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_5352376.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_5352376.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5352376.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 1 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: 1.77, per 1000 atoms: 0.52 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: 0.46 Conformation dependent library (CDL) restraints added in 107.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 575 0.92 - 1.18: 1088 1.18 - 1.45: 716 1.45 - 1.71: 753 1.71 - 1.97: 21 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.539 1.411 0.128 5.40e-03 3.43e+04 5.60e+02 bond pdb=" CA THR A 125 " pdb=" C THR A 125 " ideal model delta sigma weight residual 1.523 1.778 -0.255 1.24e-02 6.50e+03 4.23e+02 bond pdb=" N LEU A 72 " pdb=" CA LEU A 72 " ideal model delta sigma weight residual 1.463 1.683 -0.220 1.08e-02 8.57e+03 4.16e+02 bond pdb=" C LEU A 38 " pdb=" O LEU A 38 " ideal model delta sigma weight residual 1.236 1.469 -0.233 1.16e-02 7.43e+03 4.04e+02 bond pdb=" C ILE A 9 " pdb=" O ILE A 9 " ideal model delta sigma weight residual 1.237 1.033 0.204 1.10e-02 8.26e+03 3.44e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 2950 4.24 - 8.47: 1875 8.47 - 12.71: 757 12.71 - 16.94: 167 16.94 - 21.18: 28 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O LYS A 89 " pdb=" C LYS A 89 " pdb=" N BGLU A 90 " ideal model delta sigma weight residual 122.09 137.17 -15.08 1.04e+00 9.25e-01 2.10e+02 angle pdb=" O LEU A 92 " pdb=" C LEU A 92 " pdb=" N BLYS A 93 " ideal model delta sigma weight residual 122.15 138.02 -15.87 1.14e+00 7.69e-01 1.94e+02 angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.42 129.31 -8.89 6.40e-01 2.44e+00 1.93e+02 angle pdb=" O ILE A 152 " pdb=" C ILE A 152 " pdb=" N BLEU A 153 " ideal model delta sigma weight residual 122.99 108.81 14.18 1.07e+00 8.73e-01 1.76e+02 angle pdb=" O BLYS A 132 " pdb=" C BLYS A 132 " pdb=" N MET A 133 " ideal model delta sigma weight residual 122.15 136.49 -14.34 1.14e+00 7.69e-01 1.58e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.33: 1318 18.33 - 36.66: 118 36.66 - 54.98: 36 54.98 - 73.31: 8 73.31 - 91.64: 1 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C AGLU A 64 " pdb=" N AGLU A 64 " pdb=" CA AGLU A 64 " pdb=" CB AGLU A 64 " ideal model delta harmonic sigma weight residual -122.60 -141.99 19.39 0 2.50e+00 1.60e-01 6.02e+01 dihedral pdb=" N AGLU A 64 " pdb=" C AGLU A 64 " pdb=" CA AGLU A 64 " pdb=" CB AGLU A 64 " ideal model delta harmonic sigma weight residual 122.80 141.06 -18.26 0 2.50e+00 1.60e-01 5.33e+01 dihedral pdb=" N VAL A 50 " pdb=" C VAL A 50 " pdb=" CA VAL A 50 " pdb=" CB VAL A 50 " ideal model delta harmonic sigma weight residual 123.40 140.79 -17.39 0 2.50e+00 1.60e-01 4.84e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.197: 107 0.197 - 0.392: 61 0.392 - 0.587: 46 0.587 - 0.782: 20 0.782 - 0.977: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA AGLU A 64 " pdb=" N AGLU A 64 " pdb=" C AGLU A 64 " pdb=" CB AGLU A 64 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.39e+01 chirality pdb=" CA GLU A 163 " pdb=" N GLU A 163 " pdb=" C GLU A 163 " pdb=" CB GLU A 163 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.97e+01 chirality pdb=" CB VAL A 8 " pdb=" CA VAL A 8 " pdb=" CG1 VAL A 8 " pdb=" CG2 VAL A 8 " both_signs ideal model delta sigma weight residual False -2.63 -1.78 -0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.072 2.00e-02 2.50e+03 5.84e-02 1.02e+02 pdb=" CG PHE A 119 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.087 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.086 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.091 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.082 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.024 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.037 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.024 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.040 2.00e-02 2.50e+03 5.68e-02 9.67e+01 