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_6727304.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_6727304.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6727304.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 2 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: 2.06, per 1000 atoms: 0.61 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: 0.43 Conformation dependent library (CDL) restraints added in 104.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.60 - 0.87: 330 0.87 - 1.15: 1271 1.15 - 1.42: 675 1.42 - 1.69: 851 1.69 - 1.96: 26 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 91 " pdb=" CB ILE A 91 " ideal model delta sigma weight residual 1.540 1.756 -0.217 1.11e-02 8.12e+03 3.80e+02 bond pdb=" C ALA A 61 " pdb=" O ALA A 61 " ideal model delta sigma weight residual 1.237 1.459 -0.223 1.19e-02 7.06e+03 3.51e+02 bond pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 1.523 1.744 -0.221 1.27e-02 6.20e+03 3.03e+02 bond pdb=" CA ILE A 117 " pdb=" CB ILE A 117 " ideal model delta sigma weight residual 1.537 1.336 0.202 1.17e-02 7.31e+03 2.97e+02 bond pdb=" N LYS A 130 " pdb=" CA LYS A 130 " ideal model delta sigma weight residual 1.459 1.261 0.198 1.16e-02 7.43e+03 2.91e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.00: 3270 5.00 - 9.99: 1905 9.99 - 14.98: 523 14.98 - 19.98: 74 19.98 - 24.97: 5 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 106.55 15.22 1.00e+00 1.00e+00 2.32e+02 angle pdb=" CA PHE A 164 " pdb=" CB PHE A 164 " pdb=" CG PHE A 164 " ideal model delta sigma weight residual 113.80 127.87 -14.07 1.00e+00 1.00e+00 1.98e+02 angle pdb=" O ALA A 104 " pdb=" C ALA A 104 " pdb=" N ILE A 105 " ideal model delta sigma weight residual 123.31 108.07 15.24 1.17e+00 7.31e-01 1.70e+02 angle pdb=" O ILE A 168 " pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 121.80 107.45 14.35 1.13e+00 7.83e-01 1.61e+02 angle pdb=" CA LYS A 89 " pdb=" C LYS A 89 " pdb=" O LYS A 89 " ideal model delta sigma weight residual 120.20 106.35 13.85 1.12e+00 7.97e-01 1.53e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.96: 1312 17.96 - 35.91: 120 35.91 - 53.86: 36 53.86 - 71.81: 10 71.81 - 89.76: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N LEU A 112 " pdb=" C LEU A 112 " pdb=" CA LEU A 112 " pdb=" CB LEU A 112 " ideal model delta harmonic sigma weight residual 122.80 143.52 -20.72 0 2.50e+00 1.60e-01 6.87e+01 dihedral pdb=" N VAL A 186 " pdb=" C VAL A 186 " pdb=" CA VAL A 186 " pdb=" CB VAL A 186 " ideal model delta harmonic sigma weight residual 123.40 142.70 -19.30 0 2.50e+00 1.60e-01 5.96e+01 dihedral pdb=" C LEU A 112 " pdb=" N LEU A 112 " pdb=" CA LEU A 112 " pdb=" CB LEU A 112 " ideal model delta harmonic sigma weight residual -122.60 -141.87 19.27 0 2.50e+00 1.60e-01 5.94e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.214: 99 0.214 - 0.428: 81 0.428 - 0.641: 46 0.641 - 0.855: 13 0.855 - 1.068: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" C3 ADTT A 201 " pdb=" C2 ADTT A 201 " pdb=" C4 ADTT A 201 " pdb=" O3 ADTT A 201 " both_signs ideal model delta sigma weight residual False 2.56 3.62 -1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" CA LEU A 185 " pdb=" N LEU A 185 " pdb=" C LEU A 185 " pdb=" CB LEU A 185 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.34e+01 chirality pdb=" CA LEU A 112 " pdb=" N LEU A 112 " pdb=" C LEU A 112 " pdb=" CB LEU A 112 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.93 2.00e-01 2.50e+01 2.18e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.064 2.00e-02 2.50e+03 6.92e-02 1.44e+02 pdb=" CG PHE A 119 " -0.145 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.101 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.060 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.069 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.066 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.039 