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_5637181.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" 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5637181.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5637181.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.36, per 1000 atoms: 0.40 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 123.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.93: 646 0.93 - 1.19: 1017 1.19 - 1.45: 744 1.45 - 1.71: 729 1.71 - 1.97: 17 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 123 " pdb=" O VAL A 123 " ideal model delta sigma weight residual 1.235 1.440 -0.205 9.90e-03 1.02e+04 4.27e+02 bond pdb=" N AGLU A 64 " pdb=" CA AGLU A 64 " ideal model delta sigma weight residual 1.457 1.680 -0.223 1.10e-02 8.26e+03 4.12e+02 bond pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta sigma weight residual 1.450 1.231 0.219 1.16e-02 7.43e+03 3.56e+02 bond pdb=" N GLU A 18 " pdb=" CA GLU A 18 " ideal model delta sigma weight residual 1.457 1.705 -0.248 1.32e-02 5.74e+03 3.54e+02 bond pdb=" CA AGLN A 80 " pdb=" C AGLN A 80 " ideal model delta sigma weight residual 1.524 1.759 -0.236 1.27e-02 6.20e+03 3.44e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.14: 2872 4.14 - 8.29: 1875 8.29 - 12.43: 785 12.43 - 16.57: 219 16.57 - 20.71: 26 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH2 ARG A 5 " ideal model delta sigma weight residual 119.20 135.45 -16.25 9.00e-01 1.23e+00 3.26e+02 angle pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " pdb=" NH2 ARG A 28 " ideal model delta sigma weight residual 119.20 106.11 13.09 9.00e-01 1.23e+00 2.11e+02 angle pdb=" O LEU A 112 " pdb=" C LEU A 112 " pdb=" N LEU A 113 " ideal model delta sigma weight residual 122.12 137.46 -15.34 1.06e+00 8.90e-01 2.09e+02 angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.36 137.31 -15.95 1.11e+00 8.12e-01 2.07e+02 angle pdb=" O LEU A 166 " pdb=" C LEU A 166 " pdb=" N ALA A 167 " ideal model delta sigma weight residual 122.12 107.57 14.55 1.06e+00 8.90e-01 1.88e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.51: 1306 16.51 - 33.00: 117 33.00 - 49.49: 38 49.49 - 65.99: 14 65.99 - 82.48: 6 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N LEU A 77 " pdb=" C LEU A 77 " pdb=" CA LEU A 77 " pdb=" CB LEU A 77 " ideal model delta harmonic sigma weight residual 122.80 141.47 -18.67 0 2.50e+00 1.60e-01 5.58e+01 dihedral pdb=" C GLU A 143 " pdb=" N GLU A 143 " pdb=" CA GLU A 143 " pdb=" CB GLU A 143 " ideal model delta harmonic sigma weight residual -122.60 -140.91 18.31 0 2.50e+00 1.60e-01 5.37e+01 dihedral pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CA VAL A 25 " pdb=" CB VAL A 25 " ideal model delta harmonic sigma weight residual 123.40 140.85 -17.45 0 2.50e+00 1.60e-01 4.87e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.201: 100 0.201 - 0.400: 61 0.400 - 0.598: 49 0.598 - 0.797: 25 0.797 - 0.995: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.59 -1.00 2.00e-01 2.50e+01 2.48e+01 chirality pdb=" CA THR A 154 " pdb=" N THR A 154 " pdb=" C THR A 154 " pdb=" CB THR A 154 " both_signs ideal model delta sigma weight residual False 2.53 3.51 -0.99 2.00e-01 2.50e+01 2.44e+01 chirality pdb=" CB VAL A 181 " pdb=" CA VAL A 181 " pdb=" CG1 VAL A 181 " pdb=" CG2 VAL A 181 " both_signs ideal model delta sigma weight residual False -2.63 -3.54 0.91 2.00e-01 2.50e+01 2.08e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.111 2.00e-02 2.50e+03 6.02e-02 1.09e+02 pdb=" CG PHE A 164 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.028 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.117 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.061 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.099 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.021 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.073 2.00e-02 2.50e+03 5.56e-02 9.28e+01 pdb=" CG PHE A 119 " 0.096 