Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5431713.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_5431713.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5431713.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 1.70, per 1000 atoms: 0.50 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: 0.53 Conformation dependent library (CDL) restraints added in 167.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.90: 481 0.90 - 1.16: 1143 1.16 - 1.41: 623 1.41 - 1.67: 871 1.67 - 1.92: 35 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 8 " pdb=" O VAL A 8 " ideal model delta sigma weight residual 1.237 1.004 0.233 1.08e-02 8.57e+03 4.67e+02 bond pdb=" N ALA A 178 " pdb=" CA ALA A 178 " ideal model delta sigma weight residual 1.459 1.706 -0.247 1.20e-02 6.94e+03 4.23e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.526 -0.205 1.00e-02 1.00e+04 4.20e+02 bond pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " ideal model delta sigma weight residual 1.326 1.123 0.203 1.10e-02 8.26e+03 3.40e+02 bond pdb=" N LEU A 72 " pdb=" CA LEU A 72 " ideal model delta sigma weight residual 1.460 1.266 0.194 1.10e-02 8.26e+03 3.10e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.76: 3189 4.76 - 9.52: 1851 9.52 - 14.29: 626 14.29 - 19.05: 104 19.05 - 23.81: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O BASN A 97 " pdb=" C BASN A 97 " pdb=" N ARG A 98 " ideal model delta sigma weight residual 122.12 137.77 -15.65 1.06e+00 8.90e-01 2.18e+02 angle pdb=" N MET A 26 " pdb=" CA MET A 26 " pdb=" C MET A 26 " ideal model delta sigma weight residual 111.28 125.26 -13.98 1.09e+00 8.42e-01 1.64e+02 angle pdb=" CA LEU A 101 " pdb=" C LEU A 101 " pdb=" O LEU A 101 " ideal model delta sigma weight residual 121.05 135.61 -14.56 1.14e+00 7.69e-01 1.63e+02 angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.29 111.03 8.26 6.50e-01 2.37e+00 1.62e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 131.43 -10.20 8.10e-01 1.52e+00 1.59e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 1300 17.00 - 34.00: 124 34.00 - 51.00: 40 51.00 - 68.00: 16 68.00 - 85.00: 1 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 -151.44 28.84 0 2.50e+00 1.60e-01 1.33e+02 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 122.80 147.76 -24.96 0 2.50e+00 1.60e-01 9.97e+01 dihedral pdb=" C THR A 140 " pdb=" N THR A 140 " pdb=" CA THR A 140 " pdb=" CB THR A 140 " ideal model delta harmonic sigma weight residual -122.00 -140.71 18.71 0 2.50e+00 1.60e-01 5.60e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.239: 107 0.239 - 0.476: 85 0.476 - 0.712: 34 0.712 - 0.949: 14 0.949 - 1.185: 3 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 1.33 1.18 2.00e-01 2.50e+01 3.51e+01 chirality pdb=" CA ASP A 55 " pdb=" N ASP A 55 " pdb=" C ASP A 55 " pdb=" CB ASP A 55 " both_signs ideal model delta sigma weight residual False 2.51 3.50 -0.98 2.00e-01 2.50e+01 2.42e+01 chirality pdb=" CA LEU A 113 " pdb=" N LEU A 113 " pdb=" C LEU A 113 " pdb=" CB LEU A 113 " both_signs ideal model delta sigma weight residual False 2.51 3.47 -0.96 2.00e-01 2.50e+01 2.30e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " 0.003 2.00e-02 2.50e+03 6.39e-02 1.23e+02 pdb=" CG ATYR A 67 " -0.012 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.034 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.124 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.132 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.004 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.019 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.071 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.038 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.032 2.00e-02 2.50e+03 5.32e-02 8.49e+01 pdb=" CG TYR A 141 " 0.099 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.064 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.105 