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.033 2.00e-02 2.50e+03 5.55e-02 9.25e+01 pdb=" CG TYR A 139 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.083 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.034 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.082 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.013 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.120 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.010 2.00e-02 2.50e+03 5.50e-02 9.07e+01 pdb=" CG PHE A 164 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.069 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.069 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.081 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.030 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.025 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.039 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.065 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.061 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.071 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 990 2.31 - 2.88: 7948 2.88 - 3.45: 10630 3.45 - 4.03: 15219 4.03 - 4.60: 21827 Nonbonded interactions: 56614 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.737 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.796 2.450 nonbonded pdb=" H LYS A 122 " pdb=" OD2 ASP A 149 " model vdw 1.810 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.825 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.840 2.450 ... (remaining 56609 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_6727304_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= 0.2790 r_free= 0.1843 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.393891 | | target function (ml) not normalized (work): 71369.972838 | | target function (ml) not normalized (free): 3269.370900 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3205 0.2141 7.4667 5.0239| | 2: 3.63 - 2.88 1.00 2711 122 0.2655 0.1885 4.3374 4.3634| | 3: 2.88 - 2.52 1.00 2682 148 0.2529 0.1679 4.191 4.2064| | 4: 2.52 - 2.29 1.00 2661 139 0.2567 0.1554 3.5241 3.5302| | 5: 2.29 - 2.13 1.00 2678 122 0.2633 0.1542 3.383 3.4968| | 6: 2.13 - 2.00 1.00 2692 117 0.2750 0.1741 3.3006 3.4051| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.91 0.77 0.23 1338.09| | 2: 3.63 - 2.88 2711 122 0.82 24.22 1.32 0.23 1338.09| | 3: 2.88 - 2.52 2682 148 0.73 33.17 1.28 0.23 1338.09| | 4: 2.52 - 2.29 2661 139 0.94 11.03 1.30 0.26 129.69| | 5: 2.29 - 2.13 2678 122 0.92 13.13 1.32 0.26 129.69| | 6: 2.13 - 2.00 2692 117 0.90 16.01 1.33 0.26 129.69| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 129.69 max = 1338.09 mean = 740.62| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.99 mean = 19.25| |phase err.(test): min = 0.00 max = 89.14 mean = 19.35| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.275 1557 Z= 5.356 Angle : 5.237 16.778 2118 Z= 3.690 Chirality : 0.368 1.068 243 Planarity : 0.032 0.087 284 Dihedral : 14.189 89.760 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 30.27 % 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: -3.64 (0.43), residues: 224 helix: -3.42 (0.30), residues: 109 sheet: -2.32 (0.88), residues: 28 loop : -0.61 (0.53), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.057 0.019 ARG A 98 TYR 0.061 0.031 TYR A 141 PHE 0.123 0.036 PHE A 119 HIS 0.033 0.016 HIS A 126 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= 0.2790 r_free= 0.1843 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.393891 | | target function (ml) not normalized (work): 71369.972838 | | target function (ml) not normalized (free): 3269.370900 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2797 percent. r_work = 0.2918 r_free = 0.2003 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2866 0.2918 0.2003 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2866 0.2918 0.2003 n_refl.: 17050 remove outliers: r(all,work,free)=0.2161 0.2171 0.2003 