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.116 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.030 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.042 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.033 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.018 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " 0.061 2.00e-02 2.50e+03 5.49e-02 9.04e+01 pdb=" CG ATYR A 67 " -0.072 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.001 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " -0.003 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.057 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.073 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.040 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.041 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.071 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.033 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.095 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 810 2.28 - 2.86: 7854 2.86 - 3.44: 10597 3.44 - 4.02: 15300 4.02 - 4.60: 22047 Nonbonded interactions: 56608 Sorted by model distance: nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.702 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.723 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.800 2.450 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.834 2.450 nonbonded pdb=" H VAL A 44 " pdb=" O ILE A 52 " model vdw 1.842 2.450 ... (remaining 56603 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_5637181_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= 0.2794 r_free= 0.1822 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.408440 | | target function (ml) not normalized (work): 71606.287866 | | target function (ml) not normalized (free): 3263.892602 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3178 0.2140 7.5181 5.0274| | 2: 3.63 - 2.88 1.00 2711 122 0.2642 0.1701 4.3292 4.3463| | 3: 2.88 - 2.52 1.00 2682 148 0.2595 0.1796 4.1867 4.191| | 4: 2.52 - 2.29 1.00 2661 139 0.2578 0.1568 3.519 3.6277| | 5: 2.29 - 2.13 1.00 2678 122 0.2664 0.1355 3.4169 3.3427| | 6: 2.13 - 2.00 1.00 2692 117 0.2745 0.1909 3.3184 3.4355| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.60 0.77 0.23 1308.92| | 2: 3.63 - 2.88 2711 122 0.83 23.84 1.32 0.23 1308.92| | 3: 2.88 - 2.52 2682 148 0.73 33.03 1.29 0.23 1308.92| | 4: 2.52 - 2.29 2661 139 0.93 11.42 1.30 0.26 136.36| | 5: 2.29 - 2.13 2678 122 0.92 13.55 1.32 0.26 136.36| | 6: 2.13 - 2.00 2692 117 0.90 16.40 1.33 0.26 136.36| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 136.36 max = 1308.92 mean = 729.17| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.87 mean = 19.31| |phase err.(test): min = 0.00 max = 89.07 mean = 19.56| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.249 1557 Z= 5.616 Angle : 5.384 16.340 2118 Z= 3.824 Chirality : 0.383 0.995 243 Planarity : 0.032 0.146 284 Dihedral : 14.086 82.483 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 39.46 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.48), residues: 224 helix: -2.56 (0.38), residues: 108 sheet: -0.55 (0.92), residues: 28 loop : -0.48 (0.60), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.100 0.021 ARG A 98 TYR 0.141 0.047 TYR A 141 PHE 0.093 0.041 PHE A 119 HIS 0.072 0.035 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2794 r_free= 0.1822 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.408440 | | target function (ml) not normalized (work): 71606.287866 | | target function (ml) not normalized (free): 3263.892602 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3245 percent. r_work = 0.2926 r_free = 0.2010 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2872 0.2926 0.2010 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2872 0.2926 0.2010 n_refl.: 17050 remove outliers: r(all,work,free)=0.2164 0.2175 0.2010 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2137 0.2147 0.1992 