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.050 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.041 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.016 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.028 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.021 2.00e-02 2.50e+03 5.13e-02 7.88e+01 pdb=" CG PHE A 119 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.077 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.061 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.050 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.033 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.106 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.015 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.050 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.030 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1083 2.33 - 2.90: 8181 2.90 - 3.46: 10442 3.46 - 4.03: 15295 4.03 - 4.60: 21653 Nonbonded interactions: 56654 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.759 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.793 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.794 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.814 2.450 nonbonded pdb=" O GLU A 147 " pdb=" H BTHR A 154 " model vdw 1.839 2.450 ... (remaining 56649 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_5431713_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= 0.2787 r_free= 0.1798 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.404379 | | target function (ml) not normalized (work): 71540.326714 | | target function (ml) not normalized (free): 3260.224334 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3184 0.2116 7.5794 5.0374| | 2: 3.63 - 2.88 1.00 2711 122 0.2648 0.1722 4.3214 4.3146| | 3: 2.88 - 2.52 1.00 2682 148 0.2568 0.1644 4.182 4.1723| | 4: 2.52 - 2.29 1.00 2661 139 0.2538 0.1464 3.4831 3.5257| | 5: 2.29 - 2.13 1.00 2678 122 0.2633 0.1430 3.387 3.4402| | 6: 2.13 - 2.00 1.00 2692 117 0.2776 0.2022 3.3074 3.4667| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.48 0.77 0.23 1293.01| | 2: 3.63 - 2.88 2711 122 0.83 23.67 1.32 0.23 1293.01| | 3: 2.88 - 2.52 2682 148 0.73 32.56 1.29 0.23 1293.01| | 4: 2.52 - 2.29 2661 139 0.93 11.27 1.30 0.26 135.83| | 5: 2.29 - 2.13 2678 122 0.92 13.51 1.31 0.26 135.83| | 6: 2.13 - 2.00 2692 117 0.90 16.50 1.34 0.26 135.83| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 135.83 max = 1293.01 mean = 720.87| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.99 mean = 19.17| |phase err.(test): min = 0.00 max = 89.72 mean = 19.61| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.248 1557 Z= 5.412 Angle : 5.242 17.749 2118 Z= 3.615 Chirality : 0.385 1.185 243 Planarity : 0.031 0.077 284 Dihedral : 13.529 84.996 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 0.62 % Allowed : 3.11 % Favored : 96.27 % Cbeta Deviations : 29.19 % 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: -3.03 (0.46), residues: 224 helix: -3.13 (0.35), residues: 102 sheet: -0.48 (0.95), residues: 28 loop : -0.87 (0.54), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.061 0.017 ARG A 27 TYR 0.110 0.034 TYR A 141 PHE 0.102 0.042 PHE A 162 HIS 0.067 0.029 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= 0.2787 r_free= 0.1798 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.404379 | | target function (ml) not normalized (work): 71540.326714 | | target function (ml) not normalized (free): 3260.224334 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3485 percent. r_work = 0.2921 r_free = 0.1986 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2869 0.2921 0.1986 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2869 0.2921 0.1986 n_refl.: 17050 remove outliers: r(all,work,free)=0.2155 0.2166 0.1986 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2127 0.2137 0.1968 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1610 0.1608 0.1653 n_refl.: 17045 remove