n_refl.: 17045 overall B=-0.39 to atoms: r(all,work,free)=0.2135 0.2145 0.1988 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1621 0.1618 0.1682 n_refl.: 17045 remove outliers: r(all,work,free)=0.1619 0.1616 0.1682 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 0.3814 398.842 362.362 0.649 1.020 0.397 11.894-9.307 99.02 97 4 0.1844 633.456 612.418 0.920 1.021 0.375 9.237-7.194 100.00 213 7 0.2227 518.103 507.947 0.951 1.019 0.371 7.162-5.571 100.00 427 22 0.2313 388.837 375.623 0.912 1.017 0.293 5.546-4.326 100.00 867 58 0.1393 533.810 528.281 0.956 1.014 0.241 4.315-3.360 100.00 1859 96 0.1291 507.659 503.206 1.012 1.008 0.181 3.356-2.611 100.00 3867 181 0.1675 333.503 329.126 1.013 0.999 0.034 2.608-2.000 99.99 8818 434 0.1647 217.387 213.548 1.034 0.982 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3903 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1616 r_free=0.1682 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1619 r_free=0.1685 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.573390 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.904121 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 0.1347 0.1640 0.0293 0.009 1.0 1.6 0.5 0.0 0 12.787 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.47 16.40 2.93 3.013 18.469 0.904 0.022 12.74 16.61 3.87 3.652 18.713 0.904 0.020 Individual atomic B min max mean iso aniso Overall: 5.95 113.91 19.96 4.11 1785 0 Protein: 5.95 112.88 17.19 4.12 1519 0 Water: 7.90 113.91 36.07 N/A 258 0 Other: 21.61 36.81 26.24 N/A 8 0 Chain A: 5.95 113.91 19.96 N/A 1785 0 Histogram: Values Number of atoms 5.95 - 16.74 1074 16.74 - 27.54 350 27.54 - 38.33 186 38.33 - 49.13 97 49.13 - 59.93 50 59.93 - 70.72 13 70.72 - 81.52 7 81.52 - 92.32 4 92.32 - 103.11 1 103.11 - 113.91 3 =========================== Idealize ADP of riding H ========================== r_work=0.1274 r_free=0.1661 r_work=0.1278 r_free=0.1669 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1278 r_free = 0.1669 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 = 0.1274 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= 0.1274 r_free= 0.1669 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019917 | | target function (ls_wunit_k1) not normalized (work): 323.377379 | | target function (ls_wunit_k1) not normalized (free): 27.659532 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1274 0.1669 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1906 0.1905 0.1989 n_refl.: 17043 remove outliers: r(all,work,free)=0.1906 0.1905 0.1989 n_refl.: 17043 overall B=-0.37 to atoms: r(all,work,free)=0.1879 0.1878 0.1973 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1291 0.1273 0.1658 n_refl.: 17043 remove outliers: r(all,work,free)=0.1290 0.1271 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 0.3523 306.056 281.122 0.621 1.006 0.369 11.894-9.307 99.02 97 4 0.1673 486.980 476.150 0.916 1.006 0.368 9.237-7.194 100.00 213 7 0.1850 398.300 394.060 0.956 1.006 0.351 7.162-5.571 100.00 427 22 0.1856 298.925 293.433 0.924 1.006 0.271 5.546-4.326 100.00 867 58 0.1045 410.376 407.590 0.958 1.005 0.231 4.315-3.360 100.00 1859 96 0.0924 390.271 389.708 1.016 1.004 0.191 3.356-2.611 100.00 3867 181 0.1293 256.386 255.113 1.012 1.001 0.071 2.608-2.000 99.99 8818 434 0.1344 167.120 165.832 1.016 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3272 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1271 r_free=0.1658 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 r_work=0.1273 r_free=0.1661 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1661 | n_water=258 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.1277 r_free=0.1652 | n_water=254 | time (s): 20.860 (total time: 21.540) Filter (q & B) r_work=0.1278 r_free=0.1652 | n_water=252 | time (s): 2.230 (total time: 23.770) Compute maps r_work=0.1278 r_free=0.1652 | n_water=252 | time (s): 0.590 (total time: 24.360) Filter (map) r_work=0.1315 