 0.670 (total time: 36.830) Add new water r_work=0.1341 r_free=0.1702 | n_water=460 | time (s): 2.150 (total time: 38.980) Refine new water occ: r_work=0.1174 r_free=0.1531 adp: r_work=0.1167 r_free=0.1533 occ: r_work=0.1148 r_free=0.1503 adp: r_work=0.1139 r_free=0.1504 occ: r_work=0.1130 r_free=0.1490 adp: r_work=0.1122 r_free=0.1489 ADP+occupancy (water only), MIN, final r_work=0.1122 r_free=0.1489 r_work=0.1122 r_free=0.1489 | n_water=460 | time (s): 28.120 (total time: 67.100) Filter (q & B) r_work=0.1125 r_free=0.1494 | n_water=452 | time (s): 1.770 (total time: 68.870) Filter (dist only) r_work=0.1125 r_free=0.1494 | n_water=452 | time (s): 32.720 (total time: 101.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.950982 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.175048 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 0.1109 0.1543 0.0435 0.010 1.0 4.2 0.5 0.0 0 0.975 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.09 15.43 4.35 4.512 21.208 0.175 4.953 10.98 15.42 4.44 4.684 21.246 0.175 4.947 Individual atomic B min max mean iso aniso Overall: 5.72 102.56 21.19 4.92 1979 0 Protein: 5.72 102.56 16.62 4.91 1519 0 Water: 8.45 65.87 36.31 N/A 452 0 Other: 26.96 46.20 34.72 N/A 8 0 Chain A: 5.72 102.56 18.30 N/A 1733 0 Chain S: 13.89 65.87 41.49 N/A 246 0 Histogram: Values Number of atoms 5.72 - 15.40 1029 15.40 - 25.09 373 25.09 - 34.77 221 34.77 - 44.46 200 44.46 - 54.14 98 54.14 - 63.83 40 63.83 - 73.51 9 73.51 - 83.19 2 83.19 - 92.88 3 92.88 - 102.56 4 =========================== Idealize ADP of riding H ========================== r_work=0.1098 r_free=0.1542 r_work=0.1098 r_free=0.1541 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1098 r_free = 0.1541 target_work(ml) = 4.947 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1089 r_free = 0.1541 target_work(ml) = 4.945 | | occupancies: max = 1.00 min = 0.22 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= 0.1089 r_free= 0.1541 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.944699 | | target function (ml) not normalized (work): 80267.304372 | | target function (ml) not normalized (free): 4183.382861 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1111 0.1089 0.1541 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1581 0.1567 0.1858 n_refl.: 17040 remove outliers: r(all,work,free)=0.1581 0.1567 0.1858 n_refl.: 17040 overall B=-0.30 to atoms: r(all,work,free)=0.1562 0.1548 0.1848 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1109 0.1087 0.1533 n_refl.: 17040 remove outliers: r(all,work,free)=0.1108 0.1087 0.1533 n_refl.: 17039 ======================== 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 92.71 84 5 0.3532 300.140 285.418 0.558 1.000 0.314 11.894-9.307 99.02 97 4 0.1799 488.281 482.096 0.912 1.001 0.304 9.237-7.194 100.00 213 7 0.1683 399.364 399.943 0.990 1.002 0.240 7.162-5.571 100.00 427 22 0.1519 299.723 293.653 0.939 1.002 0.210 5.546-4.326 100.00 867 58 0.0901 411.472 407.919 0.971 1.002 0.211 4.315-3.360 100.00 1859 