outliers: r(all,work,free)=0.1609 0.1607 0.1653 n_refl.: 17044 ======================== 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 32.574-12.150 100.00 89 5 0.4064 394.945 358.750 0.640 1.017 0.387 11.894-9.307 99.02 97 4 0.1856 633.899 614.184 0.915 1.018 0.370 9.237-7.194 100.00 213 7 0.2163 518.466 509.106 0.955 1.018 0.341 7.162-5.571 100.00 427 22 0.2318 389.109 376.259 0.920 1.016 0.289 5.546-4.326 100.00 867 58 0.1411 534.184 528.771 0.956 1.013 0.230 4.315-3.360 100.00 1859 96 0.1271 508.014 503.650 1.013 1.008 0.201 3.356-2.611 100.00 3867 181 0.1671 333.736 329.554 1.016 0.999 0.039 2.608-2.000 99.99 8818 434 0.1629 217.539 213.591 1.037 0.983 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4801 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1607 r_free=0.1653 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A A 144 ASN A 180 GLN Total number of N/Q/H flips: 3 r_work=0.1612 r_free=0.1660 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.701765 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.819240 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 0.1644 0.0291 0.009 1.0 1.3 0.5 0.0 0 11.351 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.53 16.44 2.91 3.013 18.444 0.819 0.023 12.77 16.67 3.90 3.583 18.738 0.819 0.020 Individual atomic B min max mean iso aniso Overall: 6.56 113.88 20.03 4.03 1785 0 Protein: 6.56 112.70 17.27 4.03 1519 0 Water: 9.22 113.88 36.09 N/A 258 0 Other: 21.94 37.36 26.58 N/A 8 0 Chain A: 6.56 113.88 20.03 N/A 1785 0 Histogram: Values Number of atoms 6.56 - 17.30 1105 17.30 - 28.03 325 28.03 - 38.76 184 38.76 - 49.49 98 49.49 - 60.22 46 60.22 - 70.96 13 70.96 - 81.69 6 81.69 - 92.42 4 92.42 - 103.15 1 103.15 - 113.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1277 r_free=0.1667 r_work=0.1280 r_free=0.1673 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1280 r_free = 0.1673 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 = 0.1663 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1275 r_free= 0.1663 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019995 | | target function (ls_wunit_k1) not normalized (work): 324.659605 | | target function (ls_wunit_k1) not normalized (free): 27.078866 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1275 0.1663 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1916 0.1916 0.1987 n_refl.: 17044 remove outliers: r(all,work,free)=0.1916 0.1916 0.1987 n_refl.: 17044 overall B=-0.41 to atoms: r(all,work,free)=0.1886 0.1885 0.1971 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1294 0.1276 0.1657 n_refl.: 17044 remove outliers: r(all,work,free)=0.1293 0.1274 0.1657 n_refl.: 17042 ======================== 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 95.83 87 5 0.3532 302.796 277.365 0.612 1.010 0.360 11.894-9.307 99.02 97 4 0.1700 486.999 477.010 0.915 1.010 0.357 9.237-7.194 100.00 213 7 0.1834 398.316 395.026 0.959 1.010 0.349 7.162-5.571 100.00 427 22 0.1817 298.937 294.385 0.933 1.009 0.301 5.546-4.326 100.00 867 58 0.1043 410.392 408.165 0.959 1.008 0.213 4.315-3.360 100.00 1859 96 0.0921 390.287 389.976 1.018 1.005 0.197 3.356-2.611 100.00 3867 181 0.1300 256.396 255.110 1.018 1.000 0.091 2.608-2.000 99.99 8818 434 0.1354 167.126 165.628 1.027 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-1.4687 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1657 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1279 r_free=0.1664 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1279 r_free=0.1664 | n_water=258 | time (s): 0.800 (total time: 0.800) Filter (dist) r_work=0.1284 r_free=0.1657 | n_water=253 | time (s): 20.090 (total time: 20.890) Filter (q & B) r_work=0.1284 r_free=0.1656 | n_water=251 | time (s): 1.530 (total time: 22.420) Compute maps r_work=0.1284 r_free=0.1656 | n_water=251 | time (s): 0.530 (total time: 22.950) Filter (map) r_work=0.1316 r_free=0.1647 | n_water=213 | time (s): 1.480 (total time: 24.430) Find peaks r_work=0.1316 r_free=0.1647 | n_water=213 | time (s): 0.520 (total time: 24.950) Add new water r_work=0.1528 r_free=0.1861 | n_water=367 | time (s): 1.510 (total time: 26.460) Refine new water occ: r_work=0.1326 r_free=0.1584 adp: r_work=0.1272 r_free=0.1577 occ: r_work=0.1277 r_free=0.1548 adp: r_work=0.1246 r_free=0.1553 occ: r_work=0.1248 r_free=0.1542 adp: r_work=0.1236 r_free=0.1547 ADP+occupancy (water only), MIN, final r_work=0.1236 r_free=0.1547 r_work=0.1236 r_free=0.1547 | n_water=367 | time (s): 24.000 (total time: 50.460) Filter (q & B) r_work=0.1238 r_free=0.1553 | n_water=359 | time (s): 1.500 (total time: 51.960) Filter (dist only) r_work=0.1237 r_free=0.1556 | n_water=358 | time (s): 26.780 (total time: 78.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.337620 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.977888 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 0.1603 0.0387 0.008 0.9 2.6 0.5 0.0 0 12.169 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.16 16.03 3.87 4.149 21.061 0.978 0.018 12.01 16.37 4.36 4.229 21.351 0.978 0.018 Individual atomic B min max mean iso aniso Overall: 6.89 107.29 21.39 4.30 1885 0 Protein: 6.89 107.29 17.82 4.28 1519 0 Water: 9.14 66.56 36.20 N/A 358 0 Other: 25.11 44.62 35.08 N/A 8 0 Chain A: 6.89 107.29 19.58 N/A 1740 0 Chain S: 19.14 66.56 43.11 N/A 145 0 Histogram: Values Number of atoms 6.89 - 16.93 1031 16.93 - 26.97 381 26.97 - 37.01 208 37.01 - 47.05 157 47.05 - 57.09 70 57.09 - 67.13 28 67.13 - 77.17 3 77.17 - 87.21 3 87.21 - 97.25 2 97.25 - 107.29 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1637 r_work=0.1203 r_free=0.1642 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1642 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 = 0.1633 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1200 r_free= 0.1633 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.017219 | | target function (ls_wunit_k1) not normalized (work): 279.550070 | | target function (ls_wunit_k1) not normalized (free): 25.226821 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1221 0.1200 0.1633 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1766 0.1756 0.1989 n_refl.: 17042 remove outliers: r(all,work,free)=0.1766 0.1756 0.1989 n_refl.: 17042 overall B=-0.40 to atoms: r(all,work,free)=0.1739 0.1730 0.1971 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1194 0.1626 n_refl.: 17042 remove outliers: r(all,work,free)=0.1213 0.1192 0.1626 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 0.3284 299.640 282.759 0.602 1.001 0.350 11.894-9.307 99.02 97 4 0.1546 486.999 483.550 0.916 1.003 0.350 9.237-7.194 100.00 213 7 0.1662 398.316 398.057 0.975 1.003 0.280 7.162-5.571 100.00 427 22 0.1542 298.937 295.397 0.936 1.003 0.271 5.546-4.326 100.00 867 58 0.0880 410.392 407.910 0.962 1.003 0.221 4.315-3.360 100.00 1859 96 0.0835 390.287 389.345 1.017 1.002 0.212 3.356-2.611 100.00 3867 181 0.1199 256.396 255.357 1.014 1.001 0.053 2.608-2.000 99.99 8818 434 0.1334 167.126 166.102 1.018 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4256 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1626 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1194 r_free=0.1629 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1629 | n_water=358 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.1196 r_free=0.1627 | n_water=356 | time (s): 27.530 (total time: 28.190) Filter (q & B) r_work=0.1196 r_free=0.1627 | n_water=356 | time (s): 0.800 (total time: 28.990) Compute maps r_work=0.1196 r_free=0.1627 | n_water=356 | time (s): 0.640 (total time: 29.630) Filter (map) r_work=0.1259 r_free=0.1647 | n_water=263 | time (s): 1.960 (total time: 31.590) Find peaks r_work=0.1259 r_free=0.1647 | n_water=263 | time (s): 0.670 (total time: 32.260) Add new water r_work=0.1449 r_free=0.1799 | n_water=414 | time (s): 2.050 (total time: 34.310) Refine new water occ: r_work=0.1247 r_free=0.1570 adp: r_work=0.1237 r_free=0.1572 occ: r_work=0.1223 r_free=0.1549 adp: r_work=0.1210 r_free=0.1550 occ: r_work=0.1206 r_free=0.1541 adp: r_work=0.1193 r_free=0.1540 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1540 r_work=0.1193 r_free=0.1540 | n_water=414 | time (s): 22.520 (total time: 56.830) Filter (q & B) r_work=0.1196 r_free=0.1547 | n_water=407 | time (s): 1.960 (total time: 58.790) Filter (dist only) r_work=0.1196 r_free=0.1547 | n_water=407 | time (s): 32.040 (total time: 90.