r_free=0.1648 | n_water=209 | time (s): 2.180 (total time: 26.540) Find peaks r_work=0.1315 r_free=0.1648 | n_water=209 | time (s): 0.660 (total time: 27.200) Add new water r_work=0.1535 r_free=0.1876 | n_water=374 | time (s): 1.800 (total time: 29.000) Refine new water occ: r_work=0.1331 r_free=0.1576 adp: r_work=0.1271 r_free=0.1575 occ: r_work=0.1277 r_free=0.1551 adp: r_work=0.1244 r_free=0.1560 occ: r_work=0.1245 r_free=0.1552 adp: r_work=0.1233 r_free=0.1553 ADP+occupancy (water only), MIN, final r_work=0.1233 r_free=0.1553 r_work=0.1233 r_free=0.1553 | n_water=374 | time (s): 11.430 (total time: 40.430) Filter (q & B) r_work=0.1235 r_free=0.1557 | n_water=365 | time (s): 1.560 (total time: 41.990) Filter (dist only) r_work=0.1235 r_free=0.1558 | n_water=364 | time (s): 29.180 (total time: 71.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.836465 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.016653 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 0.1208 0.1628 0.0420 0.008 0.9 3.2 0.5 0.0 0 12.418 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 16.28 4.20 4.188 21.073 1.017 0.018 11.91 16.40 4.49 4.243 21.266 1.017 0.018 Individual atomic B min max mean iso aniso Overall: 6.98 107.51 21.25 4.28 1891 0 Protein: 6.98 107.51 17.63 4.28 1519 0 Water: 8.44 68.20 36.29 N/A 364 0 Other: 20.63 33.97 25.15 N/A 8 0 Chain A: 6.98 107.51 19.29 N/A 1736 0 Chain S: 17.55 62.71 43.29 N/A 155 0 Histogram: Values Number of atoms 6.98 - 17.03 1056 17.03 - 27.09 361 27.09 - 37.14 214 37.14 - 47.19 141 47.19 - 57.24 78 57.24 - 67.30 30 67.30 - 77.35 4 77.35 - 87.40 3 87.40 - 97.46 2 97.46 - 107.51 2 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1640 r_work=0.1192 r_free=0.1641 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1641 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1187 r_free = 0.1650 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.27 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= 0.1187 r_free= 0.1650 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016856 | | target function (ls_wunit_k1) not normalized (work): 273.634993 | | target function (ls_wunit_k1) not normalized (free): 25.983642 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1210 0.1187 0.1650 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1735 0.1726 0.1968 n_refl.: 17041 remove outliers: r(all,work,free)=0.1735 0.1726 0.1968 n_refl.: 17041 overall B=-0.37 to atoms: r(all,work,free)=0.1711 0.1701 0.1953 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1185 0.1647 n_refl.: 17041 remove outliers: r(all,work,free)=0.1207 0.1185 0.1647 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 0.3208 306.056 286.901 0.602 1.005 0.350 11.894-9.307 99.02 97 4 0.1571 486.980 482.732 0.909 1.006 0.344 9.237-7.194 100.00 213 7 0.1657 398.300 397.035 0.972 1.006 0.289 7.162-5.571 100.00 427 22 0.1543 298.925 295.042 0.931 1.006 0.239 5.546-4.326 100.00 867 58 0.0878 410.376 407.472 0.958 1.005 0.210 4.315-3.360 100.00 1859 96 0.0819 390.271 389.547 1.014 1.003 0.201 3.356-2.611 100.00 3867 181 0.1199 256.386 255.690 1.012 1.001 0.111 2.608-2.000 99.99 8818 434 0.1323 167.120 166.101 1.017 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3261 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1185 r_free=0.1647 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1185 r_free=0.1647 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1647 | n_water=364 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.1186 r_free=0.1642 | n_water=363 | time (s): 30.030 (total time: 30.680) Filter (q & B) r_work=0.1186 r_free=0.1642 | n_water=363 | time (s): 1.180 (total time: 31.860) Compute maps r_work=0.1186 r_free=0.1642 | n_water=363 | time (s): 0.830 (total time: 32.690) Filter (map) r_work=0.1253 r_free=0.1643 | n_water=264 | time (s): 2.130 (total time: 34.820) Find peaks r_work=0.1253 r_free=0.1643 | n_water=264 | time (s): 0.490 (total time: 35.310) Add new water r_work=0.1427 r_free=0.1796 | n_water=409 | time (s): 1.440 (total time: 36.750) Refine new water occ: r_work=0.1236 r_free=0.1587 adp: r_work=0.1231 r_free=0.1591 occ: r_work=0.1210 r_free=0.1566 adp: r_work=0.1204 r_free=0.1567 occ: r_work=0.1193 r_free=0.1546 adp: r_work=0.1186 r_free=0.1550 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1550 r_work=0.1186 r_free=0.1550 | n_water=409 | time (s): 40.650 (total time: 77.400) Filter (q & B) r_work=0.1188 r_free=0.1558 | n_water=402 | time (s): 1.770 (total time: 79.170) Filter (dist only) r_work=0.1187 r_free=0.1557 | n_water=401 | time (s): 33.140 (total time: 112.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.961951 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.183428 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 0.1162 0.1552 0.0389 0.009 1.0 4.8 0.5 0.0 0 0.981 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.62 15.52 3.89 4.323 21.362 0.183 4.987 11.45 15.61 4.16 4.828 21.293 0.183 4.965 Individual atomic B min max mean iso aniso Overall: 6.55 106.59 20.77 4.76 1928 0 Protein: 6.55 106.59 16.98 4.76 1519 0 Water: 9.03 64.33 34.99 N/A 401 0 Other: 19.74 37.02 25.96 N/A 8 0 Chain A: 6.55 106.59 18.66 N/A 1734 0 Chain S: 19.03 64.33 39.61 N/A 194 0 Histogram: Values Number of atoms 6.55 - 16.56 1091 16.56 - 26.56 336 26.56 - 36.57 243 36.57 - 46.57 147 46.57 - 56.57 74 56.57 - 66.58 24 66.58 - 76.58 5 76.58 - 86.58 3 86.58 - 96.59 3 96.59 - 106.59 2 =========================== Idealize ADP of riding H ========================== r_work=0.1145 r_free=0.1561 r_work=0.1145 r_free=0.1562 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1145 r_free = 0.1562 target_work(ml) = 4.965 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1136 r_free = 0.1552 target_work(ml) = 4.959 | | occupancies: max = 1.00 min = 0.17 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= 0.1136 r_free= 0.1552 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.959462 | | target function (ml) not normalized (work): 80511.912628 | | target function (ml) not normalized (free): 4188.579497 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1156 0.1136 0.1552 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1640 0.1632 0.1831 n_refl.: 17041 remove outliers: r(all,work,free)=0.1640 0.1632 0.1831 n_refl.: 17041 overall B=-0.38 to atoms: r(all,work,free)=0.1614 0.1606 0.1820 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1154 0.1134 0.1548 n_refl.: 17041 remove outliers: r(all,work,free)=0.1154 0.1134 0.1548 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 0.3573 306.056 281.699 0.568 1.006 0.340 11.894-9.307 99.02 97 4 0.1799 486.980 478.991 0.905 1.007 0.338 9.237-7.194 100.00 213 7 0.1838 398.300 397.637 0.982 1.007 0.280 7.162-5.571 100.00 427 22 0.1618 298.925 293.351 0.937 1.006 0.221 5.546-4.326 100.00 867 58 0.0938 410.376 407.320 0.963 1.006 0.190 4.315-3.360 100.00 1859 96 0.0878 390.271 387.825 1.010 1.004 0.181 3.356-2.611 100.00 3867 181 0.1268 256.386 254.203 1.013 1.001 0.142 2.608-2.000 99.99 8818 434 0.1070 167.120 165.886 1.018 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3536 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1134 r_free=0.1548 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1136 r_free=0.1547 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1136 r_free=0.1547 | n_water=401 | time (s): 0.800 (total time: 0.800) Filter (dist) r_work=0.1136 r_free=0.1547 | n_water=401 | time (s): 31.910 (total time: 32.710) Filter (q & B) r_work=0.1136 r_free=0.1548 | n_water=400 | time (s): 2.250 (total time: 34.960) Compute maps r_work=0.1136 r_free=0.1548 | n_water=400 | time (s): 0.750 (total time: 35.710) Filter (map) r_work=0.1194 r_free=0.1588 | n_water=311 | time (s): 1.750 (total time: 37.460) Find peaks r_work=0.1194 r_free=0.1588 | n_water=311 | time (s): 0.620 (total time: 38.080) Add