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_6462862.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 { 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6462862.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6462862.pdb" } 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 3 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: 1.61, per 1000 atoms: 0.48 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: 0.34 Conformation dependent library (CDL) restraints added in 109.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 532 0.92 - 1.17: 1105 1.17 - 1.43: 688 1.43 - 1.69: 810 1.69 - 1.95: 18 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALEU A 153 " pdb=" CA ALEU A 153 " ideal model delta sigma weight residual 1.456 1.726 -0.269 1.21e-02 6.83e+03 4.96e+02 bond pdb=" C VAL A 69 " pdb=" O VAL A 69 " ideal model delta sigma weight residual 1.235 1.423 -0.188 1.02e-02 9.61e+03 3.40e+02 bond pdb=" N BLYS A 132 " pdb=" CA BLYS A 132 " ideal model delta sigma weight residual 1.459 1.669 -0.210 1.19e-02 7.06e+03 3.12e+02 bond pdb=" N ASP A 60 " pdb=" CA ASP A 60 " ideal model delta sigma weight residual 1.459 1.255 0.204 1.17e-02 7.31e+03 3.03e+02 bond pdb=" N LEU A 72 " pdb=" CA LEU A 72 " ideal model delta sigma weight residual 1.454 1.661 -0.207 1.21e-02 6.83e+03 2.91e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 2904 4.22 - 8.44: 1893 8.44 - 12.65: 760 12.65 - 16.87: 193 16.87 - 21.09: 27 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ILE A 117 " pdb=" C ILE A 117 " pdb=" O ILE A 117 " ideal model delta sigma weight residual 120.84 136.82 -15.98 1.16e+00 7.43e-01 1.90e+02 angle pdb=" CA LYS A 12 " pdb=" C LYS A 12 " pdb=" O LYS A 12 " ideal model delta sigma weight residual 120.96 105.98 14.98 1.09e+00 8.42e-01 1.89e+02 angle pdb=" O VAL A 169 " pdb=" C VAL A 169 " pdb=" N GLU A 170 " ideal model delta sigma weight residual 121.91 135.32 -13.41 9.80e-01 1.04e+00 1.87e+02 angle pdb=" O ARG A 28 " pdb=" C ARG A 28 " pdb=" N ALA A 29 " ideal model delta sigma weight residual 122.12 107.87 14.25 1.06e+00 8.90e-01 1.81e+02 angle pdb=" C LEU A 72 " pdb=" CA LEU A 72 " pdb=" CB LEU A 72 " ideal model delta sigma weight residual 110.17 123.12 -12.95 9.90e-01 1.02e+00 1.71e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 1322 17.98 - 35.96: 108 35.96 - 53.93: 38 53.93 - 71.91: 10 71.91 - 89.89: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ASP A 49 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual -122.60 -147.92 25.32 0 2.50e+00 1.60e-01 1.03e+02 dihedral pdb=" C ALA A 86 " pdb=" N ALA A 86 " pdb=" CA ALA A 86 " pdb=" CB ALA A 86 " ideal model delta harmonic sigma weight residual -122.60 -146.84 24.24 0 2.50e+00 1.60e-01 9.40e+01 dihedral pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual 122.80 146.09 -23.29 0 2.50e+00 1.60e-01 8.68e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.272: 117 0.272 - 0.544: 84 0.544 - 0.815: 28 0.815 - 1.086: 12 1.086 - 1.358: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 49 " pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CB ASP A 49 " both_signs ideal model delta sigma weight residual False 2.51 1.15 1.36 2.00e-01 2.50e+01 4.61e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.35 -1.24 2.00e-01 2.50e+01 3.83e+01 chirality pdb=" CA ALA A 86 " pdb=" N ALA A 86 " pdb=" C ALA A 86 " pdb=" CB ALA A 86 " both_signs ideal model delta sigma weight residual False 2.48 1.47 1.01 2.00e-01 2.50e+01 2.57e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.072 2.00e-02 2.50e+03 6.94e-02 1.44e+02 pdb=" CG PHE A 164 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.134 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.079 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.065 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.034 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.058 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.016 