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_8831905.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 { 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_8831905.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8831905.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" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.15, per 1000 atoms: 0.34 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: 0.31 Conformation dependent library (CDL) restraints added in 115.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.90: 446 0.90 - 1.16: 1198 1.16 - 1.43: 666 1.43 - 1.69: 820 1.69 - 1.96: 23 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.537 1.667 -0.130 5.00e-03 4.00e+04 6.81e+02 bond pdb=" CA ALA A 183 " pdb=" C ALA A 183 " ideal model delta sigma weight residual 1.521 1.750 -0.229 1.14e-02 7.69e+03 4.05e+02 bond pdb=" C VAL A 23 " pdb=" O VAL A 23 " ideal model delta sigma weight residual 1.237 1.452 -0.215 1.13e-02 7.83e+03 3.63e+02 bond pdb=" N ALA A 61 " pdb=" CA ALA A 61 " ideal model delta sigma weight residual 1.459 1.239 0.220 1.21e-02 6.83e+03 3.30e+02 bond pdb=" C SER A 47 " pdb=" O SER A 47 " ideal model delta sigma weight residual 1.236 1.031 0.205 1.18e-02 7.18e+03 3.02e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.56: 3102 4.56 - 9.11: 1867 9.11 - 13.67: 670 13.67 - 18.23: 122 18.23 - 22.79: 16 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ALA A 165 " pdb=" C ALA A 165 " pdb=" N LEU A 166 " ideal model delta sigma weight residual 122.12 135.74 -13.62 1.06e+00 8.90e-01 1.65e+02 angle pdb=" N PRO A 184 " pdb=" CA PRO A 184 " pdb=" CB PRO A 184 " ideal model delta sigma weight residual 103.52 115.46 -11.94 9.50e-01 1.11e+00 1.58e+02 angle pdb=" O TYR A 141 " pdb=" C TYR A 141 " pdb=" N SER A 142 " ideal model delta sigma weight residual 123.10 137.24 -14.14 1.15e+00 7.56e-01 1.51e+02 angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH1 ARG A 156 " ideal model delta sigma weight residual 121.50 133.58 -12.08 1.00e+00 1.00e+00 1.46e+02 angle pdb=" CA ALA A 178 " pdb=" C ALA A 178 " pdb=" O ALA A 178 " ideal model delta sigma weight residual 120.82 133.15 -12.33 1.05e+00 9.07e-01 1.38e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.33: 1297 16.33 - 32.65: 123 32.65 - 48.97: 38 48.97 - 65.29: 20 65.29 - 81.62: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C BLYS A 99 " pdb=" N BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -145.58 22.98 0 2.50e+00 1.60e-01 8.45e+01 dihedral pdb=" C ALA A 6 " pdb=" N ALA A 6 " pdb=" CA ALA A 6 " pdb=" CB ALA A 6 " ideal model delta harmonic sigma weight residual -122.60 -104.70 -17.90 0 2.50e+00 1.60e-01 5.13e+01 dihedral pdb=" C SER A 142 " pdb=" N SER A 142 " pdb=" CA SER A 142 " pdb=" CB SER A 142 " ideal model delta harmonic sigma weight residual -122.60 -105.12 -17.48 0 2.50e+00 1.60e-01 4.89e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.209: 81 0.209 - 0.417: 91 0.417 - 0.626: 42 0.626 - 0.834: 20 0.834 - 1.042: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA SER A 142 " pdb=" N SER A 142 " pdb=" C SER A 142 " pdb=" CB SER A 142 " both_signs ideal model delta sigma weight residual False 2.51 3.55 -1.04 2.00e-01 2.50e+01 2.72e+01 chirality pdb=" CB VAL A 146 " pdb=" CA VAL A 146 " pdb=" CG1 VAL A 146 " pdb=" CG2 VAL A 146 " both_signs ideal model delta sigma weight residual False -2.63 -1.61 -1.02 2.00e-01 2.50e+01 2.62e+01 chirality pdb=" CG LEU A 10 " pdb=" CB LEU A 10 " pdb=" CD1 LEU A 10 " pdb=" CD2 LEU A 10 " both_signs ideal model delta sigma weight residual False -2.59 -1.57 -1.02 2.00e-01 2.50e+01 2.58e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.153 2.00e-02 2.50e+03 6.28e-02 1.18e+02 pdb=" CG ATYR A 67 " 0.052 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.100 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.044 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.011 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.050 