96 0.0828 391.314 389.325 1.008 1.002 0.201 3.356-2.611 100.00 3867 181 0.1214 257.071 255.026 1.005 1.001 0.121 2.608-2.000 99.99 8818 434 0.1036 167.566 166.364 1.002 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.0402 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1087 r_free=0.1533 After: r_work=0.1089 r_free=0.1532 ================================== NQH flips ================================== r_work=0.1089 r_free=0.1532 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=0.1089 r_free=0.1532 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1089 r_free=0.1532 | n_water=452 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.1089 r_free=0.1532 | n_water=452 | time (s): 36.160 (total time: 36.840) Filter (q & B) r_work=0.1089 r_free=0.1532 | n_water=452 | time (s): 1.620 (total time: 38.460) Compute maps r_work=0.1089 r_free=0.1532 | n_water=452 | time (s): 0.740 (total time: 39.200) Filter (map) r_work=0.1167 r_free=0.1580 | n_water=338 | time (s): 2.100 (total time: 41.300) Find peaks r_work=0.1167 r_free=0.1580 | n_water=338 | time (s): 0.660 (total time: 41.960) Add new water r_work=0.1293 r_free=0.1662 | n_water=465 | time (s): 1.950 (total time: 43.910) Refine new water occ: r_work=0.1143 r_free=0.1503 adp: r_work=0.1135 r_free=0.1511 occ: r_work=0.1122 r_free=0.1487 adp: r_work=0.1114 r_free=0.1494 occ: r_work=0.1108 r_free=0.1482 adp: r_work=0.1101 r_free=0.1487 ADP+occupancy (water only), MIN, final r_work=0.1101 r_free=0.1487 r_work=0.1101 r_free=0.1487 | n_water=465 | time (s): 26.350 (total time: 70.260) Filter (q & B) r_work=0.1104 r_free=0.1492 | n_water=457 | time (s): 1.980 (total time: 72.240) Filter (dist only) r_work=0.1108 r_free=0.1496 | n_water=456 | time (s): 36.970 (total time: 109.210) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.985676 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.164207 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 0.1117 0.1517 0.0399 0.010 1.1 4.8 0.5 0.0 0 0.993 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.17 15.17 3.99 4.600 20.897 0.164 4.943 11.08 15.09 4.02 4.644 20.963 0.164 4.936 Individual atomic B min max mean iso aniso Overall: 5.63 101.25 21.00 5.02 1983 0 Protein: 5.63 101.25 16.36 5.00 1519 0 Water: 8.09 64.19 36.23 N/A 456 0 Other: 25.71 43.61 33.57 N/A 8 0 Chain A: 5.63 101.25 17.96 N/A 1730 0 Chain S: 16.16 64.19 41.78 N/A 253 0 Histogram: Values Number of atoms 5.63 - 15.20 1039 15.20 - 24.76 360 24.76 - 34.32 222 34.32 - 43.88 192 43.88 - 53.44 119 53.44 - 63.00 31 63.00 - 72.57 10 72.57 - 82.13 3 82.13 - 91.69 3 91.69 - 101.25 4 =========================== Idealize ADP of riding H ========================== r_work=0.1108 r_free=0.1509 r_work=0.1108 r_free=0.1509 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1108 r_free = 0.1509 target_work(ml) = 4.936 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1102 r_free = 0.1515 target_work(ml) = 4.935 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17039 (all), 4.74 % free)------------| | | | r_work= 0.1102 r_free= 0.1515 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.934502 | | target function (ml) not normalized (work): 80096.844485 | | target function (ml) not normalized (free): 4169.781879 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2809 159 0.1118 0.1466 5.4609 5.6939| | 2: 3.63 - 2.88 1.00 2711 122 0.1084 0.1416 5.2253 5.3416| | 3: 2.88 - 2.52 1.00 2681 148 0.1344 0.1761 5.1415 5.2348| | 4: 2.52 - 2.29 1.00 2661 139 0.0933 0.1496 4.6171 4.9641| | 5: 2.29 - 2.13 1.00 2678 122 0.0955 0.1366 4.5671 4.8457| | 6: 2.13 - 2.00 1.00 2692 117 0.1117 0.1688 4.5655 4.7593| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2809 159 0.94 9.32 0.99 0.96 6673.92| | 2: 3.63 - 2.88 2711 122 0.92 13.20 1.01 0.96 6673.92| | 3: 2.88 - 2.52 2681 148 0.87 19.40 0.99 0.96 6673.92| | 4: 2.52 - 2.29 2661 139 0.93 11.84 1.01 0.98 2069.87| | 5: 2.29 - 2.13 2678 122 0.92 13.94 1.00 0.98 2069.87| | 6: 2.13 - 2.00 2692 117 0.90 16.58 0.99 0.98 2069.87| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2069.87 max = 6673.92 mean = 4396.01| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.73 mean = 14.01| |phase err.(test): min = 0.00 max = 89.84 mean = 13.64| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1122 0.1102 0.1515 n_refl.: 17039 re-set all scales: r(all,work,free)=0.1561 0.1546 0.1858 n_refl.: 17039 remove outliers: r(all,work,free)=0.1561 0.1546 0.1858 n_refl.: 17039 overall B=-0.26 to atoms: r(all,work,free)=0.1546 0.1531 0.1848 n_refl.: 17039 bulk-solvent and scaling: r(all,work,free)=0.1121 0.1102 0.1512 n_refl.: 17039 remove outliers: r(all,work,free)=0.1121 0.1102 0.1512 n_refl.: 17039 ======================== 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 92.71 84 5 0.3566 300.140 275.710 0.539 1.004 0.330 11.894-9.307 99.02 97 4 0.1717 488.281 483.371 0.903 1.005 0.330 9.237-7.194 100.00 213 7 0.1833 399.364 399.851 0.982 1.005 0.230 7.162-5.571 100.00 427 22 0.1585 299.723 292.982 0.936 1.005 0.200 5.546-4.326 100.00 867 58 0.0909 411.472 407.852 0.967 1.004 0.201 4.315-3.360 100.00 1859 96 0.0863 391.314 389.152 1.006 1.003 0.201 3.356-2.611 100.00 3867 181 0.1229 257.071 254.795 1.003 1.000 0.058 2.608-2.000 99.99 8818 434 0.1034 167.566 166.315 0.998 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9021 ================= 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 : 0.2788 0.1872 0.082 5.342 8.8 119.3 19.9 258 0.000 1_bss: 0.1603 0.1685 0.082 5.342 8.4 118.9 19.5 258 0.000 1_settarget: 0.1603 0.1685 0.082 5.342 8.4 118.9 19.5 258 0.000 1_nqh: 0.1603 0.1685 0.082 5.342 8.4 118.9 19.5 258 0.000 1_weight: 0.1603 0.1685 0.082 5.342 8.4 118.9 19.5 258 0.000 1_xyzrec: 0.1351 0.1650 0.009 0.963 8.4 118.9 19.5 258 0.152 1_adp: 0.1277 0.1671 0.009 0.963 6.2 113.9 20.0 258 0.152 1_regHadp: 0.1280 0.1677 0.009 0.963 6.2 113.9 20.0 258 0.152 1_occ: 0.1276 0.1669 0.009 0.963 6.2 113.9 20.0 258 0.152 2_bss: 0.1275 0.1658 0.009 0.963 5.8 113.5 19.6 258 0.152 2_settarget: 0.1275 0.1658 0.009 0.963 