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.868227 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.124760 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 0.1177 0.1579 0.0402 0.009 1.0 4.8 0.5 0.0 0 0.934 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.77 15.79 4.02 4.361 21.643 0.125 5.001 11.58 15.74 4.16 4.846 21.568 0.125 4.978 Individual atomic B min max mean iso aniso Overall: 6.33 104.29 21.02 4.48 1934 0 Protein: 6.33 104.29 17.12 4.48 1519 0 Water: 8.71 62.82 35.31 N/A 407 0 Other: 27.76 45.67 35.62 N/A 8 0 Chain A: 6.33 104.29 18.85 N/A 1736 0 Chain S: 16.82 62.82 40.05 N/A 198 0 Histogram: Values Number of atoms 6.33 - 16.13 1046 16.13 - 25.92 365 25.92 - 35.72 229 35.72 - 45.51 180 45.51 - 55.31 72 55.31 - 65.11 30 65.11 - 74.90 4 74.90 - 84.70 3 84.70 - 94.50 3 94.50 - 104.29 2 =========================== Idealize ADP of riding H ========================== r_work=0.1158 r_free=0.1574 r_work=0.1158 r_free=0.1575 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1158 r_free = 0.1575 target_work(ml) = 4.978 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1149 r_free = 0.1570 target_work(ml) = 4.973 | | occupancies: max = 1.00 min = 0.13 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= 0.1149 r_free= 0.1570 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 4.972650 | | target function (ml) not normalized (work): 80725.998265 | | target function (ml) not normalized (free): 4199.657670 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1169 0.1149 0.1570 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1677 0.1669 0.1866 n_refl.: 17041 remove outliers: r(all,work,free)=0.1677 0.1669 0.1866 n_refl.: 17041 overall B=-0.41 to atoms: r(all,work,free)=0.1647 0.1639 0.1851 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1164 0.1144 0.1565 n_refl.: 17041 remove outliers: r(all,work,free)=0.1163 0.1143 0.1565 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 0.3407 296.082 277.839 0.559 1.004 0.335 11.894-9.307 99.02 97 4 0.1743 486.999 480.747 0.909 1.005 0.332 9.237-7.194 100.00 213 7 0.1817 398.316 397.051 0.979 1.006 0.290 7.162-5.571 100.00 427 22 0.1628 298.937 292.839 0.941 1.005 0.220 5.546-4.326 100.00 867 58 0.0938 410.392 406.859 0.964 1.005 0.206 4.315-3.360 100.00 1859 96 0.0888 390.287 388.294 1.014 1.003 0.201 3.356-2.611 100.00 3867 181 0.1266 256.396 253.965 1.017 1.001 0.132 2.608-2.000 99.99 8818 434 0.1095 167.126 165.764 1.024 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4821 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1143 r_free=0.1565 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=0.1143 r_free=0.1562 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1143 r_free=0.1562 | n_water=407 | time (s): 0.770 (total time: 0.770) Filter (dist) r_work=0.1143 r_free=0.1563 | n_water=406 | time (s): 33.620 (total time: 34.390) Filter (q & B) r_work=0.1143 r_free=0.1563 | n_water=405 | time (s): 1.780 (total time: 36.170) Compute maps r_work=0.1143 r_free=0.1563 | n_water=405 | time (s): 0.760 (total time: 36.930) Filter (map) r_work=0.1195 r_free=0.1569 | n_water=318 | time (s): 1.630 (total time: 38.560) Find peaks r_work=0.1195 r_free=0.1569 | n_water=318 | time (s): 0.590 (total time: 39.150) Add new water r_work=0.1338 r_free=0.1717 | n_water=456 | time (s): 2.000 (total time: 41.150) Refine new water occ: r_work=0.1176 r_free=0.1525 adp: r_work=0.1169 r_free=0.1530 occ: r_work=0.1152 r_free=0.1507 adp: r_work=0.1144 r_free=0.1507 occ: r_work=0.1137 r_free=0.1503 adp: r_work=0.1129 r_free=0.1498 ADP+occupancy (water only), MIN, final r_work=0.1129 r_free=0.1498 r_work=0.1129 r_free=0.1498 | n_water=456 | time (s): 38.030 (total time: 79.180) Filter (q & B) r_work=0.1134 r_free=0.1512 | n_water=442 | time (s): 2.080 (total time: 81.260) Filter (dist only) r_work=0.1137 r_free=0.1512 | n_water=441 | time (s): 35.770 (total time: 117.