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1630 0.1625 0.1718 n_refl.: 17045 remove outliers: r(all,work,free)=0.1629 0.1624 0.1718 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 0.4056 394.958 361.326 0.646 1.012 0.397 11.894-9.307 99.02 97 4 0.1930 633.919 613.997 0.932 1.013 0.380 9.237-7.194 100.00 213 7 0.2172 518.482 509.771 0.965 1.012 0.371 7.162-5.571 100.00 427 22 0.2335 389.121 376.123 0.921 1.011 0.284 5.546-4.326 100.00 867 58 0.1383 534.201 528.986 0.961 1.009 0.251 4.315-3.360 100.00 1859 96 0.1300 508.030 503.903 1.016 1.006 0.181 3.356-2.611 100.00 3867 181 0.1666 333.747 329.151 1.014 1.000 0.029 2.608-2.000 99.99 8818 434 0.1666 217.546 213.598 1.031 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4730 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1624 r_free=0.1718 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1624 r_free=0.1718 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.066636 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.853663 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 0.1653 0.0299 0.008 1.0 0.6 0.5 0.0 0 11.033 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.53 16.53 2.99 3.013 18.446 0.854 0.023 12.79 16.80 4.00 3.558 18.682 0.854 0.021 Individual atomic B min max mean iso aniso Overall: 6.12 113.89 19.92 4.04 1785 0 Protein: 6.12 112.99 17.14 4.04 1519 0 Water: 8.83 113.89 36.07 N/A 258 0 Other: 21.74 37.39 26.29 N/A 8 0 Chain A: 6.12 113.89 19.92 N/A 1785 0 Histogram: Values Number of atoms 6.12 - 16.89 1082 16.89 - 27.67 346 27.67 - 38.45 183 38.45 - 49.22 95 49.22 - 60.00 52 60.00 - 70.78 12 70.78 - 81.56 7 81.56 - 92.33 4 92.33 - 103.11 1 103.11 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1279 r_free=0.1680 r_work=0.1282 r_free=0.1688 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1282 r_free = 0.1688 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1277 r_free = 0.1674 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 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= 0.1277 r_free= 0.1674 coordinate error (max.-lik. estimate): 0.12 A | | | | normalized target function (ls_wunit_k1) (work): 0.020110 | | target function (ls_wunit_k1) not normalized (work): 326.533739 | | target function (ls_wunit_k1) not normalized (free): 27.827722 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1297 0.1277 0.1674 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1913 0.1912 0.1993 n_refl.: 17044 remove outliers: r(all,work,free)=0.1913 0.1912 0.1993 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1885 0.1883 0.1978 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1297 0.1278 0.1667 n_refl.: 17044 remove outliers: r(all,work,free)=0.1295 0.1276 0.1667 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 0.3545 303.829 279.333 0.625 1.009 0.370 11.894-9.307 99.02 97 4 0.1693 488.660 478.585 0.919 1.010 0.367 9.237-7.194 100.00 213 7 0.1839 399.675 396.952 0.961 1.009 0.351 7.162-5.571 100.00 427 22 0.1833 299.956 295.242 0.932 1.008 0.301 5.546-4.326 100.00 867 58 0.1060 411.792 409.528 0.958 1.007 0.210 4.315-3.360 100.00 1859 96 0.0928 391.618 391.226 1.017 1.004 0.191 3.356-2.611 100.00 3867 181 0.1301 257.271 256.003 1.015 1.000 0.081 2.608-2.000 99.99 8818 434 0.1348 167.696 166.211 1.022 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3811 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1667 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1276 r_free=0.1667 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1667 | n_water=258 | time (s): 0.900 (total time: 0.900) Filter (dist) r_work=0.1284 r_free=0.1658 | n_water=252 | time (s): 21.610 (total time: 22.510) Filter (q & B) r_work=0.1285 r_free=0.1658 | n_water=250 | time (s): 2.030 (total time: 24.540) Compute maps r_work=0.1285 r_free=0.1658 | n_water=250 | time (s): 0.820 (total time: 25.360) Filter (map) r_work=0.1316 r_free=0.1647 | n_water=213 | time (s): 