5.8 113.5 19.6 258 0.152 2_updatecdl: 0.1275 0.1658 0.009 0.980 5.8 113.5 19.6 258 0.152 2_nqh: 0.1275 0.1658 0.009 0.980 5.8 113.5 19.6 258 0.152 2_sol: 0.1240 0.1544 0.009 0.980 5.8 112.6 20.8 364 n/a 2_weight: 0.1240 0.1544 0.009 0.980 5.8 112.6 20.8 364 n/a 2_xyzrec: 0.1205 0.1586 0.008 0.928 5.8 112.6 20.8 364 n/a 2_adp: 0.1190 0.1618 0.008 0.928 6.6 107.6 21.4 364 n/a 2_regHadp: 0.1192 0.1619 0.008 0.928 6.6 107.6 21.4 364 n/a 2_occ: 0.1190 0.1618 0.008 0.928 6.6 107.6 21.4 364 n/a 3_bss: 0.1183 0.1613 0.008 0.928 6.2 107.2 21.0 364 n/a 3_settarget: 0.1183 0.1613 0.008 0.928 6.2 107.2 21.0 364 n/a 3_updatecdl: 0.1183 0.1613 0.008 0.933 6.2 107.2 21.0 364 n/a 3_nqh: 0.1184 0.1615 0.008 0.933 6.2 107.2 21.0 364 n/a 3_sol: 0.1193 0.1531 0.008 0.933 6.2 107.2 21.3 412 n/a 3_weight: 0.1193 0.1531 0.008 0.933 6.2 107.2 21.3 412 n/a 3_xyzrec: 0.1165 0.1554 0.009 0.971 6.2 107.2 21.3 412 n/a 3_adp: 0.1143 0.1556 0.009 0.971 6.3 105.1 21.1 412 n/a 3_regHadp: 0.1143 0.1557 0.009 0.971 6.3 105.1 21.1 412 n/a 3_occ: 0.1134 0.1544 0.009 0.971 6.3 105.1 21.1 412 n/a 4_bss: 0.1133 0.1547 0.009 0.971 5.9 104.7 20.7 412 n/a 4_settarget: 0.1133 0.1547 0.009 0.971 5.9 104.7 20.7 412 n/a 4_updatecdl: 0.1133 0.1547 0.009 0.970 5.9 104.7 20.7 412 n/a 4_nqh: 0.1133 0.1547 0.009 0.970 5.9 104.7 20.7 412 n/a 4_sol: 0.1125 0.1494 0.009 0.970 5.9 104.7 21.1 452 n/a 4_weight: 0.1125 0.1494 0.009 0.970 5.9 104.7 21.1 452 n/a 4_xyzrec: 0.1109 0.1543 0.010 0.988 5.9 104.7 21.1 452 n/a 4_adp: 0.1098 0.1542 0.010 0.988 5.7 102.6 21.2 452 n/a 4_regHadp: 0.1098 0.1541 0.010 0.988 5.7 102.6 21.2 452 n/a 4_occ: 0.1089 0.1541 0.010 0.988 5.7 102.6 21.2 452 n/a 5_bss: 0.1087 0.1533 0.010 0.988 5.4 102.3 20.9 452 n/a 5_settarget: 0.1087 0.1533 0.010 0.988 5.4 102.3 20.9 452 n/a 5_updatecdl: 0.1087 0.1533 0.010 0.986 5.4 102.3 20.9 452 n/a 5_setrh: 0.1089 0.1532 0.010 0.986 5.4 102.3 20.9 452 n/a 5_nqh: 0.1089 0.1532 0.010 0.986 5.4 102.3 20.9 452 n/a 5_sol: 0.1108 0.1496 0.010 0.986 5.4 102.3 20.9 456 n/a 5_weight: 0.1108 0.1496 0.010 0.986 5.4 102.3 20.9 456 n/a 5_xyzrec: 0.1117 0.1517 0.010 1.087 5.4 102.3 20.9 456 n/a 5_adp: 0.1108 0.1509 0.010 1.087 5.6 101.2 21.0 456 n/a 5_regHadp: 0.1108 0.1509 0.010 1.087 5.6 101.2 21.0 456 n/a 5_occ: 0.1102 0.1515 0.010 1.087 5.6 101.2 21.0 456 n/a end: 0.1102 0.1512 0.010 1.087 5.4 101.0 20.7 456 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8960824_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8960824_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.4800 Refinement macro-cycles (run) : 926.6300 Write final files (write_after_run_outputs) : 21.5700 Total : 951.6800 Total CPU time: 16.21 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:13 PST -0800 (1735494073.95 s) Start R-work = 0.1603, R-free = 0.1685 Final R-work = 0.1102, R-free = 0.1512 =============================================================================== Job complete usr+sys time: 994.59 seconds wall clock time: 16 minutes 57.69 seconds (1017.69 seconds total)