2.00e-02 2.50e+03 6.26e-02 1.18e+02 pdb=" CG PHE A 162 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.096 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.089 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.010 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.095 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.085 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.019 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.079 2.00e-02 2.50e+03 5.99e-02 1.08e+02 pdb=" CG ATYR A 67 " -0.065 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.035 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.115 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.011 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.042 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.043 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.021 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.088 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.026 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 398 2.19 - 2.80: 7074 2.80 - 3.40: 10882 3.40 - 4.00: 15533 4.00 - 4.60: 22718 Nonbonded interactions: 56605 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.592 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.789 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.803 2.450 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.810 2.100 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.823 2.100 ... (remaining 56600 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_6462862_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= 0.2791 r_free= 0.1824 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.399781 | | target function (ml) not normalized (work): 71465.643093 | | target function (ml) not normalized (free): 3269.733706 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3193 0.2124 7.5142 5.0304| | 2: 3.63 - 2.88 1.00 2711 122 0.2641 0.1798 4.3297 4.3354| | 3: 2.88 - 2.52 1.00 2682 148 0.2593 0.1683 4.1862 4.1977| | 4: 2.52 - 2.29 1.00 2661 139 0.2551 0.1563 3.503 3.5894| | 5: 2.29 - 2.13 1.00 2678 122 0.2650 0.1506 3.3921 3.4579| | 6: 2.13 - 2.00 1.00 2692 117 0.2730 0.1805 3.3107 3.4097| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.66 0.77 0.23 1313.00| | 2: 3.63 - 2.88 2711 122 0.83 23.93 1.31 0.23 1313.00| | 3: 2.88 - 2.52 2682 148 0.73 33.04 1.29 0.23 1313.00| | 4: 2.52 - 2.29 2661 139 0.94 11.05 1.30 0.26 131.77| | 5: 2.29 - 2.13 2678 122 0.92 13.27 1.31 0.26 131.77| | 6: 2.13 - 2.00 2692 117 0.90 16.15 1.34 0.26 131.77| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 131.77 max = 1313.00 mean = 728.97| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.98 mean = 19.19| |phase err.(test): min = 0.00 max = 88.62 mean = 19.24| |-----------------------------------------------------------------------------| ----------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 0.269 1557 Z= 5.407 Angle : 5.189 18.284 2118 Z= 3.660 Chirality : 0.408 1.358 243 Planarity : 0.032 0.088 284 Dihedral : 13.844 89.886 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.41 % Favored : 94.05 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 35.14 % 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: -3.21 (0.42), residues: 224 helix: -2.76 (0.33), residues: 107 sheet: -2.02 (0.79), residues: 24 loop : -1.05 (0.51), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.093 0.026 ARG A 98 TYR 0.072 0.044 TYR A 139 PHE 0.095 0.041 PHE A 164 HIS 0.045 0.026 HIS A 115 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= 0.2791 r_free= 0.1824 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.399781 | | target function (ml) not normalized (work): 71465.643093 | | target function (ml) not normalized (free): 3269.733706 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3049 percent. r_work = 0.2921 r_free = 0.2010 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2868 0.2921 0.2010 