new water r_work=0.1337 r_free=0.1687 | n_water=456 | time (s): 1.870 (total time: 39.950) Refine new water occ: r_work=0.1171 r_free=0.1511 adp: r_work=0.1164 r_free=0.1511 occ: r_work=0.1148 r_free=0.1483 adp: r_work=0.1141 r_free=0.1484 occ: r_work=0.1133 r_free=0.1465 adp: r_work=0.1127 r_free=0.1468 ADP+occupancy (water only), MIN, final r_work=0.1127 r_free=0.1468 r_work=0.1127 r_free=0.1468 | n_water=456 | time (s): 28.730 (total time: 68.680) Filter (q & B) r_work=0.1131 r_free=0.1481 | n_water=446 | time (s): 1.800 (total time: 70.480) Filter (dist only) r_work=0.1131 r_free=0.1483 | n_water=445 | time (s): 37.220 (total time: 107.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.917996 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.160148 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 0.1532 0.0415 0.010 1.0 5.1 0.5 0.0 0 0.959 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.17 15.32 4.15 4.528 21.028 0.160 4.950 11.08 15.35 4.27 4.669 21.058 0.160 4.944 Individual atomic B min max mean iso aniso Overall: 5.99 104.30 20.94 4.88 1972 0 Protein: 5.99 104.30 16.60 4.88 1519 0 Water: 8.72 63.57 35.67 N/A 445 0 Other: 19.16 35.96 25.25 N/A 8 0 Chain A: 5.99 104.30 18.23 N/A 1734 0 Chain S: 16.89 63.57 40.61 N/A 238 0 Histogram: Values Number of atoms 5.99 - 15.82 1064 15.82 - 25.65 360 25.65 - 35.48 222 35.48 - 45.31 199 45.31 - 55.15 80 55.15 - 64.98 33 64.98 - 74.81 7 74.81 - 84.64 2 84.64 - 94.47 3 94.47 - 104.30 2 =========================== Idealize ADP of riding H ========================== r_work=0.1108 r_free=0.1535 r_work=0.1108 r_free=0.1536 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1108 r_free = 0.1536 target_work(ml) = 4.944 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1100 r_free = 0.1539 target_work(ml) = 4.939 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1100 r_free= 0.1539 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.939108 | | target function (ml) not normalized (work): 80181.483613 | | target function (ml) not normalized (free): 4174.711530 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1121 0.1100 0.1539 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1572 0.1560 0.1836 n_refl.: 17041 remove outliers: r(all,work,free)=0.1572 0.1560 0.1836 n_refl.: 17041 overall B=-0.29 to atoms: r(all,work,free)=0.1554 0.1541 0.1827 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1120 0.1098 0.1538 n_refl.: 17041 remove outliers: r(all,work,free)=0.1119 0.1097 0.1538 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 0.3661 302.569 281.230 0.553 1.002 0.334 11.894-9.307 99.02 97 4 0.1812 486.980 478.049 0.910 1.004 0.330 9.237-7.194 100.00 213 7 0.1808 398.300 398.736 0.984 1.004 0.238 7.162-5.571 100.00 427 22 0.1516 298.925 293.712 0.941 1.004 0.200 5.546-4.326 100.00 867 58 0.0906 410.376 406.657 0.965 1.003 0.185 4.315-3.360 100.00 1859 96 0.0841 390.271 387.919 1.007 1.003 0.171 3.356-2.611 100.00 3867 181 0.1228 256.386 254.322 1.006 1.001 0.131 2.608-2.000 99.99 8818 434 0.1037 167.120 165.966 1.003 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.0172 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1097 r_free=0.1538 After: r_work=0.1100 r_free=0.1538 ================================== NQH flips ================================== r_work=0.1100 r_free=0.1538 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1101 r_free=0.1538 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1101 r_free=0.1538 | n_water=445 | time (s): 0.950 (total time: 0.950) Filter (dist) r_work=0.1101 r_free=0.1538 | n_water=445 | time (s): 37.370 (total time: 38.320) Filter (q & B) r_work=0.1101 r_free=0.1538 | n_water=444 | time (s): 2.320 (total time: 40.640) Compute maps r_work=0.1101 r_free=0.1538 | n_water=444 | time (s): 0.740 (total time: 41.380) Filter (map) r_work=0.1179 r_free=0.1549 | n_water=332 | time (s): 1.770 (total time: 43.150) Find peaks