1.800 (total time: 27.160) Find peaks r_work=0.1316 r_free=0.1647 | n_water=213 | time (s): 0.660 (total time: 27.820) Add new water r_work=0.1537 r_free=0.1857 | n_water=370 | time (s): 2.020 (total time: 29.840) Refine new water occ: r_work=0.1334 r_free=0.1571 adp: r_work=0.1273 r_free=0.1565 occ: r_work=0.1279 r_free=0.1545 adp: r_work=0.1245 r_free=0.1549 occ: r_work=0.1246 r_free=0.1540 adp: r_work=0.1235 r_free=0.1545 ADP+occupancy (water only), MIN, final r_work=0.1235 r_free=0.1545 r_work=0.1235 r_free=0.1545 | n_water=370 | time (s): 11.090 (total time: 40.930) Filter (q & B) r_work=0.1237 r_free=0.1550 | n_water=362 | time (s): 2.290 (total time: 43.220) Filter (dist only) r_work=0.1237 r_free=0.1551 | n_water=361 | time (s): 28.480 (total time: 71.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.012975 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.977538 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 0.1211 0.1591 0.0380 0.008 0.9 2.2 0.5 0.0 0 12.506 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 15.91 3.80 4.147 21.030 0.978 0.018 11.96 16.17 4.21 4.183 21.354 0.978 0.017 Individual atomic B min max mean iso aniso Overall: 6.66 107.61 21.46 4.27 1888 0 Protein: 6.66 107.61 17.82 4.25 1519 0 Water: 8.57 68.45 36.46 N/A 361 0 Other: 25.42 47.64 35.71 N/A 8 0 Chain A: 6.66 107.61 19.58 N/A 1740 0 Chain S: 17.76 60.66 43.61 N/A 148 0 Histogram: Values Number of atoms 6.66 - 16.75 1015 16.75 - 26.85 390 26.85 - 36.94 214 36.94 - 47.04 157 47.04 - 57.13 78 57.13 - 67.23 23 67.23 - 77.32 4 77.32 - 87.42 4 87.42 - 97.51 1 97.51 - 107.61 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1617 r_work=0.1197 r_free=0.1620 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1620 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 = 0.1197 r_free = 0.1620 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 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= 0.1197 r_free= 0.1620 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016997 | | target function (ls_wunit_k1) not normalized (work): 275.949513 | | target function (ls_wunit_k1) not normalized (free): 25.307931 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1217 0.1197 0.1620 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1781 0.1773 0.1989 n_refl.: 17042 remove outliers: r(all,work,free)=0.1781 0.1773 0.1989 n_refl.: 17042 overall B=-0.39 to atoms: r(all,work,free)=0.1756 0.1747 0.1970 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1191 0.1612 n_refl.: 17042 remove outliers: r(all,work,free)=0.1212 0.1191 0.1612 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 0.3314 303.829 283.362 0.610 1.004 0.350 11.894-9.307 99.02 97 4 0.1515 488.660 485.606 0.919 1.005 0.340 9.237-7.194 100.00 213 7 0.1671 399.675 400.174 0.975 1.005 0.295 7.162-5.571 100.00 427 22 0.1559 299.956 296.267 0.934 1.005 0.281 5.546-4.326 100.00 867 58 0.0861 411.792 408.644 0.959 1.004 0.211 4.315-3.360 100.00 1859 96 0.0833 391.618 390.576 1.015 1.003 0.201 3.356-2.611 100.00 3867 181 0.1206 257.271 256.327 1.013 1.001 0.111 2.608-2.000 99.99 8818 434 0.1329 167.696 166.647 1.018 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3849 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1612 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B Total number of N/Q/H flips: 1 r_work=0.1191 r_free=0.1615 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1615 | n_water=361 | time (s): 0.700 (total time: 0.700) Filter (dist) r_work=0.1191 r_free=0.1614 | n_water=360 | time (s): 28.580 (total time: 29.280) Filter (q & B) r_work=0.1191 r_free=0.1614 | n_water=360 | time (s): 1.170 (total time: 30.450) Compute maps r_work=0.1191 r_free=0.1614 | n_water=360 | time (s): 0.800 (total time: 31.250) Filter (map) r_work=0.1267 r_free=0.1625 | n_water=253 | time (s): 1.980 (total time: 33.230) Find peaks r_work=0.1267 r_free=0.1625 | n_water=253 | time (s): 0.650 (total