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2868 0.2921 0.2010 n_refl.: 17050 remove outliers: r(all,work,free)=0.2159 0.2169 0.2010 n_refl.: 17045 overall B=-0.42 to atoms: r(all,work,free)=0.2130 0.2140 0.1991 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1613 0.1609 0.1686 n_refl.: 17045 remove outliers: r(all,work,free)=0.1611 0.1607 0.1686 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 0.3935 398.997 369.812 0.670 1.004 0.397 11.894-9.307 99.02 97 4 0.1872 633.702 614.794 0.938 1.005 0.380 9.237-7.194 100.00 213 7 0.2179 518.304 510.318 0.965 1.005 0.345 7.162-5.571 100.00 427 22 0.2334 388.988 375.447 0.927 1.005 0.321 5.546-4.326 100.00 867 58 0.1391 534.018 529.395 0.965 1.005 0.225 4.315-3.360 100.00 1859 96 0.1303 507.856 504.302 1.020 1.003 0.159 3.356-2.611 100.00 3867 181 0.1653 333.633 328.646 1.015 1.001 0.058 2.608-2.000 99.99 8818 434 0.1631 217.471 213.671 1.025 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4911 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1607 r_free=0.1686 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1607 r_free=0.1685 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.968661 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.837836 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 0.1353 0.1633 0.0279 0.008 1.0 1.0 0.5 0.0 0 10.984 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.53 16.33 2.79 3.013 18.441 0.838 0.023 12.78 16.63 3.85 3.599 18.719 0.838 0.020 Individual atomic B min max mean iso aniso Overall: 6.26 113.88 20.00 4.05 1785 0 Protein: 6.26 112.48 17.23 4.05 1519 0 Water: 9.15 113.88 36.09 N/A 258 0 Other: 21.66 37.44 26.40 N/A 8 0 Chain A: 6.26 113.88 20.00 N/A 1785 0 Histogram: Values Number of atoms 6.26 - 17.02 1088 17.02 - 27.78 341 27.78 - 38.55 183 38.55 - 49.31 98 49.31 - 60.07 48 60.07 - 70.83 13 70.83 - 81.59 6 81.59 - 92.36 4 92.36 - 103.12 1 103.12 - 113.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1278 r_free=0.1663 r_work=0.1280 r_free=0.1669 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1280 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 = 0.1275 r_free = 0.1661 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.14 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= 0.1275 r_free= 0.1661 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019963 | | target function (ls_wunit_k1) not normalized (work): 324.116063 | | target function (ls_wunit_k1) not normalized (free): 27.212069 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1294 0.1275 0.1661 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1905 0.1904 0.1988 n_refl.: 17043 remove outliers: r(all,work,free)=0.1905 0.1904 0.1988 n_refl.: 17043 overall B=-0.38 to atoms: r(all,work,free)=0.1878 0.1876 0.1971 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1275 0.1650 n_refl.: 17043 remove outliers: r(all,work,free)=0.1293 0.1275 0.1650 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 96.88 88 5 0.3589 307.412 286.054 0.656 1.000 0.389 11.894-9.307 99.02 97 4 0.1711 488.243 478.309 0.928 0.999 0.380 9.237-7.194 100.00 213 7 0.1814 399.334 397.592 0.971 0.998 0.325 7.162-5.571 100.00 427 22 0.1856 299.700 295.108 0.943 0.997 0.311 5.546-4.326 100.00 867 58 0.1042 411.441 409.674 0.968 0.995 0.200 4.315-3.360 100.00 1859 96 0.0922 391.284 391.158 1.028 0.991 0.139 3.356-2.611 100.00 3867 181 0.1297 257.051 255.624 1.028 0.986 0.101 2.608-2.000 99.99 8818 434 0.1352 167.553 165.677 1.037 0.976 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3450 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1650 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1277 r_free=0.1652 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1652 | n_water=258 | time (s): 0.910 (total time: 0.910) Filter (dist) r_work=0.1288 r_free=0.1639 | n_water=251 | time (s): 20.520 (total time: 21.430) Filter (q & B) r_work=0.1288 r_free=0.1637 | n_water=249 | time (s): 1.440 (total time: 22.870) Compute maps r_work=0.1288 r_free=0.1637 | n_water=249 | time (s): 0.520 (total time: 23.390) Filter (map) r_work=0.1329 r_free=0.1638 | n_water=206 | time (s): 1.660 (total time: 25.050) Find peaks r_work=0.1329 r_free=0.1638 | n_water=206 | time (s): 0.470 (total time: 25.520) Add new water r_work=0.1548 r_free=0.1865 | n_water=368 | time (s): 1.430 (total time: 26.950) Refine new water occ: r_work=0.1344 r_free=0.1608 adp: r_work=0.1283 r_free=0.1578 occ: r_work=0.1288 r_free=0.1569 adp: r_work=0.1254 r_free=0.1558 occ: r_work=0.1253 r_free=0.1555 adp: r_work=0.1244 r_free=0.1552 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1552 r_work=0.1244 r_free=0.1552 | n_water=368 | time (s): 23.350 (total time: 50.300) Filter (q & B) r_work=0.1245 r_free=0.1552 | n_water=360 | time (s): 2.080 (total time: 52.380) Filter (dist only) r_work=0.1246 r_free=0.1549 | n_water=358 | time (s): 28.620 (total time: 81.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.400664 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.982661 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 0.1216 0.1576 0.0360 0.008 0.9 4.2 0.5 0.0 0 12.200 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.16 15.76 3.60 4.158 21.098 0.983 0.018 11.99 16.00 4.01 4.239 21.390 0.983 0.018 Individual atomic B min max mean iso aniso Overall: 6.33 107.10 21.44 4.33 1885 0 Protein: 6.33 107.10 17.82 4.32 1519 0 Water: 8.66 65.79 36.48 N/A 358 0 Other: 25.46 46.09 35.85 N/A 8 0 Chain A: 6.33 107.10 19.45 N/A 1733 0 Chain S: 17.15 62.75 44.06 N/A 152 0 Histogram: Values Number of atoms 6.33 - 16.41 1006 16.41 - 26.49 384 26.49 - 36.56 218 36.56 - 46.64 158 46.64 - 56.72 81 56.72 - 66.80 26 66.80 - 76.87 5 76.87 - 86.95 3 86.95 - 97.03 2 97.03 - 107.10 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1600 r_work=0.1201 r_free=0.1602 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1602 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 = 0.1200 r_free = 0.1607 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1200 r_free= 0.1607 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017106 | | target function (ls_wunit_k1) not normalized (work): 277.734279 | | target function (ls_wunit_k1) not normalized (free): 25.346481 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1200 0.1607 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1815 0.1811 0.1952 n_refl.: 17043 remove outliers: r(all,work,free)=0.1815 0.1811 0.1952 n_refl.: 17043 overall B=-0.51 to atoms: r(all,work,free)=0.1780 0.1775 0.1929 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1192 0.1598 n_refl.: 17043 remove outliers: r(all,work,free)=0.1212 0.1192 0.1598 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 96.88 88 5 0.3336 307.412 288.160 0.635 1.006 0.377 11.894-9.307 99.02 97 4 0.1475 488.243 484.416 0.923 1.006 0.360 9.237-7.194 100.00 213 7 0.1660 399.334 399.404 0.974 1.006 0.285 7.162-5.571 100.00 427 22 0.1601 299.700 296.290 0.935 1.005 0.271 5.546-4.326 100.00 867 58 0.0868 411.441 408.941 0.957 1.005 0.206 4.315-3.360 100.00 1859 96 0.0832 391.284 390.618 1.014 1.003 0.193 3.356-2.611 100.00 3867 181 0.1204 257.051 256.171 1.009 1.001 0.112 2.608-2.000 99.99 8818 434 0.1329 167.553 166.464 1.010 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1591 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1598 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1598 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1598 | n_water=358 | time (s): 0.830 (total time: 0.830) Filter (dist) r_work=0.1192 r_free=0.1600 | n_water=357 | time (s): 29.840 (total time: 30.670) Filter (q & B) r_work=0.1192 r_free=0.1601 | n_water=356 | time (s): 1.680 (total time: 32.350) Compute maps r_work=0.1192 r_free=0.1601 | n_water=356 | time (s): 0.640 (total time: 32.990) Filter (map) r_work=0.1266 r_free=0.1628 | n_water=255 | time (s): 2.070 (total time: 35.060) Find peaks r_work=0.1266 