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.930101 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.170909 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 0.1120 0.1552 0.0431 0.010 1.0 2.9 0.5 0.0 0 0.965 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.20 15.52 4.31 4.386 21.191 0.171 4.955 11.08 15.48 4.40 4.629 21.227 0.171 4.945 Individual atomic B min max mean iso aniso Overall: 5.94 101.85 21.14 4.79 1968 0 Protein: 5.94 101.85 16.66 4.78 1519 0 Water: 8.70 62.85 36.34 N/A 441 0 Other: 26.47 44.82 34.16 N/A 8 0 Chain A: 5.94 101.85 18.36 N/A 1735 0 Chain S: 16.48 62.85 41.84 N/A 233 0 Histogram: Values Number of atoms 5.94 - 15.53 1025 15.53 - 25.12 376 25.12 - 34.71 218 34.71 - 44.30 193 44.30 - 53.89 101 53.89 - 63.48 41 63.48 - 73.08 5 73.08 - 82.67 4 82.67 - 92.26 3 92.26 - 101.85 2 =========================== Idealize ADP of riding H ========================== r_work=0.1108 r_free=0.1548 r_work=0.1108 r_free=0.1549 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1108 r_free = 0.1549 target_work(ml) = 4.946 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1100 r_free = 0.1554 target_work(ml) = 4.942 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1100 r_free= 0.1554 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.941833 | | target function (ml) not normalized (work): 80220.775831 | | target function (ml) not normalized (free): 4179.772882 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1122 0.1100 0.1554 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1597 0.1584 0.1881 n_refl.: 17040 remove outliers: r(all,work,free)=0.1597 0.1584 0.1881 n_refl.: 17040 overall B=-0.33 to atoms: r(all,work,free)=0.1576 0.1562 0.1867 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1120 0.1098 0.1551 n_refl.: 17040 remove outliers: r(all,work,free)=0.1120 0.1098 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 0.3664 296.082 272.064 0.546 1.004 0.330 11.894-9.307 99.02 97 4 0.1713 486.999 478.474 0.917 1.004 0.289 9.237-7.194 100.00 213 7 0.1772 398.316 397.764 0.981 1.004 0.250 7.162-5.571 100.00 427 22 0.1563 298.937 292.822 0.943 1.004 0.215 5.546-4.326 100.00 867 58 0.0901 410.392 406.747 0.966 1.003 0.196 4.315-3.360 100.00 1859 96 0.0852 390.287 388.211 1.009 1.002 0.191 3.356-2.611 100.00 3867 181 0.1222 256.396 253.997 1.010 1.000 0.121 2.608-2.000 99.99 8818 434 0.1040 167.126 165.966 1.012 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1489 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1098 r_free=0.1551 After: r_work=0.1100 r_free=0.1550 ================================== NQH flips ================================== r_work=0.1100 r_free=0.1550 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1100 r_free=0.1550 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1100 r_free=0.1550 | n_water=441 | time (s): 0.790 (total time: 0.790) Filter (dist) r_work=0.1100 r_free=0.1551 | n_water=440 | time (s): 34.720 (total time: 35.510) Filter (q & B) r_work=0.1100 r_free=0.1551 | n_water=440 | time (s): 1.160 (total time: 36.670) Compute maps r_work=0.1100 r_free=0.1551 | n_water=440 | time (s): 0.600 (total time: 37.270) Filter (map) r_work=0.1162 r_free=0.1586 | n_water=349 | time (s): 1.750 (total time: 39.020) Find peaks r_work=0.1162 r_free=0.1586 | n_water=349 | time (s): 0.480 (total time: 39.500) Add new water r_work=0.1276 r_free=0.1691 | n_water=480 | time (s): 1.630 (total time: 41.130) Refine new water occ: r_work=0.1135 r_free=0.1526 adp: r_work=0.1127 r_free=0.1530 occ: r_work=0.1116 r_free=0.1507 adp: r_work=0.1106 r_free=0.1510 occ: r_work=0.1101 r_free=0.1498 adp: r_work=0.1094 r_free=0.1499 ADP+occupancy (water only), MIN, final r_work=0.1094 r_free=0.1499 r_work=0.1094 r_free=0.1499 | n_water=480 | time (s): 26.080 (total time: 67.210) Filter (q & B) r_work=0.1096 r_free=0.1509 | n_water=471 | time (s): 1.810 (total time: 69.020) Filter (dist only) r_work=0.1096 r_free=0.1509 | n_water=470 | time (s): 36.250 (total time: 105.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.941640 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.162692 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 0.1113 0.1528 0.0415 0.010 1.0 5.8 0.5 0.0 0 0.971 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.13 15.28 4.15 4.511 20.980 0.163 4.940 11.00 15.09 4.09 4.564 21.022 0.163 4.930 Individual atomic B min max mean iso aniso Overall: 5.14 101.10 21.14 4.91 1997 0 Protein: 5.14 101.10 16.33 4.90 1519 0 Water: 8.10 68.53 36.47 N/A 470 0 Other: 26.18 44.59 33.70 N/A 8 0 Chain A: 5.14 101.10 18.00 N/A 1735 0 Chain S: 16.65 68.53 41.98 N/A 262 0 Histogram: Values Number of atoms 5.14 - 14.74 990 14.74 - 24.33 402 24.33 - 33.93 220 33.93 - 43.52 192 43.52 - 53.12 137 53.12 - 62.72 36 62.72 - 72.31 11 72.31 - 81.91 3 81.91 - 91.50 2 91.50 - 101.10 4 =========================== Idealize ADP of riding H ========================== r_work=0.1100 r_free=0.1509 r_work=0.1100 r_free=0.1510 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1100 r_free = 0.1510 target_work(ml) = 4.930 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1093 r_free = 0.1519 target_work(ml) = 4.926 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1093 r_free= 0.1519 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.926202 | | target function (ml) not normalized (work): 79967.031909 | | target function (ml) not normalized (free): 4153.642446 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1092 0.1349 5.4341 5.5909| | 2: 3.63 - 2.88 1.00 2711 122 0.1069 0.1561 5.2002 5.3748| | 3: 2.88 - 2.52 1.00 2681 148 0.1344 0.1745 5.1112 5.2021| | 4: 2.52 - 2.29 1.00 2661 139 0.0929 0.1481 4.6262 4.918| | 5: 2.29 - 2.13 1.00 2678 122 0.0964 0.1528 4.5828 4.9032| | 6: 2.13 - 2.00 1.00 2692 117 0.1131 0.1723 4.574 4.7629| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.87 1.00 0.95 6082.47| | 2: 3.63 - 2.88 2711 122 0.93 12.54 1.01 0.95 6082.47| | 3: 2.88 - 2.52 2681 148 0.88 18.54 0.99 0.95 6082.47| | 4: 2.52 - 2.29 2661 139 0.93 12.17 1.01 0.97 2132.31| | 5: 2.29 - 2.13 2678 122 0.91 14.19 1.00 0.97 2132.31| | 6: 2.13 - 2.00 2692 117 0.89 16.91 0.99 0.97 2132.31| |alpha: min = 0.95 max = 0.97 mean = 0.96| |beta: min = 2132.31 max = 6082.47 mean = 4128.20| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.90 mean = 13.83| |phase err.(test): min = 0.00 max = 88.38 mean = 13.58| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1114 0.1093 0.1519 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1573 0.1561 0.1823 n_refl.: 17040 remove outliers: r(all,work,free)=0.1573 0.1561 0.1823 n_refl.: 17040 overall B=-0.25 to atoms: r(all,work,free)=0.1558 0.1546 0.1814 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1115 0.1094 0.1523 n_refl.: 17040 remove outliers: r(all,work,free)=0.1115 0.1094 0.1523 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 0.3617 296.082 275.972 0.545 1.002 0.330 11.894-9.307 99.02 97 4 0.1646 486.999 480.453 0.919 1.003 0.279 9.237-7.194 100.00 213 7 0.1667 398.316 400.624 0.992 1.003 0.230 7.162-5.571 100.00 427 22 0.1482 298.937 293.497 0.938 1.003 0.210 5.546-4.326 100.00 867 58 0.0921 410.392 406.778 0.964 1.003 0.191 4.315-3.360 100.00 1859 96 0.0868 390.287 388.237 1.005 1.002 