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.016 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.041 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.041 2.00e-02 2.50e+03 6.27e-02 1.18e+02 pdb=" CG PHE A 119 " -0.177 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.062 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.017 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.031 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.074 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.033 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.010 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.021 2.00e-02 2.50e+03 6.01e-02 1.08e+02 pdb=" CG BTYR A 67 " -0.049 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.050 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.012 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.078 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.036 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.103 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.062 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.034 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.110 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.042 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 1266 2.35 - 2.91: 8328 2.91 - 3.48: 10416 3.48 - 4.04: 15153 4.04 - 4.60: 21502 Nonbonded interactions: 56665 Sorted by model distance: nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.792 2.270 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.809 2.100 nonbonded pdb=" O GLU A 147 " pdb=" H ATHR A 154 " model vdw 1.836 2.450 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.847 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.858 2.450 ... (remaining 56660 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_8831905_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= 0.2786 r_free= 0.1860 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.407593 | | target function (ml) not normalized (work): 71592.538991 | | target function (ml) not normalized (free): 3275.774703 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3186 0.2157 7.5296 5.0315| | 2: 3.63 - 2.88 1.00 2711 122 0.2640 0.1819 4.3314 4.3414| | 3: 2.88 - 2.52 1.00 2682 148 0.2548 0.1637 4.1832 4.1736| | 4: 2.52 - 2.29 1.00 2661 139 0.2588 0.1683 3.5258 3.677| | 5: 2.29 - 2.13 1.00 2678 122 0.2634 0.1543 3.3929 3.4537| | 6: 2.13 - 2.00 1.00 2692 117 0.2746 0.1900 3.3197 3.3843| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.54 0.77 0.23 1299.98| | 2: 3.63 - 2.88 2711 122 0.83 23.84 1.31 0.23 1299.98| | 3: 2.88 - 2.52 2682 148 0.73 32.83 1.28 0.23 1299.98| | 4: 2.52 - 2.29 2661 139 0.93 11.53 1.30 0.26 140.08| | 5: 2.29 - 2.13 2678 122 0.92 13.69 1.32 0.26 140.08| | 6: 2.13 - 2.00 2692 117 0.90 16.47 1.34 0.26 140.08| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 140.08 max = 1299.98 mean = 726.50| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.94 mean = 19.32| |phase err.(test): min = 0.00 max = 88.43 mean = 19.41| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.229 1557 Z= 5.677 Angle : 5.295 16.972 2118 Z= 3.642 Chirality : 0.407 1.042 243 Planarity : 0.030 0.077 284 Dihedral : 14.023 81.616 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 1.08 % Allowed : 3.24 % Favored : 95.68 % Rotamer: Outliers : 0.62 % Allowed : 4.97 % Favored : 94.41 % Cbeta Deviations : 31.35 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.46), residues: 224 helix: -2.72 (0.37), residues: 103 sheet: -0.98 (0.81), residues: 38 loop : -1.28 (0.57), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.097 0.026 ARG A 156 TYR 0.084 0.045 TYR A 139 PHE 0.154 0.048 PHE A 119 HIS 0.060 0.034 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= 0.2786 r_free= 0.1860 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.407593 | | target function (ml) not normalized (work): 71592.538991 | | target function (ml) not normalized (free): 3275.774703 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2950 