r_free=0.1628 | n_water=255 | time (s): 0.650 (total time: 35.710) Add new water r_work=0.1454 r_free=0.1838 | n_water=405 | time (s): 2.070 (total time: 37.780) Refine new water occ: r_work=0.1257 r_free=0.1612 adp: r_work=0.1249 r_free=0.1616 occ: r_work=0.1231 r_free=0.1583 adp: r_work=0.1220 r_free=0.1585 occ: r_work=0.1213 r_free=0.1565 adp: r_work=0.1202 r_free=0.1565 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1565 r_work=0.1202 r_free=0.1565 | n_water=405 | time (s): 40.240 (total time: 78.020) Filter (q & B) r_work=0.1206 r_free=0.1576 | n_water=394 | time (s): 1.450 (total time: 79.470) Filter (dist only) r_work=0.1206 r_free=0.1576 | n_water=393 | time (s): 31.900 (total time: 111.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.899458 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.124617 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1182 0.1566 0.0383 0.009 1.0 3.5 0.5 0.0 0 0.950 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.82 15.66 3.83 4.383 21.485 0.125 4.999 11.66 15.77 4.11 4.953 21.336 0.125 4.981 Individual atomic B min max mean iso aniso Overall: 6.08 102.98 20.67 4.59 1920 0 Protein: 6.08 102.98 16.91 4.58 1519 0 Water: 8.68 63.34 34.95 N/A 393 0 Other: 25.59 44.67 33.38 N/A 8 0 Chain A: 6.08 102.98 18.54 N/A 1729 0 Chain S: 15.07 63.34 40.03 N/A 191 0 Histogram: Values Number of atoms 6.08 - 15.77 1030 15.77 - 25.46 374 25.46 - 35.15 226 35.15 - 44.84 167 44.84 - 54.53 76 54.53 - 64.22 34 64.22 - 73.91 4 73.91 - 83.60 5 83.60 - 93.29 2 93.29 - 102.98 2 =========================== Idealize ADP of riding H ========================== r_work=0.1166 r_free=0.1577 r_work=0.1166 r_free=0.1578 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1166 r_free = 0.1578 target_work(ml) = 4.981 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1157 r_free = 0.1571 target_work(ml) = 4.974 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1157 r_free= 0.1571 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.974224 | | target function (ml) not normalized (work): 80761.502832 | | target function (ml) not normalized (free): 4200.390812 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1177 0.1157 0.1571 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1725 0.1719 0.1901 n_refl.: 17043 remove outliers: r(all,work,free)=0.1725 0.1719 0.1901 n_refl.: 17043 overall B=-0.51 to atoms: r(all,work,free)=0.1688 0.1681 0.1882 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1173 0.1153 0.1567 n_refl.: 17043 remove outliers: r(all,work,free)=0.1171 0.1151 0.1567 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 0.3562 306.017 277.794 0.580 1.007 0.353 11.894-9.307 99.02 97 4 0.1742 488.243 479.298 0.909 1.007 0.340 9.237-7.194 100.00 213 7 0.1855 399.334 398.821 0.976 1.007 0.260 7.162-5.571 100.00 427 22 0.1685 299.700 294.748 0.944 1.006 0.251 5.546-4.326 100.00 867 58 0.0952 411.441 408.216 0.965 1.005 0.206 4.315-3.360 100.00 1859 96 0.0919 391.284 389.040 1.012 1.004 0.202 3.356-2.611 100.00 3867 181 0.1287 257.051 254.746 1.009 1.001 0.142 2.608-2.000 99.99 8818 434 0.1073 167.553 166.167 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9584 b_overall=-1.1541 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1151 r_free=0.1567 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1151 r_free=0.1567 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1151 r_free=0.1567 | n_water=393 | time (s): 0.930 (total time: 0.930) Filter (dist) r_work=0.1151 r_free=0.1567 | n_water=393 | time (s): 30.370 (total time: 31.300) Filter (q & B) r_work=0.1151 r_free=0.1567 | n_water=393 | time (s): 0.780 (total time: 32.080) Compute maps r_work=0.1151 r_free=0.1567 | n_water=393 | time (s): 0.580 (total time: 32.660) Filter (map) r_work=0.1206 r_free=0.1575 | n_water=305 | time (s): 1.920 (total time: 34.580) Find peaks r_work=0.1206 r_free=0.1575 | n_water=305 | time (s): 0.670 (total time: 35.250) Add new water