r_work=0.1179 r_free=0.1549 | n_water=332 | time (s): 0.450 (total time: 43.600) Add new water r_work=0.1292 r_free=0.1656 | n_water=462 | time (s): 1.470 (total time: 45.070) Refine new water occ: r_work=0.1147 r_free=0.1478 adp: r_work=0.1142 r_free=0.1482 occ: r_work=0.1128 r_free=0.1466 adp: r_work=0.1122 r_free=0.1465 occ: r_work=0.1114 r_free=0.1460 adp: r_work=0.1107 r_free=0.1458 ADP+occupancy (water only), MIN, final r_work=0.1107 r_free=0.1458 r_work=0.1107 r_free=0.1458 | n_water=462 | time (s): 22.170 (total time: 67.240) Filter (q & B) r_work=0.1110 r_free=0.1470 | n_water=454 | time (s): 1.510 (total time: 68.750) Filter (dist only) r_work=0.1110 r_free=0.1472 | n_water=452 | time (s): 38.250 (total time: 107.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.935760 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.142109 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 0.1124 0.1484 0.0360 0.011 1.1 3.8 0.5 0.0 0 0.968 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.24 14.84 3.60 4.564 20.760 0.142 4.938 11.13 14.76 3.63 4.600 20.835 0.142 4.930 Individual atomic B min max mean iso aniso Overall: 5.31 102.18 20.84 4.95 1979 0 Protein: 5.31 102.18 16.35 4.94 1519 0 Water: 8.52 64.39 35.86 N/A 452 0 Other: 17.96 35.07 24.93 N/A 8 0 Chain A: 5.31 102.18 17.97 N/A 1734 0 Chain S: 20.15 64.39 41.16 N/A 245 0 Histogram: Values Number of atoms 5.31 - 15.00 1023 15.00 - 24.69 382 24.69 - 34.37 213 34.37 - 44.06 202 44.06 - 53.75 110 53.75 - 63.44 31 63.44 - 73.12 9 73.12 - 82.81 2 82.81 - 92.50 3 92.50 - 102.18 4 =========================== Idealize ADP of riding H ========================== r_work=0.1113 r_free=0.1476 r_work=0.1113 r_free=0.1476 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1113 r_free = 0.1476 target_work(ml) = 4.930 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1110 r_free = 0.1475 target_work(ml) = 4.926 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1110 r_free= 0.1475 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.926314 | | target function (ml) not normalized (work): 79968.855678 | | target function (ml) not normalized (free): 4152.130930 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1130 0.1376 5.4639 5.6422| | 2: 3.63 - 2.88 1.00 2711 122 0.1093 0.1409 5.2063 5.3311| | 3: 2.88 - 2.52 1.00 2681 148 0.1343 0.1631 5.1127 5.2019| | 4: 2.52 - 2.29 1.00 2661 139 0.0944 0.1447 4.6176 4.8937| | 5: 2.29 - 2.13 1.00 2678 122 0.0966 0.1522 4.5678 4.9122| | 6: 2.13 - 2.00 1.00 2692 117 0.1116 0.1698 4.5593 4.7456| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.59 1.00 0.96 6105.60| | 2: 3.63 - 2.88 2711 122 0.93 12.52 1.01 0.96 6105.60| | 3: 2.88 - 2.52 2681 148 0.88 18.65 0.99 0.96 6105.60| | 4: 2.52 - 2.29 2661 139 0.93 11.77 1.01 0.98 2033.83| | 5: 2.29 - 2.13 2678 122 0.92 13.83 1.00 0.98 2033.83| | 6: 2.13 - 2.00 2692 117 0.90 16.46 0.99 0.98 2033.83| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2033.83 max = 6105.60 mean = 4091.16| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.60| |phase err.(test): min = 0.00 max = 87.66 mean = 13.09| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1127 0.1110 0.1475 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1553 0.1539 0.1837 n_refl.: 17040 remove outliers: r(all,work,free)=0.1553 0.1539 0.1837 n_refl.: 17040 overall B=-0.26 to atoms: r(all,work,free)=0.1538 0.1524 0.1828 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1129 0.1112 0.1474 n_refl.: 17040 remove outliers: r(all,work,free)=0.1129 0.1112 0.1474 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 0.3681 302.569 279.942 0.531 1.003 0.311 11.894-9.307 99.02 97 4 0.1881 486.980 478.123 0.903 1.005 0.297 9.237-7.194 100.00 213 7 0.1774 398.300 400.268 0.988 1.005 0.210 7.162-5.571 100.00 427 22 0.1569 298.925 294.018 0.937 1.005 0.200 5.546-4.326 100.00 867 58 0.0929 410.376 407.069 0.965 1.004 0.175 4.315-3.360 100.00 1859 96 0.0882 390.271 