time: 33.880) Add new water r_work=0.1471 r_free=0.1831 | n_water=403 | time (s): 1.940 (total time: 35.820) Refine new water occ: r_work=0.1257 r_free=0.1591 adp: r_work=0.1249 r_free=0.1595 occ: r_work=0.1227 r_free=0.1576 adp: r_work=0.1216 r_free=0.1574 occ: r_work=0.1207 r_free=0.1569 adp: r_work=0.1196 r_free=0.1567 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1567 r_work=0.1196 r_free=0.1567 | n_water=403 | time (s): 32.350 (total time: 68.170) Filter (q & B) r_work=0.1198 r_free=0.1571 | n_water=397 | time (s): 1.650 (total time: 69.820) Filter (dist only) r_work=0.1198 r_free=0.1573 | n_water=396 | time (s): 30.960 (total time: 100.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.918995 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.148765 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 0.1175 0.1556 0.0382 0.009 1.0 4.5 0.5 0.0 0 0.959 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.75 15.56 3.82 4.336 21.557 0.149 4.996 11.56 15.53 3.98 4.809 21.467 0.149 4.971 Individual atomic B min max mean iso aniso Overall: 6.53 105.85 20.84 4.58 1923 0 Protein: 6.53 105.85 17.09 4.57 1519 0 Water: 8.62 63.62 34.95 N/A 396 0 Other: 27.26 46.31 35.41 N/A 8 0 Chain A: 6.53 105.85 18.78 N/A 1732 0 Chain S: 16.60 63.62 39.60 N/A 191 0 Histogram: Values Number of atoms 6.53 - 16.46 1068 16.46 - 26.39 354 26.39 - 36.32 231 36.32 - 46.26 164 46.26 - 56.19 69 56.19 - 66.12 25 66.12 - 76.05 5 76.05 - 85.99 3 85.99 - 95.92 2 95.92 - 105.85 2 =========================== Idealize ADP of riding H ========================== r_work=0.1156 r_free=0.1553 r_work=0.1156 r_free=0.1555 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1156 r_free = 0.1555 target_work(ml) = 4.971 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1144 r_free = 0.1555 target_work(ml) = 4.964 | | 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.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1144 r_free= 0.1555 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 4.964442 | | target function (ml) not normalized (work): 80597.713618 | | target function (ml) not normalized (free): 4189.072573 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1164 0.1144 0.1555 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1689 0.1682 0.1874 n_refl.: 17042 remove outliers: r(all,work,free)=0.1689 0.1682 0.1874 n_refl.: 17042 overall B=-0.40 to atoms: r(all,work,free)=0.1661 0.1653 0.1858 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1160 0.1141 0.1553 n_refl.: 17042 remove outliers: r(all,work,free)=0.1160 0.1141 0.1553 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 0.3603 303.829 277.894 0.570 1.003 0.340 11.894-9.307 99.02 97 4 0.1765 488.660 480.413 0.916 1.004 0.330 9.237-7.194 100.00 213 7 0.1803 399.675 400.275 0.987 1.004 0.265 7.162-5.571 100.00 427 22 0.1601 299.956 294.945 0.940 1.004 0.241 5.546-4.326 100.00 867 58 0.0939 411.792 408.031 0.966 1.004 0.211 4.315-3.360 100.00 1859 96 0.0888 391.618 389.705 1.013 1.003 0.212 3.356-2.611 100.00 3867 181 0.1276 257.271 255.132 1.014 1.002 0.132 2.608-2.000 99.99 8818 434 0.1081 167.696 166.273 1.018 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.4202 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1141 r_free=0.1553 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1141 r_free=0.1553 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1141 r_free=0.1553 | n_water=396 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.1141 r_free=0.1553 | n_water=396 | time (s): 30.910 (total time: 31.630) Filter (q & B) r_work=0.1141 r_free=0.1553 | n_water=395 | time (s): 2.000 (total time: 33.630) Compute maps r_work=0.1141 r_free=0.1553 | n_water=395 | time (s): 0.790 (total time: 34.420) Filter (map) r_work=0.1206 r_free=0.1544 | n_water=309 | time (s): 2.010 (total time: 36.430) Find peaks r_work=0.1206 r_free=0.1544 | n_water=309 | time (s): 0.520 (total time: 36.950) Add new water