r_work=0.1362 r_free=0.1721 | n_water=449 | time (s): 2.270 (total time: 37.520) Refine new water occ: r_work=0.1189 r_free=0.1553 adp: r_work=0.1180 r_free=0.1550 occ: r_work=0.1164 r_free=0.1540 adp: r_work=0.1153 r_free=0.1532 occ: r_work=0.1146 r_free=0.1538 adp: r_work=0.1137 r_free=0.1530 ADP+occupancy (water only), MIN, final r_work=0.1137 r_free=0.1530 r_work=0.1137 r_free=0.1530 | n_water=449 | time (s): 38.330 (total time: 75.850) Filter (q & B) r_work=0.1140 r_free=0.1537 | n_water=438 | time (s): 1.430 (total time: 77.280) Filter (dist only) r_work=0.1143 r_free=0.1537 | n_water=437 | time (s): 34.540 (total time: 111.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.934998 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.144338 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 0.1126 0.1553 0.0427 0.009 1.0 3.2 0.5 0.0 0 0.967 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 15.53 4.27 4.431 20.844 0.144 4.961 11.16 15.51 4.36 4.561 20.862 0.144 4.953 Individual atomic B min max mean iso aniso Overall: 5.58 101.22 20.72 4.71 1964 0 Protein: 5.58 101.22 16.37 4.70 1519 0 Water: 8.37 64.39 35.68 N/A 437 0 Other: 24.16 42.77 30.77 N/A 8 0 Chain A: 5.58 101.22 17.94 N/A 1728 0 Chain S: 18.52 64.39 41.13 N/A 236 0 Histogram: Values Number of atoms 5.58 - 15.14 1021 15.14 - 24.71 386 24.71 - 34.27 210 34.27 - 43.84 191 43.84 - 53.40 102 53.40 - 62.97 36 62.97 - 72.53 8 72.53 - 82.09 5 82.09 - 91.66 3 91.66 - 101.22 2 =========================== Idealize ADP of riding H ========================== r_work=0.1116 r_free=0.1551 r_work=0.1116 r_free=0.1552 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1116 r_free = 0.1552 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1108 r_free = 0.1558 target_work(ml) = 4.951 | | occupancies: max = 1.00 min = 0.21 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= 0.1108 r_free= 0.1558 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.951260 | | target function (ml) not normalized (work): 80378.748941 | | target function (ml) not normalized (free): 4189.455904 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1130 0.1108 0.1558 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1590 0.1579 0.1846 n_refl.: 17041 remove outliers: r(all,work,free)=0.1590 0.1579 0.1846 n_refl.: 17041 overall B=-0.27 to atoms: r(all,work,free)=0.1573 0.1562 0.1836 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1126 0.1105 0.1551 n_refl.: 17041 remove outliers: r(all,work,free)=0.1126 0.1104 0.1551 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 0.3631 303.354 278.250 0.566 1.005 0.350 11.894-9.307 99.02 97 4 0.1763 488.243 481.853 0.907 1.005 0.340 9.237-7.194 100.00 213 7 0.1802 399.334 399.402 0.982 1.005 0.230 7.162-5.571 100.00 427 22 0.1598 299.700 293.136 0.936 1.005 0.196 5.546-4.326 100.00 867 58 0.0915 411.441 407.856 0.965 1.004 0.181 4.315-3.360 100.00 1859 96 0.0859 391.284 389.299 1.006 1.003 0.181 3.356-2.611 100.00 3867 181 0.1221 257.051 254.750 1.002 1.001 0.131 2.608-2.000 99.99 8818 434 0.1042 167.553 166.304 0.998 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.9151 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1104 r_free=0.1551 After: r_work=0.1106 r_free=0.1550 ================================== NQH flips ================================== r_work=0.1106 r_free=0.1550 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1106 r_free=0.1550 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1106 r_free=0.1550 | n_water=437 | time (s): 0.950 (total time: 0.950) Filter (dist) r_work=0.1106 r_free=0.1550 | n_water=437 | time (s): 34.630 (total time: 35.580) Filter (q & B) r_work=0.1106 r_free=0.1550 | n_water=437 | time (s): 1.390 (total time: 36.970) Compute maps r_work=0.1106 r_free=0.1550 | n_water=437 | time (s): 0.890 (total time: 37.860) Filter (map) r_work=0.1185 r_free=0.1528 | n_water=332 | time (s): 2.140 (total time: 40.000) Find peaks r_work=0.1185 