388.046 1.006 1.003 0.171 3.356-2.611 100.00 3867 181 0.1230 256.386 254.276 1.004 1.000 0.063 2.608-2.000 99.99 8818 434 0.1041 167.120 165.914 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=-0.8894 ================= 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 : 0.2790 0.1843 0.081 5.237 8.8 119.3 19.9 258 0.000 1_bss: 0.1616 0.1682 0.081 5.237 8.5 118.9 19.5 258 0.000 1_settarget: 0.1616 0.1682 0.081 5.237 8.5 118.9 19.5 258 0.000 1_nqh: 0.1619 0.1685 0.081 5.237 8.5 118.9 19.5 258 0.006 1_weight: 0.1619 0.1685 0.081 5.237 8.5 118.9 19.5 258 0.006 1_xyzrec: 0.1347 0.1640 0.009 1.025 8.5 118.9 19.5 258 0.149 1_adp: 0.1274 0.1661 0.009 1.025 5.9 113.9 20.0 258 0.149 1_regHadp: 0.1278 0.1669 0.009 1.025 5.9 113.9 20.0 258 0.149 1_occ: 0.1274 0.1669 0.009 1.025 5.9 113.9 20.0 258 0.149 2_bss: 0.1271 0.1658 0.009 1.025 5.6 113.5 19.6 258 0.149 2_settarget: 0.1271 0.1658 0.009 1.025 5.6 113.5 19.6 258 0.149 2_updatecdl: 0.1271 0.1658 0.009 1.031 5.6 113.5 19.6 258 0.149 2_nqh: 0.1273 0.1661 0.009 1.031 5.6 113.5 19.6 258 0.146 2_sol: 0.1235 0.1558 0.009 1.031 5.6 112.5 20.9 364 n/a 2_weight: 0.1235 0.1558 0.009 1.031 5.6 112.5 20.9 364 n/a 2_xyzrec: 0.1208 0.1628 0.008 0.934 5.6 112.5 20.9 364 n/a 2_adp: 0.1191 0.1640 0.008 0.934 7.0 107.5 21.3 364 n/a 2_regHadp: 0.1192 0.1641 0.008 0.934 7.0 107.5 21.3 364 n/a 2_occ: 0.1187 0.1650 0.008 0.934 7.0 107.5 21.3 364 n/a 3_bss: 0.1185 0.1647 0.008 0.934 6.6 107.1 20.9 364 n/a 3_settarget: 0.1185 0.1647 0.008 0.934 6.6 107.1 20.9 364 n/a 3_updatecdl: 0.1185 0.1647 0.008 0.934 6.6 107.1 20.9 364 n/a 3_nqh: 0.1185 0.1647 0.008 0.934 6.6 107.1 20.9 364 n/a 3_sol: 0.1187 0.1557 0.008 0.934 6.6 107.1 20.9 401 n/a 3_weight: 0.1187 0.1557 0.008 0.934 6.6 107.1 20.9 401 n/a 3_xyzrec: 0.1162 0.1552 0.009 0.972 6.6 107.1 20.9 401 n/a 3_adp: 0.1145 0.1561 0.009 0.972 6.6 106.6 20.8 401 n/a 3_regHadp: 0.1145 0.1562 0.009 0.972 6.6 106.6 20.8 401 n/a 3_occ: 0.1136 0.1552 0.009 0.972 6.6 106.6 20.8 401 n/a 4_bss: 0.1134 0.1548 0.009 0.972 6.2 106.2 20.4 401 n/a 4_settarget: 0.1134 0.1548 0.009 0.972 6.2 106.2 20.4 401 n/a 4_updatecdl: 0.1134 0.1548 0.009 0.973 6.2 106.2 20.4 401 n/a 4_nqh: 0.1136 0.1547 0.009 0.973 6.2 106.2 20.4 401 n/a 4_sol: 0.1131 0.1483 0.009 0.973 6.2 106.2 20.9 445 n/a 4_weight: 0.1131 0.1483 0.009 0.973 6.2 106.2 20.9 445 n/a 4_xyzrec: 0.1117 0.1532 0.010 0.996 6.2 106.2 20.9 445 n/a 4_adp: 0.1108 0.1535 0.010 0.996 6.0 104.3 20.9 445 n/a 4_regHadp: 0.1108 0.1536 0.010 0.996 6.0 104.3 20.9 445 n/a 4_occ: 0.1100 0.1539 0.010 0.996 6.0 104.3 20.9 445 n/a 5_bss: 0.1097 0.1538 0.010 0.996 5.7 104.0 20.6 445 n/a 5_settarget: 0.1097 0.1538 0.010 0.996 5.7 104.0 20.6 445 n/a 5_updatecdl: 0.1097 0.1538 0.010 0.996 5.7 104.0 20.6 445 n/a 5_setrh: 0.1100 0.1538 0.010 0.996 5.7 104.0 20.6 445 n/a 5_nqh: 0.1101 0.1538 0.010 0.996 5.7 104.0 20.6 445 n/a 5_sol: 0.1110 0.1472 0.010 0.996 5.7 104.0 20.7 452 n/a 5_weight: 0.1110 0.1472 0.010 0.996 5.7 104.0 20.7 452 n/a 5_xyzrec: 0.1124 0.1484 0.011 1.110 5.7 104.0 20.7 452 n/a 5_adp: 0.1113 0.1476 0.011 1.110 5.3 102.2 20.8 452 n/a 5_regHadp: 0.1113 0.1476 0.011 1.110 5.3 102.2 20.8 452 n/a 5_occ: 0.1110 0.1475 0.011 1.110 5.3 102.2 20.8 452 n/a end: 0.1112 0.1474 0.011 1.110 5.1 101.9 20.6 452 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6727304_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6727304_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.2400 Refinement macro-cycles (run) : 923.9200 Write final files (write_after_run_outputs) : 19.8000 Total : 947.9600 Total CPU time: 16.23 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:17 PST -0800 (1735494077.09 s) Start R-work = 0.1616, R-free = 0.1682 Final R-work = 0.1112, R-free = 0.1474 =============================================================================== Job complete usr+sys time: 994.42 seconds wall clock time: 16 minutes 59.31 seconds (1019.31 seconds total)