percent. r_work = 0.2916 r_free = 0.2027 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2864 0.2916 0.2027 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2864 0.2916 0.2027 n_refl.: 17050 remove outliers: r(all,work,free)=0.2153 0.2162 0.2027 n_refl.: 17045 overall B=-0.42 to atoms: r(all,work,free)=0.2125 0.2134 0.2008 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1613 0.1610 0.1687 n_refl.: 17045 remove outliers: r(all,work,free)=0.1611 0.1608 0.1687 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 0.3882 399.107 360.853 0.658 1.013 0.403 11.894-9.307 99.02 97 4 0.1872 633.876 615.634 0.931 1.013 0.390 9.237-7.194 100.00 213 7 0.2176 518.447 509.545 0.959 1.012 0.381 7.162-5.571 100.00 427 22 0.2294 389.095 375.029 0.923 1.011 0.284 5.546-4.326 100.00 867 58 0.1356 534.165 529.038 0.962 1.009 0.225 4.315-3.360 100.00 1859 96 0.1296 507.996 503.932 1.020 1.006 0.212 3.356-2.611 100.00 3867 181 0.1647 333.724 329.008 1.010 1.000 0.071 2.608-2.000 99.99 8818 434 0.1653 217.531 213.640 1.032 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4829 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1608 r_free=0.1687 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 r_work=0.1611 r_free=0.1694 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.330745 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.958563 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1351 0.1634 0.0283 0.009 1.0 1.0 0.5 0.0 0 11.665 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.34 2.83 3.013 18.443 0.959 0.023 12.79 16.53 3.74 3.687 18.714 0.959 0.020 Individual atomic B min max mean iso aniso Overall: 6.07 113.88 19.98 4.15 1785 0 Protein: 6.07 113.53 17.23 4.16 1519 0 Water: 8.57 113.88 36.01 N/A 258 0 Other: 21.63 37.22 26.61 N/A 8 0 Chain A: 6.07 113.88 19.98 N/A 1785 0 Histogram: Values Number of atoms 6.07 - 16.85 1082 16.85 - 27.63 341 27.63 - 38.42 187 38.42 - 49.20 99 49.20 - 59.98 48 59.98 - 70.76 13 70.76 - 81.54 7 81.54 - 92.32 4 92.32 - 103.10 1 103.10 - 113.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1279 r_free=0.1653 r_work=0.1282 r_free=0.1661 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1282 r_free = 0.1661 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1276 r_free = 0.1653 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1276 r_free= 0.1653 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019976 | | target function (ls_wunit_k1) not normalized (work): 324.325362 | | target function (ls_wunit_k1) not normalized (free): 27.130834 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1294 0.1276 0.1653 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1905 0.1904 0.1990 n_refl.: 17043 remove outliers: r(all,work,free)=0.1905 0.1904 0.1990 n_refl.: 17043 overall B=-0.38 to atoms: r(all,work,free)=0.1878 0.1876 0.1974 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1294 0.1276 0.1642 n_refl.: 17043 remove outliers: r(all,work,free)=0.1294 0.1276 0.1642 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 0.3563 307.420 285.611 0.654 1.011 0.388 11.894-9.307 99.02 97 4 0.1686 488.256 477.815 0.918 1.011 0.380 9.237-7.194 100.00 213 7 0.1862 399.344 395.181 0.957 1.010 0.351 7.162-5.571 100.00 427 22 0.1843 299.708 294.832 0.929 1.009 0.261 5.546-4.326 100.00 867 58 0.1040 411.452 409.177 0.958 1.007 0.221 4.315-3.360 100.00 1859 96 0.0929 391.294 391.040 1.017 1.005 0.191 3.356-2.611 100.00 3867 181 0.1296 257.058 255.790 1.012 1.000 0.091 2.608-2.000 99.99 8818 434 0.1352 167.558 166.045 1.022 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3695 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1642 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1278 r_free=0.1642 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1278 r_free=0.1642 | n_water=258 | time (s): 0.630 (total time: 0.630) Filter (dist) r_work=0.1287 r_free=0.1636 | n_water=252 | time (s): 20.290 (total time: 20.920) Filter (q & B) r_work=0.1288 