r_free=0.1528 | n_water=332 | time (s): 0.670 (total time: 40.670) Add new water r_work=0.1304 r_free=0.1625 | n_water=474 | time (s): 2.160 (total time: 42.830) Refine new water occ: r_work=0.1143 r_free=0.1509 adp: r_work=0.1135 r_free=0.1500 occ: r_work=0.1122 r_free=0.1502 adp: r_work=0.1112 r_free=0.1494 occ: r_work=0.1108 r_free=0.1495 adp: r_work=0.1100 r_free=0.1492 ADP+occupancy (water only), MIN, final r_work=0.1100 r_free=0.1492 r_work=0.1100 r_free=0.1492 | n_water=474 | time (s): 36.650 (total time: 79.480) Filter (q & B) r_work=0.1107 r_free=0.1506 | n_water=459 | time (s): 1.590 (total time: 81.070) Filter (dist only) r_work=0.1107 r_free=0.1508 | n_water=458 | time (s): 36.000 (total time: 117.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.969979 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.149991 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 0.1519 0.0402 0.010 1.0 4.8 0.5 0.0 0 0.985 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.17 15.19 4.02 4.455 20.638 0.150 4.944 11.07 15.06 3.99 4.531 20.711 0.150 4.936 Individual atomic B min max mean iso aniso Overall: 5.33 100.75 20.79 4.89 1985 0 Protein: 5.33 100.75 16.17 4.88 1519 0 Water: 8.22 67.28 35.91 N/A 458 0 Other: 24.85 42.70 32.06 N/A 8 0 Chain A: 5.33 100.75 17.73 N/A 1728 0 Chain S: 15.12 67.28 41.33 N/A 257 0 Histogram: Values Number of atoms 5.33 - 14.87 1007 14.87 - 24.41 397 24.41 - 33.95 211 33.95 - 43.50 202 43.50 - 53.04 112 53.04 - 62.58 35 62.58 - 72.12 12 72.12 - 81.66 3 81.66 - 91.21 2 91.21 - 100.75 4 =========================== Idealize ADP of riding H ========================== r_work=0.1107 r_free=0.1506 r_work=0.1107 r_free=0.1505 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1107 r_free = 0.1505 target_work(ml) = 4.936 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1102 r_free = 0.1510 target_work(ml) = 4.934 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1102 r_free= 0.1510 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.933556 | | target function (ml) not normalized (work): 80086.413098 | | target function (ml) not normalized (free): 4176.593922 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1117 0.1429 5.4539 5.6923| | 2: 3.63 - 2.88 1.00 2711 122 0.1095 0.1495 5.229 5.3815| | 3: 2.88 - 2.52 1.00 2681 148 0.1346 0.1588 5.1416 5.1974| | 4: 2.52 - 2.29 1.00 2661 139 0.0919 0.1549 4.6154 4.9681| | 5: 2.29 - 2.13 1.00 2678 122 0.0961 0.1512 4.5704 4.903| | 6: 2.13 - 2.00 1.00 2692 117 0.1109 0.1647 4.5614 4.7609| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.94 9.38 1.00 0.96 6690.02| | 2: 3.63 - 2.88 2711 122 0.92 13.18 1.01 0.96 6690.02| | 3: 2.88 - 2.52 2681 148 0.87 19.36 0.99 0.96 6690.02| | 4: 2.52 - 2.29 2661 139 0.93 11.95 1.01 0.97 2072.39| | 5: 2.29 - 2.13 2678 122 0.91 14.03 1.00 0.97 2072.39| | 6: 2.13 - 2.00 2692 117 0.90 16.69 0.99 0.97 2072.39| |alpha: min = 0.96 max = 0.97 mean = 0.97| |beta: min = 2072.39 max = 6690.02 mean = 4405.53| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.96 mean = 14.06| |phase err.(test): min = 0.00 max = 86.12 mean = 13.55| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1122 0.1102 0.1510 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1549 0.1536 0.1825 n_refl.: 17040 remove outliers: r(all,work,free)=0.1549 0.1536 0.1825 n_refl.: 17040 overall B=-0.21 to atoms: r(all,work,free)=0.1537 0.1524 0.1819 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1123 0.1103 0.1509 n_refl.: 17040 remove outliers: r(all,work,free)=0.1123 0.1103 0.1509 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 0.3523 303.354 278.087 0.572 1.003 0.360 11.894-9.307 99.02 97 4 0.1705 488.243 482.041 0.912 1.003 0.320 9.237-7.194 100.00 213 7 0.1764 399.334 399.684 0.987 1.003 0.230 7.162-5.571 100.00 427 22 0.1592 299.700 293.180 0.934 1.003 0.185 5.546-4.326 100.00 867 58 0.0918 411.441 407.986 0.964 1.003 0.180 4.315-3.360 100.00 1859 96 0.0882 391.284 388.931 