r_work=0.1348 r_free=0.1686 | n_water=458 | time (s): 1.430 (total time: 38.380) Refine new water occ: r_work=0.1178 r_free=0.1534 adp: r_work=0.1171 r_free=0.1535 occ: r_work=0.1153 r_free=0.1506 adp: r_work=0.1144 r_free=0.1506 occ: r_work=0.1138 r_free=0.1489 adp: r_work=0.1129 r_free=0.1489 ADP+occupancy (water only), MIN, final r_work=0.1129 r_free=0.1489 r_work=0.1129 r_free=0.1489 | n_water=458 | time (s): 37.730 (total time: 76.110) Filter (q & B) r_work=0.1134 r_free=0.1498 | n_water=444 | time (s): 2.010 (total time: 78.120) Filter (dist only) r_work=0.1137 r_free=0.1493 | n_water=443 | time (s): 35.840 (total time: 113.960) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.826765 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.151048 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1124 0.1546 0.0422 0.009 1.0 5.8 0.5 0.0 0 0.913 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.24 15.46 4.22 4.441 21.183 0.151 4.965 11.12 15.43 4.31 4.613 21.196 0.151 4.956 Individual atomic B min max mean iso aniso Overall: 5.99 103.81 21.06 4.78 1970 0 Protein: 5.99 103.81 16.65 4.78 1519 0 Water: 8.46 62.51 35.95 N/A 443 0 Other: 26.03 44.48 34.13 N/A 8 0 Chain A: 5.99 103.81 18.28 N/A 1730 0 Chain S: 19.35 62.51 41.09 N/A 240 0 Histogram: Values Number of atoms 5.99 - 15.77 1047 15.77 - 25.55 370 25.55 - 35.33 219 35.33 - 45.12 193 45.12 - 54.90 96 54.90 - 64.68 32 64.68 - 74.46 5 74.46 - 84.24 3 84.24 - 94.03 3 94.03 - 103.81 2 =========================== Idealize ADP of riding H ========================== r_work=0.1112 r_free=0.1543 r_work=0.1112 r_free=0.1544 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1112 r_free = 0.1544 target_work(ml) = 4.956 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1102 r_free = 0.1547 target_work(ml) = 4.952 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1102 r_free= 0.1547 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.952470 | | target function (ml) not normalized (work): 80403.350556 | | target function (ml) not normalized (free): 4183.091286 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1124 0.1102 0.1547 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1616 0.1604 0.1888 n_refl.: 17042 remove outliers: r(all,work,free)=0.1616 0.1604 0.1888 n_refl.: 17042 overall B=-0.32 to atoms: r(all,work,free)=0.1595 0.1582 0.1877 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1122 0.1101 0.1543 n_refl.: 17042 remove outliers: r(all,work,free)=0.1121 0.1100 0.1543 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 0.3799 300.333 278.385 0.550 1.002 0.340 11.894-9.307 99.02 97 4 0.1797 488.660 481.781 0.912 1.003 0.330 9.237-7.194 100.00 213 7 0.1755 399.675 402.774 0.990 1.004 0.247 7.162-5.571 100.00 427 22 0.1516 299.956 294.304 0.940 1.003 0.220 5.546-4.326 100.00 867 58 0.0911 411.792 408.281 0.967 1.003 0.211 4.315-3.360 100.00 1859 96 0.0826 391.618 389.419 1.009 1.002 0.191 3.356-2.611 100.00 3867 181 0.1219 257.271 255.010 1.009 1.001 0.131 2.608-2.000 99.99 8818 434 0.1056 167.696 166.435 1.007 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1063 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1100 r_free=0.1543 After: r_work=0.1102 r_free=0.1541 ================================== NQH flips ================================== r_work=0.1102 r_free=0.1541 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1102 r_free=0.1541 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1102 r_free=0.1541 | n_water=443 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.1102 r_free=0.1546 | n_water=442 | time (s): 36.680 (total time: 37.330) Filter (q & B) r_work=0.1103 r_free=0.1549 | n_water=440 | time (s): 1.700 (total time: 39.030) Compute maps r_work=0.1103 r_free=0.1549 | n_water=440 | time (s): 0.640 (total time: 39.670) Filter (map) r_work=0.1186 r_free=0.1548 | n_water=330 | time (s): 1.900 (total time: 41.570) Find peaks r_work=0.1186 r_free=0.1548 | n_water=330 | time (s): 0.420 (total time: 41.990) Add new water r_work=0.1315 r_free=0.1656 | n_water=468 | time (s): 1.460 (total time: 43.450) Refine new water occ: r_work=0.1149 r_free=0.1527 adp: r_work=0.1141 r_free=0.1519 occ: r_work=0.1129 r_free=0.1515 adp: r_work=0.1119 r_free=0.1504 occ: r_work=0.1115 r_free=0.1505 adp: r_work=0.1107 r_free=0.1495 ADP+occupancy (water only), MIN, final r_work=0.1107 r_free=0.1495 r_work=0.1107 r_free=0.1495 | n_water=468 | time (s): 25.850 (total time: 69.300) Filter (q & B) r_work=0.1109 r_free=0.1499 | n_water=460 | time (s): 2.400 (total time: 71.700) Filter (dist only) r_work=0.1110 r_free=0.1501 | n_water=459 | time (s): 37.140 (total time: 108.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.932135 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.157008 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 0.1130 0.1515 0.0385 0.010 1.1 4.5 0.5 0.0 0 0.966 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.30 15.15 3.85 4.520 20.881 0.157 4.949 11.17 15.02 3.85 4.619 20.950 0.157 4.939 Individual atomic B min max mean iso aniso Overall: 5.30 102.47 20.97 4.94 1986 0 Protein: 5.30 102.47 16.34 4.93 1519 0 Water: 8.36 61.56 36.09 N/A 459 0 Other: 25.81 41.87 32.81 N/A 8 0 Chain A: 5.30 102.47 17.94 N/A 1729 0 Chain S: 17.85 61.56 41.40 N/A 257 0 Histogram: Values Number of atoms 5.30 - 15.02 1011 15.02 - 24.73 397 24.73 - 34.45 219 34.45 - 44.17 186 44.17 - 53.88 129 53.88 - 63.60 29 63.60 - 73.32 6 73.32 - 83.03 3 83.03 - 92.75 3 92.75 - 102.47 3 =========================== Idealize ADP of riding H ========================== r_work=0.1117 r_free=0.1502 r_work=0.1117 r_free=0.1500 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1117 r_free = 0.1500 target_work(ml) = 4.939 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1113 r_free = 0.1517 target_work(ml) = 4.938 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1113 r_free= 0.1517 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.938032 | | target function (ml) not normalized (work): 80164.018011 | | target function (ml) not normalized (free): 4162.930899 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2811 159 0.1125 0.1355 5.4655 5.6274| | 2: 3.63 - 2.88 1.00 2711 122 0.1099 0.1582 5.2165 5.4005| | 3: 2.88 - 2.52 1.00 2681 148 0.1367 0.1680 5.1321 5.1867| | 4: 2.52 - 2.29 1.00 2661 139 0.0930 0.1547 4.625 4.9467| | 5: 2.29 - 2.13 1.00 2678 122 0.0970 0.1482 4.5822 4.8771| | 6: 2.13 - 2.00 1.00 2692 117 0.1127 0.1706 4.5771 4.7784| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2811 159 0.95 8.91 1.00 0.96 6306.55| | 2: 3.63 - 2.88 2711 122 0.92 12.74 1.01 0.96 6306.55| | 3: 2.88 - 2.52 2681 148 0.88 18.77 0.99 0.96 6306.55| | 4: 2.52 - 2.29 2661 139 0.93 12.16 1.01 0.98 2126.50| | 5: 2.29 - 2.13 2678 122 0.91 14.20 1.00 0.98 2126.50| | 6: 2.13 - 2.00 2692 117 0.89 16.85 0.99 0.98 2126.50| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2126.50 max = 6306.55 mean = 4238.67| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.96 mean = 13.90| |phase err.(test): min = 0.00 max = 85.55 mean = 13.34| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1132 0.1113 0.1517 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1596 0.1584 0.1872 n_refl.: 17041 remove outliers: r(all,work,free)=0.1596 0.1584 0.1872 n_refl.: 17041 overall B=-0.26 to atoms: r(all,work,free)=0.1580 0.1567 0.1863 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1133 0.1114 0.1518 n_refl.: 17041 remove outliers: r(all,work,free)=0.1133 0.1114 0.1518 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 0.3634 300.333 277.954 0.547 1.004 0.340 11.894-9.307 99.02 97 4 0.1777 488.660 482.261 0.911 1.006 0.330 9.237-7.194 100.00 213 7 0.1808 399.675 402.075 0.989 1.006 0.250 7.162-5.571 100.00 427 22 0.1556 299.956 294.660 0.934 1.005 0.220 5.546-4.326 100.00 867 58 0.0929 411.792 408.323 0.964 1.005 0.211 4.315-3.360 100.00 1859 96 0.0875 