0.191 3.356-2.611 100.00 3867 181 0.1213 256.396 254.147 1.002 1.001 0.151 2.608-2.000 99.99 8818 434 0.1039 167.126 165.762 0.994 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8722 ================= 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 : 0.2787 0.1798 0.082 5.242 8.8 119.3 19.9 258 0.000 1_bss: 0.1607 0.1653 0.082 5.242 8.4 118.9 19.5 258 0.000 1_settarget: 0.1607 0.1653 0.082 5.242 8.4 118.9 19.5 258 0.000 1_nqh: 0.1612 0.1660 0.082 5.242 8.4 118.9 19.5 258 0.010 1_weight: 0.1612 0.1660 0.082 5.242 8.4 118.9 19.5 258 0.010 1_xyzrec: 0.1353 0.1644 0.009 0.967 8.4 118.9 19.5 258 0.159 1_adp: 0.1277 0.1667 0.009 0.967 6.6 113.9 20.0 258 0.159 1_regHadp: 0.1280 0.1673 0.009 0.967 6.6 113.9 20.0 258 0.159 1_occ: 0.1275 0.1663 0.009 0.967 6.6 113.9 20.0 258 0.159 2_bss: 0.1274 0.1657 0.009 0.967 6.2 113.5 19.6 258 0.159 2_settarget: 0.1274 0.1657 0.009 0.967 6.2 113.5 19.6 258 0.159 2_updatecdl: 0.1274 0.1657 0.009 0.991 6.2 113.5 19.6 258 0.159 2_nqh: 0.1279 0.1664 0.009 0.991 6.2 113.5 19.6 258 0.153 2_sol: 0.1237 0.1556 0.009 0.991 6.2 112.3 20.9 358 n/a 2_weight: 0.1237 0.1556 0.009 0.991 6.2 112.3 20.9 358 n/a 2_xyzrec: 0.1216 0.1603 0.008 0.931 6.2 112.3 20.9 358 n/a 2_adp: 0.1201 0.1637 0.008 0.931 6.9 107.3 21.4 358 n/a 2_regHadp: 0.1203 0.1642 0.008 0.931 6.9 107.3 21.4 358 n/a 2_occ: 0.1200 0.1633 0.008 0.931 6.9 107.3 21.4 358 n/a 3_bss: 0.1192 0.1626 0.008 0.931 6.5 106.9 21.0 358 n/a 3_settarget: 0.1192 0.1626 0.008 0.931 6.5 106.9 21.0 358 n/a 3_updatecdl: 0.1192 0.1626 0.008 0.932 6.5 106.9 21.0 358 n/a 3_nqh: 0.1194 0.1629 0.008 0.932 6.5 106.9 21.0 358 n/a 3_sol: 0.1196 0.1547 0.008 0.932 6.5 106.9 21.2 407 n/a 3_weight: 0.1196 0.1547 0.008 0.932 6.5 106.9 21.2 407 n/a 3_xyzrec: 0.1177 0.1579 0.009 0.954 6.5 106.9 21.2 407 n/a 3_adp: 0.1158 0.1574 0.009 0.954 6.3 104.3 21.0 407 n/a 3_regHadp: 0.1158 0.1575 0.009 0.954 6.3 104.3 21.0 407 n/a 3_occ: 0.1149 0.1570 0.009 0.954 6.3 104.3 21.0 407 n/a 4_bss: 0.1143 0.1565 0.009 0.954 5.9 103.9 20.6 407 n/a 4_settarget: 0.1143 0.1565 0.009 0.954 5.9 103.9 20.6 407 n/a 4_updatecdl: 0.1143 0.1565 0.009 0.954 5.9 103.9 20.6 407 n/a 4_nqh: 0.1143 0.1562 0.009 0.954 5.9 103.9 20.6 407 n/a 4_sol: 0.1137 0.1512 0.009 0.954 5.9 103.9 21.1 441 n/a 4_weight: 0.1137 0.1512 0.009 0.954 5.9 103.9 21.1 441 n/a 4_xyzrec: 0.1120 0.1552 0.010 0.987 5.9 103.9 21.1 441 n/a 4_adp: 0.1108 0.1548 0.010 0.987 5.9 101.8 21.1 441 n/a 4_regHadp: 0.1108 0.1549 0.010 0.987 5.9 101.8 21.1 441 n/a 4_occ: 0.1100 0.1554 0.010 0.987 5.9 101.8 21.1 441 n/a 5_bss: 0.1098 0.1551 0.010 0.987 5.6 101.5 20.8 441 n/a 5_settarget: 0.1098 0.1551 0.010 0.987 5.6 101.5 20.8 441 n/a 5_updatecdl: 0.1098 0.1551 0.010 0.988 5.6 101.5 20.8 441 n/a 5_setrh: 0.1100 0.1550 0.010 0.988 5.6 101.5 20.8 441 n/a 5_nqh: 0.1100 0.1550 0.010 0.988 5.6 101.5 20.8 441 n/a 5_sol: 0.1096 0.1509 0.010 0.988 5.6 101.5 21.1 470 n/a 5_weight: 0.1096 0.1509 0.010 0.988 5.6 101.5 21.1 470 n/a 5_xyzrec: 0.1113 0.1528 0.010 1.026 5.6 101.5 21.1 470 n/a 5_adp: 0.1100 0.1509 0.010 1.026 5.1 101.1 21.1 470 n/a 5_regHadp: 0.1100 0.1510 0.010 1.026 5.1 101.1 21.1 470 n/a 5_occ: 0.1093 0.1519 0.010 1.026 5.1 101.1 21.1 470 n/a end: 0.1094 0.1523 0.010 1.026 4.9 100.8 20.9 470 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_5431713_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_5431713_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1600 Refinement macro-cycles (run) : 933.6400 Write final files (write_after_run_outputs) : 20.9000 Total : 957.7000 Total CPU time: 16.32 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:21 PST -0800 (1735494081.51 s) Start R-work = 0.1607, R-free = 0.1653 Final R-work = 0.1094, R-free = 0.1523 =============================================================================== Job complete usr+sys time: 1000.79 seconds wall clock time: 17 minutes 4.62 seconds (1024.62 seconds total)