1.003 1.002 0.181 3.356-2.611 100.00 3867 181 0.1228 257.051 254.794 0.998 1.001 0.121 2.608-2.000 99.99 8818 434 0.1031 167.553 166.268 0.986 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7248 ================= 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 : 0.2791 0.1824 0.081 5.189 8.8 119.3 19.9 258 0.000 1_bss: 0.1607 0.1686 0.081 5.189 8.4 118.9 19.5 258 0.000 1_settarget: 0.1607 0.1686 0.081 5.189 8.4 118.9 19.5 258 0.000 1_nqh: 0.1607 0.1685 0.081 5.189 8.4 118.9 19.5 258 0.003 1_weight: 0.1607 0.1685 0.081 5.189 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1353 0.1633 0.008 0.958 8.4 118.9 19.5 258 0.153 1_adp: 0.1278 0.1663 0.008 0.958 6.3 113.9 20.0 258 0.153 1_regHadp: 0.1280 0.1669 0.008 0.958 6.3 113.9 20.0 258 0.153 1_occ: 0.1275 0.1661 0.008 0.958 6.3 113.9 20.0 258 0.153 2_bss: 0.1275 0.1650 0.008 0.958 5.9 113.5 19.6 258 0.153 2_settarget: 0.1275 0.1650 0.008 0.958 5.9 113.5 19.6 258 0.153 2_updatecdl: 0.1275 0.1650 0.008 0.972 5.9 113.5 19.6 258 0.153 2_nqh: 0.1277 0.1652 0.008 0.972 5.9 113.5 19.6 258 0.150 2_sol: 0.1246 0.1549 0.008 0.972 5.9 112.1 20.9 358 n/a 2_weight: 0.1246 0.1549 0.008 0.972 5.9 112.1 20.9 358 n/a 2_xyzrec: 0.1216 0.1576 0.008 0.921 5.9 112.1 20.9 358 n/a 2_adp: 0.1199 0.1600 0.008 0.921 6.3 107.1 21.4 358 n/a 2_regHadp: 0.1201 0.1602 0.008 0.921 6.3 107.1 21.4 358 n/a 2_occ: 0.1200 0.1607 0.008 0.921 6.3 107.1 21.4 358 n/a 3_bss: 0.1192 0.1598 0.008 0.921 5.8 106.6 20.9 358 n/a 3_settarget: 0.1192 0.1598 0.008 0.921 5.8 106.6 20.9 358 n/a 3_updatecdl: 0.1192 0.1598 0.008 0.921 5.8 106.6 20.9 358 n/a 3_nqh: 0.1192 0.1598 0.008 0.921 5.8 106.6 20.9 358 n/a 3_sol: 0.1206 0.1576 0.008 0.921 5.8 106.6 20.9 393 n/a 3_weight: 0.1206 0.1576 0.008 0.921 5.8 106.6 20.9 393 n/a 3_xyzrec: 0.1182 0.1566 0.009 0.963 5.8 106.6 20.9 393 n/a 3_adp: 0.1166 0.1577 0.009 0.963 6.1 103.0 20.7 393 n/a 3_regHadp: 0.1166 0.1578 0.009 0.963 6.1 103.0 20.7 393 n/a 3_occ: 0.1157 0.1571 0.009 0.963 6.1 103.0 20.7 393 n/a 4_bss: 0.1151 0.1567 0.009 0.963 5.6 102.5 20.2 393 n/a 4_settarget: 0.1151 0.1567 0.009 0.963 5.6 102.5 20.2 393 n/a 4_updatecdl: 0.1151 0.1567 0.009 0.963 5.6 102.5 20.2 393 n/a 4_nqh: 0.1151 0.1567 0.009 0.963 5.6 102.5 20.2 393 n/a 4_sol: 0.1143 0.1537 0.009 0.963 5.6 102.5 20.7 437 n/a 4_weight: 0.1143 0.1537 0.009 0.963 5.6 102.5 20.7 437 n/a 4_xyzrec: 0.1126 0.1553 0.009 0.973 5.6 102.5 20.7 437 n/a 4_adp: 0.1116 0.1551 0.009 0.973 5.6 101.2 20.7 437 n/a 4_regHadp: 0.1116 0.1552 0.009 0.973 5.6 101.2 20.7 437 n/a 4_occ: 0.1108 0.1558 0.009 0.973 5.6 101.2 20.7 437 n/a 5_bss: 0.1104 0.1551 0.009 0.973 5.3 101.0 20.5 437 n/a 5_settarget: 0.1104 0.1551 0.009 0.973 5.3 101.0 20.5 437 n/a 5_updatecdl: 0.1104 0.1551 0.009 0.972 5.3 101.0 20.5 437 n/a 5_setrh: 0.1106 0.1550 0.009 0.972 5.3 101.0 20.5 437 n/a 5_nqh: 0.1106 0.1550 0.009 0.972 5.3 101.0 20.5 437 n/a 5_sol: 0.1107 0.1508 0.009 0.972 5.3 101.0 20.7 458 n/a 5_weight: 0.1107 0.1508 0.009 0.972 5.3 101.0 20.7 458 n/a 5_xyzrec: 0.1117 0.1519 0.010 1.020 5.3 101.0 20.7 458 n/a 5_adp: 0.1107 0.1506 0.010 1.020 5.3 100.7 20.8 458 n/a 5_regHadp: 0.1107 0.1505 0.010 1.020 5.3 100.7 20.8 458 n/a 5_occ: 0.1102 0.1510 0.010 1.020 5.3 100.7 20.8 458 n/a end: 0.1103 0.1509 0.010 1.020 5.1 100.5 20.6 458 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6462862_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6462862_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8700 Refinement macro-cycles (run) : 954.4000 Write final files (write_after_run_outputs) : 16.3600 Total : 974.6300 Total CPU time: 16.63 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:39 PST -0800 (1735494099.01 s) Start R-work = 0.1607, R-free = 0.1686 Final R-work = 0.1103, R-free = 0.1509 =============================================================================== Job complete usr+sys time: 1016.75 seconds wall clock time: 17 minutes 19.45 seconds (1039.45 seconds total)