391.618 389.620 1.005 1.003 0.181 3.356-2.611 100.00 3867 181 0.1249 257.271 255.015 1.003 1.001 0.058 2.608-2.000 99.99 8818 434 0.1040 167.696 166.310 0.999 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9083 ================= 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 : 0.2794 0.1822 0.084 5.384 8.8 119.3 19.9 258 0.000 1_bss: 0.1624 0.1718 0.084 5.384 8.4 118.9 19.5 258 0.000 1_settarget: 0.1624 0.1718 0.084 5.384 8.4 118.9 19.5 258 0.000 1_nqh: 0.1624 0.1718 0.084 5.384 8.4 118.9 19.5 258 0.000 1_weight: 0.1624 0.1718 0.084 5.384 8.4 118.9 19.5 258 0.000 1_xyzrec: 0.1353 0.1653 0.008 0.964 8.4 118.9 19.5 258 0.151 1_adp: 0.1279 0.1680 0.008 0.964 6.1 113.9 19.9 258 0.151 1_regHadp: 0.1282 0.1688 0.008 0.964 6.1 113.9 19.9 258 0.151 1_occ: 0.1277 0.1674 0.008 0.964 6.1 113.9 19.9 258 0.151 2_bss: 0.1276 0.1667 0.008 0.964 5.7 113.5 19.5 258 0.151 2_settarget: 0.1276 0.1667 0.008 0.964 5.7 113.5 19.5 258 0.151 2_updatecdl: 0.1276 0.1667 0.008 0.984 5.7 113.5 19.5 258 0.151 2_nqh: 0.1276 0.1667 0.008 0.984 5.7 113.5 19.5 258 0.151 2_sol: 0.1237 0.1551 0.008 0.984 5.7 112.6 20.9 361 n/a 2_weight: 0.1237 0.1551 0.008 0.984 5.7 112.6 20.9 361 n/a 2_xyzrec: 0.1211 0.1591 0.008 0.929 5.7 112.6 20.9 361 n/a 2_adp: 0.1196 0.1617 0.008 0.929 6.7 107.6 21.5 361 n/a 2_regHadp: 0.1197 0.1620 0.008 0.929 6.7 107.6 21.5 361 n/a 2_occ: 0.1197 0.1620 0.008 0.929 6.7 107.6 21.5 361 n/a 3_bss: 0.1191 0.1612 0.008 0.929 6.3 107.2 21.1 361 n/a 3_settarget: 0.1191 0.1612 0.008 0.929 6.3 107.2 21.1 361 n/a 3_updatecdl: 0.1191 0.1612 0.008 0.929 6.3 107.2 21.1 361 n/a 3_nqh: 0.1191 0.1615 0.008 0.929 6.3 107.2 21.1 361 n/a 3_sol: 0.1198 0.1573 0.008 0.929 6.3 107.2 21.0 396 n/a 3_weight: 0.1198 0.1573 0.008 0.929 6.3 107.2 21.0 396 n/a 3_xyzrec: 0.1175 0.1556 0.009 0.961 6.3 107.2 21.0 396 n/a 3_adp: 0.1156 0.1553 0.009 0.961 6.5 105.9 20.8 396 n/a 3_regHadp: 0.1156 0.1555 0.009 0.961 6.5 105.9 20.8 396 n/a 3_occ: 0.1144 0.1555 0.009 0.961 6.5 105.9 20.8 396 n/a 4_bss: 0.1141 0.1553 0.009 0.961 6.1 105.5 20.4 396 n/a 4_settarget: 0.1141 0.1553 0.009 0.961 6.1 105.5 20.4 396 n/a 4_updatecdl: 0.1141 0.1553 0.009 0.961 6.1 105.5 20.4 396 n/a 4_nqh: 0.1141 0.1553 0.009 0.961 6.1 105.5 20.4 396 n/a 4_sol: 0.1137 0.1493 0.009 0.961 6.1 105.5 21.0 443 n/a 4_weight: 0.1137 0.1493 0.009 0.961 6.1 105.5 21.0 443 n/a 4_xyzrec: 0.1124 0.1546 0.009 0.969 6.1 105.5 21.0 443 n/a 4_adp: 0.1112 0.1543 0.009 0.969 6.0 103.8 21.1 443 n/a 4_regHadp: 0.1112 0.1544 0.009 0.969 6.0 103.8 21.1 443 n/a 4_occ: 0.1102 0.1547 0.009 0.969 6.0 103.8 21.1 443 n/a 5_bss: 0.1100 0.1543 0.009 0.969 5.7 103.5 20.7 443 n/a 5_settarget: 0.1100 0.1543 0.009 0.969 5.7 103.5 20.7 443 n/a 5_updatecdl: 0.1100 0.1543 0.009 0.972 5.7 103.5 20.7 443 n/a 5_setrh: 0.1102 0.1541 0.009 0.972 5.7 103.5 20.7 443 n/a 5_nqh: 0.1102 0.1541 0.009 0.972 5.7 103.5 20.7 443 n/a 5_sol: 0.1110 0.1501 0.009 0.972 5.7 103.5 20.8 459 n/a 5_weight: 0.1110 0.1501 0.009 0.972 5.7 103.5 20.8 459 n/a 5_xyzrec: 0.1130 0.1515 0.010 1.077 5.7 103.5 20.8 459 n/a 5_adp: 0.1117 0.1502 0.010 1.077 5.3 102.5 21.0 459 n/a 5_regHadp: 0.1117 0.1500 0.010 1.077 5.3 102.5 21.0 459 n/a 5_occ: 0.1113 0.1517 0.010 1.077 5.3 102.5 21.0 459 n/a end: 0.1114 0.1518 0.010 1.077 5.0 102.2 20.7 459 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_5637181_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_5637181_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2800 Refinement macro-cycles (run) : 929.0300 Write final files (write_after_run_outputs) : 22.1700 Total : 954.4800 Total CPU time: 16.26 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:17 PST -0800 (1735494077.32 s) Start R-work = 0.1624, R-free = 0.1718 Final R-work = 0.1114, R-free = 0.1518 =============================================================================== Job complete usr+sys time: 999.30 seconds wall clock time: 17 minutes 2.23 seconds (1022.23 seconds total)