r_free=0.1635 | n_water=250 | time (s): 1.750 (total time: 22.670) Compute maps r_work=0.1288 r_free=0.1635 | n_water=250 | time (s): 0.680 (total time: 23.350) Filter (map) r_work=0.1326 r_free=0.1629 | n_water=208 | time (s): 1.570 (total time: 24.920) Find peaks r_work=0.1326 r_free=0.1629 | n_water=208 | time (s): 0.460 (total time: 25.380) Add new water r_work=0.1561 r_free=0.1944 | n_water=374 | time (s): 1.600 (total time: 26.980) Refine new water occ: r_work=0.1338 r_free=0.1607 adp: r_work=0.1279 r_free=0.1606 occ: r_work=0.1284 r_free=0.1562 adp: r_work=0.1248 r_free=0.1573 occ: r_work=0.1247 r_free=0.1556 adp: r_work=0.1236 r_free=0.1557 ADP+occupancy (water only), MIN, final r_work=0.1236 r_free=0.1557 r_work=0.1236 r_free=0.1557 | n_water=374 | time (s): 13.800 (total time: 40.780) Filter (q & B) r_work=0.1239 r_free=0.1564 | n_water=366 | time (s): 2.320 (total time: 43.100) Filter (dist only) r_work=0.1239 r_free=0.1566 | n_water=365 | time (s): 28.760 (total time: 71.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.361246 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.010512 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 0.1203 0.1601 0.0397 0.009 0.9 2.2 0.5 0.0 0 12.681 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 16.01 3.97 4.214 21.075 1.011 0.018 11.86 16.26 4.39 4.294 21.317 1.011 0.017 Individual atomic B min max mean iso aniso Overall: 6.71 108.15 21.31 4.32 1892 0 Protein: 6.71 108.15 17.71 4.31 1519 0 Water: 8.42 68.65 35.97 N/A 365 0 Other: 25.17 44.57 34.34 N/A 8 0 Chain A: 6.71 108.15 19.39 N/A 1735 0 Chain S: 17.99 68.65 42.47 N/A 157 0 Histogram: Values Number of atoms 6.71 - 16.85 1034 16.85 - 27.00 374 27.00 - 37.14 233 37.14 - 47.28 147 47.28 - 57.43 70 57.43 - 67.57 21 67.57 - 77.71 6 77.71 - 87.86 4 87.86 - 98.00 1 98.00 - 108.15 2 =========================== Idealize ADP of riding H ========================== r_work=0.1186 r_free=0.1626 r_work=0.1188 r_free=0.1628 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1188 r_free = 0.1628 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1183 r_free = 0.1632 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 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= 0.1183 r_free= 0.1632 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016751 | | target function (ls_wunit_k1) not normalized (work): 271.973925 | | target function (ls_wunit_k1) not normalized (free): 25.679543 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1183 0.1632 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1793 0.1789 0.1942 n_refl.: 17043 remove outliers: r(all,work,free)=0.1793 0.1789 0.1942 n_refl.: 17043 overall B=-0.37 to atoms: r(all,work,free)=0.1767 0.1763 0.1926 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1178 0.1625 n_refl.: 17043 remove outliers: r(all,work,free)=0.1198 0.1176 0.1625 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 0.3409 306.858 279.665 0.609 1.007 0.360 11.894-9.307 99.02 97 4 0.1530 488.256 482.022 0.911 1.007 0.357 9.237-7.194 100.00 213 7 0.1640 399.344 400.322 0.972 1.007 0.310 7.162-5.571 100.00 427 22 0.1501 299.708 296.619 0.933 1.006 0.235 5.546-4.326 100.00 867 58 0.0856 411.452 408.861 0.959 1.005 0.210 4.315-3.360 100.00 1859 96 0.0811 391.294 390.330 1.015 1.004 0.201 3.356-2.611 100.00 3867 181 0.1175 257.058 256.417 1.009 1.001 0.121 2.608-2.000 99.99 8818 434 0.1328 167.558 166.640 1.015 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-1.3094 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1176 r_free=0.1625 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1176 r_free=0.1625 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1176 r_free=0.1625 | n_water=365 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.1177 r_free=0.1630 | n_water=363 | time (s): 31.090 (total time: 31.730) Filter (q & B) r_work=0.1177 r_free=0.1630 | n_water=363 | time (s): 1.080 (total time: 32.810) Compute maps r_work=0.1177 r_free=0.1630 | n_water=363 | time (s): 0.730 (total time: 33.540) Filter (map) r_work=0.1249 r_free=0.1628 | n_water=270 | time (s): 1.670 (total time: 35.210) Find peaks r_work=0.1249 r_free=0.1628 | n_water=270 | time (s): 0.470 (total time: 35.680) Add new water r_work=0.1437 r_free=0.1819 | n_water=414 | time (s): 1.890 (total time: 37.570) Refine new water occ: r_work=0.1245 r_free=0.1580 adp: r_work=0.1238 r_free=0.1587 occ: r_work=0.1218 r_free=0.1541 adp: r_work=0.1207 r_free=0.1545 occ: r_work=0.1199 r_free=0.1525 adp: r_work=0.1190 r_free=0.1528 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1528 r_work=0.1190 r_free=0.1528 | n_water=414 | time (s): 33.280 (total time: 70.850) Filter (q & B) r_work=0.1191 r_free=0.1534 | n_water=407 | time (s): 2.010 (total time: 72.860) Filter (dist only) r_work=0.1191 r_free=0.1534 | n_water=405 | time (s): 32.970 (total time: 105.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.869743 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.200441 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 0.1173 0.1553 0.0381 0.009 1.0 4.5 0.5 0.0 0 0.935 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.73 15.53 3.81 4.366 21.553 0.200 4.994 11.52 15.55 4.03 4.995 21.483 0.200 4.970 Individual atomic B min max mean iso aniso Overall: 6.49 106.14 20.96 4.85 1932 0 Protein: 6.49 106.14 17.01 4.84 1519 0 Water: 8.57 60.85 35.57 N/A 405 0 Other: 25.50 44.88 33.10 N/A 8 0 Chain A: 6.49 106.14 18.77 N/A 1734 0 Chain S: 16.73 60.85 40.21 N/A 198 0 Histogram: Values Number of atoms 6.49 - 16.45 1083 16.45 - 26.42 336 26.42 - 36.38 223 36.38 - 46.35 178 46.35 - 56.31 75 56.31 - 66.28 24 66.28 - 76.25 5 76.25 - 86.21 4 86.21 - 96.18 2 96.18 - 106.14 2 =========================== Idealize ADP of riding H ========================== r_work=0.1152 r_free=0.1555 r_work=0.1153 r_free=0.1558 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1153 r_free = 0.1558 target_work(ml) = 4.970 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1142 r_free = 0.1541 target_work(ml) = 4.963 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1142 r_free= 0.1541 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.962710 | | target function (ml) not normalized (work): 80564.626479 | | target function (ml) not normalized (free): 4182.969750 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1162 0.1142 0.1541 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1659 0.1653 0.1839 n_refl.: 17041 remove outliers: r(all,work,free)=0.1659 0.1653 0.1839 n_refl.: 17041 overall B=-0.37 to atoms: r(all,work,free)=0.1634 0.1627 0.1826 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1160 0.1140 0.1544 n_refl.: 17041 remove outliers: r(all,work,free)=0.1159 0.1140 0.1544 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 0.3587 303.363 280.265 0.572 1.006 0.339 11.894-9.307 99.02 97 4 0.1714 488.256 481.048 0.903 1.006 0.338 9.237-7.194 100.00 213 7 0.1794 399.344 400.805 0.989 1.006 0.280 7.162-5.571 100.00 427 22 0.1540 299.708 294.271 0.942 1.006 0.215 5.546-4.326 100.00 867 58 0.0944 411.452 408.341 0.965 1.005 0.211 4.315-3.360 100.00 1859 96 0.0891 391.294 388.687 1.010 1.003 0.185 3.356-2.611 100.00 3867 181 0.1280 257.058 254.936 1.011 1.001 0.142 2.608-2.000 99.99 8818 434 0.1080 167.558 166.197 1.017 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3294 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1140 r_free=0.1544 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=0.1142 r_free=0.1541 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1142 r_free=0.1541 | n_water=405 | time (s): 0.750 (total time: 0.750) Filter (dist) r_work=0.1142 r_free=0.1541 | n_water=405 | time (s): 31.430 (total time: 32.180) Filter (q & B) r_work=0.1142 r_free=0.1542 | n_water=404 | time (s): 2.160 (total time: 34.340) Compute maps r_work=0.1142 r_free=0.1542 | n_water=404 | time (s): 0.770 (total time: 35.110) Filter (map) r_work=0.1204 r_free=0.1571 | n_water=315 | time (s): 1.840 (total time: 36.950) Find peaks r_work=0.1204 r_free=0.1571 | n_water=315 | time (s): 0.680 (total time: 37.630) Add new water r_work=0.1337 r_free=0.1689 | n_water=457 | time (s): 2.090 (total time: 39.720) Refine new water occ: r_work=0.1174 r_free=0.1500 adp: r_work=0.1168 r_free=0.1504 occ: r_work=0.1149 r_free=0.1479 adp: r_work=0.1142 r_free=0.1481 occ: r_work=0.1133 r_free=0.1471 adp: r_work=0.1127 r_free=0.1473 ADP+occupancy (water only), MIN, final r_work=0.1127 r_free=0.1473 r_work=0.1127 r_free=0.1473 | n_water=457 | time (s): 34.200 (total time: 73.920) Filter (q & B) r_work=0.1133 r_free=0.1482 | n_water=441 | time (s): 2.020 (total time: 75.940) Filter (dist only) r_work=0.1134 r_free=0.1483 | n_water=440 | time (s): 34.300 (total time: 110.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.837721 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.160065 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 0.1525 0.0409 0.009 1.0 3.2 0.5 0.0 0 0.919 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.17 15.25 4.09 4.589 21.103 0.160 4.953 11.04 15.29 4.26 4.708 21.150 0.160 4.945 Individual atomic B min max mean iso aniso Overall: 5.91 104.35 21.03 4.91 1967 0 Protein: 5.91 104.35 16.61 4.91 1519 0 Water: 8.64 64.19 36.13 N/A 440 0 Other: 24.38 43.26 31.93 N/A 8 0 Chain A: 5.91 104.35 18.30 N/A 1734 0 Chain S: 14.68 64.19 41.39 N/A 233 0 Histogram: Values Number of atoms 5.91 - 15.76 1062 15.76 - 25.60 356 25.60 - 35.45 212 35.45 - 45.29 193 45.29 - 55.13 102 55.13 - 64.98 28 64.98 - 74.82 5 74.82 - 84.66 4 84.66 - 94.51 3 94.51 - 104.35 2 =========================== Idealize ADP of riding H ========================== r_work=0.1104 r_free=0.1529 r_work=0.1104 r_free=0.1530 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1104 r_free = 0.1530 target_work(ml) = 4.945 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1097 r_free = 0.1522 target_work(ml) = 4.939 | | 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.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1097 r_free= 0.1522 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.939230 | | target function (ml) not normalized (work): 80178.521243 | | target function (ml) not normalized (free): 4169.626590 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1118 0.1097 0.1522 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1582 0.1571 0.1839 n_refl.: 17040 remove outliers: r(all,work,free)=0.1582 0.1571 0.1839 n_refl.: 17040 overall B=-0.30 to atoms: r(all,work,free)=0.1563 0.1551 0.1829 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1116 0.1095 0.1519 n_refl.: 17040 remove outliers: r(all,work,free)=0.1116 0.1095 0.1519 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 0.3650 303.363 277.434 0.559 1.002 0.340 11.894-9.307 99.02 97 4 0.1743 488.256 483.186 0.920 1.002 0.330 9.237-7.194 100.00 213 7 0.1694 399.344 401.258 0.993 1.002 0.250 7.162-5.571 100.00 427 22 0.1537 299.708 294.283 0.942 1.002 0.220 5.546-4.326 100.00 867 58 0.0892 411.452 408.644 0.967 1.002 0.191 4.315-3.360 100.00 1859 96 0.0834 391.294 388.860 1.008 1.002 0.191 3.356-2.611 100.00 3867 181 0.1216 257.058 254.853 1.004 1.002 0.131 2.608-2.000 99.99 8818 434 0.1054 167.558 166.412 1.001 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.0326 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1095 r_free=0.1519 After: r_work=0.1098 r_free=0.1518 ================================== NQH flips ================================== r_work=0.1098 r_free=0.1518 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1098 r_free=0.1518 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1098 r_free=0.1518 | n_water=440 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.1103 r_free=0.1519 | n_water=438 | time (s): 35.260 (total time: 35.870) Filter (q & B) r_work=0.1103 r_free=0.1519 | n_water=438 | time (s): 0.910 (total time: 36.780) Compute maps r_work=0.1103 r_free=0.1519 | n_water=438 | time (s): 0.620 (total time: 37.400) Filter (map) r_work=0.1174 r_free=0.1559 | n_water=336 | time (s): 1.740 (total time: 39.140) Find peaks r_work=0.1174 r_free=0.1559 | n_water=336 | time (s): 0.440 (total time: 39.580) Add new water r_work=0.1284 r_free=0.1659 | n_water=463 | time (s): 1.490 (total time: 41.070) Refine new water occ: r_work=0.1136 r_free=0.1509 adp: r_work=0.1129 r_free=0.1512 occ: r_work=0.1116 r_free=0.1490 adp: r_work=0.1107 r_free=0.1494 occ: r_work=0.1102 r_free=0.1475 adp: r_work=0.1095 r_free=0.1479 ADP+occupancy (water only), MIN, final r_work=0.1095 r_free=0.1479 r_work=0.1095 r_free=0.1479 | n_water=463 | time (s): 28.160 (total time: 69.230) Filter (q & B) r_work=0.1100 r_free=0.1491 | n_water=450 | time (s): 2.040 (total time: 71.270) Filter (dist only) r_work=0.1100 r_free=0.1492 | n_water=448 | time (s): 38.090 (total time: 109.360) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.847859 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.171491 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1116 0.1507 0.0391 0.009 1.0 4.8 0.5 0.0 0 0.924 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.16 15.07 3.91 4.589 20.848 0.171 4.944 11.06 14.98 3.92 4.634 20.921 0.171 4.937 Individual atomic B min max mean iso aniso Overall: 5.25 103.49 20.95 5.07 1975 0 Protein: 5.25 103.49 16.34 5.06 1519 0 Water: 8.10 67.25 36.38 N/A 448 0 Other: 24.45 43.94 31.50 N/A 8 0 Chain A: 5.25 103.49 17.97 N/A 1732 0 Chain S: 16.61 67.25 42.18 N/A 243 0 Histogram: Values Number of atoms 5.25 - 15.07 1028 15.07 - 24.90 383 24.90 - 34.72 207 34.72 - 44.55 199 44.55 - 54.37 106 54.37 - 64.19 32 64.19 - 74.02 10 74.02 - 83.84 3 83.84 - 93.67 4 93.67 - 103.49 3 =========================== Idealize ADP of riding H ========================== r_work=0.1106 r_free=0.1498 r_work=0.1106 r_free=0.1498 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1106 r_free = 0.1498 target_work(ml) = 4.937 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1102 r_free = 0.1498 target_work(ml) = 4.934 | | 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= 0.1102 r_free= 0.1498 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.933653 | | target function (ml) not normalized (work): 80087.986117 | | target function (ml) not normalized (free): 4158.382749 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1105 0.1374 5.4481 5.618| | 2: 3.63 - 2.88 1.00 2711 122 0.1077 0.1416 5.1956 5.3274| | 3: 2.88 - 2.52 1.00 2681 148 0.1336 0.1675 5.1064 5.1899| | 4: 2.52 - 2.29 1.00 2661 139 0.0940 0.1519 4.6393 4.9465| | 5: 2.29 - 2.13 1.00 2678 122 0.0981 0.1512 4.5953 4.9008| | 6: 2.13 - 2.00 1.00 2692 117 0.1142 0.1782 4.5883 4.8| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.49 1.00 0.96 5972.57| | 2: 3.63 - 2.88 2711 122 0.93 12.29 1.01 0.96 5972.57| | 3: 2.88 - 2.52 2681 148 0.88 18.33 0.99 0.96 5972.57| | 4: 2.52 - 2.29 2661 139 0.93 12.28 1.01 0.97 2182.18| | 5: 2.29 - 2.13 2678 122 0.91 14.41 1.00 0.97 2182.18| | 6: 2.13 - 2.00 2692 117 0.89 17.06 0.99 0.97 2182.18| |alpha: min = 0.96 max = 0.97 mean = 0.97| |beta: min = 2182.18 max = 5972.57 mean = 4097.34| |figures of merit: min = 0.01 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.49 mean = 13.77| |phase err.(test): min = 0.00 max = 88.32 mean = 13.41| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1121 0.1102 0.1498 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1568 0.1558 0.1808 n_refl.: 17040 remove outliers: r(all,work,free)=0.1568 0.1558 0.1808 n_refl.: 17040 overall B=-0.24 to atoms: r(all,work,free)=0.1554 0.1543 0.1799 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1122 0.1103 0.1496 n_refl.: 17040 remove outliers: r(all,work,free)=0.1122 0.1103 0.1496 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 0.3556 303.363 279.760 0.552 1.004 0.330 11.894-9.307 99.02 97 4 0.1666 488.256 482.030 0.914 1.004 0.330 9.237-7.194 100.00 213 7 0.1715 399.344 401.469 0.991 1.005 0.250 7.162-5.571 100.00 427 22 0.1576 299.708 294.001 0.934 1.004 0.203 5.546-4.326 100.00 867 58 0.0919 411.452 408.371 0.965 1.004 0.180 4.315-3.360 100.00 1859 96 0.0858 391.294 389.195 1.004 1.002 0.164 3.356-2.611 100.00 3867 181 0.1224 257.058 254.899 1.002 1.000 0.111 2.608-2.000 99.99 8818 434 0.1049 167.558 166.303 0.995 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8468 ================= 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 : 0.2786 0.1860 0.083 5.295 8.8 119.3 19.9 258 0.000 1_bss: 0.1608 0.1687 0.083 5.295 8.4 118.9 19.5 258 0.000 1_settarget: 0.1608 0.1687 0.083 5.295 8.4 118.9 19.5 258 0.000 1_nqh: 0.1611 0.1694 0.083 5.295 8.4 118.9 19.5 258 0.007 1_weight: 0.1611 0.1694 0.083 5.295 8.4 118.9 19.5 258 0.007 1_xyzrec: 0.1351 0.1634 0.009 0.990 8.4 118.9 19.5 258 0.146 1_adp: 0.1279 0.1653 0.009 0.990 6.1 113.9 20.0 258 0.146 1_regHadp: 0.1282 0.1661 0.009 0.990 6.1 113.9 20.0 258 0.146 1_occ: 0.1276 0.1653 0.009 0.990 6.1 113.9 20.0 258 0.146 2_bss: 0.1276 0.1642 0.009 0.990 5.7 113.5 19.6 258 0.146 2_settarget: 0.1276 0.1642 0.009 0.990 5.7 113.5 19.6 258 0.146 2_updatecdl: 0.1276 0.1642 0.009 0.999 5.7 113.5 19.6 258 0.146 2_nqh: 0.1278 0.1642 0.009 0.999 5.7 113.5 19.6 258 0.143 2_sol: 0.1239 0.1566 0.009 0.999 5.7 113.1 20.9 365 n/a 2_weight: 0.1239 0.1566 0.009 0.999 5.7 113.1 20.9 365 n/a 2_xyzrec: 0.1203 0.1601 0.009 0.938 5.7 113.1 20.9 365 n/a 2_adp: 0.1186 0.1626 0.009 0.938 6.7 108.1 21.3 365 n/a 2_regHadp: 0.1188 0.1628 0.009 0.938 6.7 108.1 21.3 365 n/a 2_occ: 0.1183 0.1632 0.009 0.938 6.7 108.1 21.3 365 n/a 3_bss: 0.1176 0.1625 0.009 0.938 6.3 107.8 20.9 365 n/a 3_settarget: 0.1176 0.1625 0.009 0.938 6.3 107.8 20.9 365 n/a 3_updatecdl: 0.1176 0.1625 0.009 0.939 6.3 107.8 20.9 365 n/a 3_nqh: 0.1176 0.1625 0.009 0.939 6.3 107.8 20.9 365 n/a 3_sol: 0.1191 0.1534 0.009 0.939 6.3 107.8 21.1 405 n/a 3_weight: 0.1191 0.1534 0.009 0.939 6.3 107.8 21.1 405 n/a 3_xyzrec: 0.1173 0.1553 0.009 0.966 6.3 107.8 21.1 405 n/a 3_adp: 0.1152 0.1555 0.009 0.966 6.5 106.1 21.0 405 n/a 3_regHadp: 0.1153 0.1558 0.009 0.966 6.5 106.1 21.0 405 n/a 3_occ: 0.1142 0.1541 0.009 0.966 6.5 106.1 21.0 405 n/a 4_bss: 0.1140 0.1544 0.009 0.966 6.1 105.8 20.6 405 n/a 4_settarget: 0.1140 0.1544 0.009 0.966 6.1 105.8 20.6 405 n/a 4_updatecdl: 0.1140 0.1544 0.009 0.967 6.1 105.8 20.6 405 n/a 4_nqh: 0.1142 0.1541 0.009 0.967 6.1 105.8 20.6 405 n/a 4_sol: 0.1134 0.1483 0.009 0.967 6.1 105.8 20.9 440 n/a 4_weight: 0.1134 0.1483 0.009 0.967 6.1 105.8 20.9 440 n/a 4_xyzrec: 0.1117 0.1525 0.009 0.969 6.1 105.8 20.9 440 n/a 4_adp: 0.1104 0.1529 0.009 0.969 5.9 104.3 21.0 440 n/a 4_regHadp: 0.1104 0.1530 0.009 0.969 5.9 104.3 21.0 440 n/a 4_occ: 0.1097 0.1522 0.009 0.969 5.9 104.3 21.0 440 n/a 5_bss: 0.1095 0.1519 0.009 0.969 5.6 104.1 20.7 440 n/a 5_settarget: 0.1095 0.1519 0.009 0.969 5.6 104.1 20.7 440 n/a 5_updatecdl: 0.1095 0.1519 0.009 0.969 5.6 104.1 20.7 440 n/a 5_setrh: 0.1098 0.1518 0.009 0.969 5.6 104.1 20.7 440 n/a 5_nqh: 0.1098 0.1518 0.009 0.969 5.6 104.1 20.7 440 n/a 5_sol: 0.1100 0.1492 0.009 0.969 5.6 104.1 20.8 448 n/a 5_weight: 0.1100 0.1492 0.009 0.969 5.6 104.1 20.8 448 n/a 5_xyzrec: 0.1116 0.1507 0.009 0.995 5.6 104.1 20.8 448 n/a 5_adp: 0.1106 0.1498 0.009 0.995 5.2 103.5 20.9 448 n/a 5_regHadp: 0.1106 0.1498 0.009 0.995 5.2 103.5 20.9 448 n/a 5_occ: 0.1102 0.1498 0.009 0.995 5.2 103.5 20.9 448 n/a end: 0.1103 0.1496 0.009 0.995 5.0 103.2 20.7 448 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8831905_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8831905_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.5000 Refinement macro-cycles (run) : 935.6500 Write final files (write_after_run_outputs) : 20.6300 Total : 959.7800 Total CPU time: 16.34 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:21 PST -0800 (1735494081.54 s) Start R-work = 0.1608, R-free = 0.1687 Final R-work = 0.1103, R-free = 0.1496 =============================================================================== Job complete usr+sys time: 1002.14 seconds wall clock time: 17 minutes 5.01 seconds (1025.01 seconds total)