pdb=" CG TYR A 139 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.084 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.084 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.013 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.088 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.062 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.046 2.00e-02 2.50e+03 5.34e-02 8.55e+01 pdb=" CG ATYR A 67 " 0.019 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.049 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.083 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.057 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.075 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.025 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.038 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.084 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.004 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.33: 1151 2.33 - 2.90: 8199 2.90 - 3.47: 10484 3.47 - 4.03: 15169 4.03 - 4.60: 21583 Nonbonded interactions: 56586 Sorted by model distance: nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.768 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.799 2.100 nonbonded pdb=" HB3 LYS A 188 " pdb=" HE2 LYS A 188 " model vdw 1.808 2.440 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.815 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.821 2.100 ... (remaining 56581 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_5352376_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= 0.2793 r_free= 0.1865 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.415000 | | target function (ml) not normalized (work): 71712.844213 | | target function (ml) not normalized (free): 3270.727324 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3184 0.2185 7.525 5.0371| | 2: 3.63 - 2.88 1.00 2711 122 0.2643 0.1734 4.3282 4.3359| | 3: 2.88 - 2.52 1.00 2682 148 0.2557 0.1680 4.1883 4.1848| | 4: 2.52 - 2.29 1.00 2661 139 0.2546 0.1647 3.521 3.5913| | 5: 2.29 - 2.13 1.00 2678 122 0.2697 0.1614 3.4242 3.4616| | 6: 2.13 - 2.00 1.00 2692 117 0.2788 0.1924 3.3409 3.4187| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.61 0.77 0.23 1315.93| | 2: 3.63 - 2.88 2711 122 0.83 23.87 1.32 0.23 1315.93| | 3: 2.88 - 2.52 2682 148 0.73 32.90 1.28 0.23 1315.93| | 4: 2.52 - 2.29 2661 139 0.93 11.79 1.29 0.26 142.92| | 5: 2.29 - 2.13 2678 122 0.92 13.97 1.32 0.26 142.92| | 6: 2.13 - 2.00 2692 117 0.89 17.05 1.34 0.26 142.92| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 142.92 max = 1315.93 mean = 735.96| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 90.00 mean = 19.53| |phase err.(test): min = 0.00 max = 89.32 mean = 20.05| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.255 1557 Z= 5.584 Angle : 5.278 20.057 2118 Z= 3.756 Chirality : 0.368 0.977 243 Planarity : 0.030 0.080 284 Dihedral : 13.689 91.641 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 4.97 % Favored : 93.79 % Cbeta Deviations : 27.03 % 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: -2.80 (0.44), residues: 224 helix: -2.46 (0.36), residues: 108 sheet: -1.01 (0.72), residues: 38 loop : -0.95 (0.56), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.082 0.019 ARG A 27 TYR 0.085 0.033 TYR A 139 PHE 0.108 0.042 PHE A 119 HIS 0.053 0.025 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2793 r_free= 0.1865 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.415000 | | target function (ml) not normalized (work): 71712.844213 | | target function (ml) not normalized (free): 3270.727324 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3311 percent. r_work = 0.2926 r_free = 0.2000 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2874 0.2926 0.2000 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2874 0.2926 0.2000 n_refl.: 17050 remove outliers: r(all,work,free)=0.2171 0.2183 0.2000 n_refl.: 17045 overall B=-0.42 to atoms: r(all,work,free)=0.2144 0.2155 0.1982 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1635 0.1631 0.1711 n_refl.: 17045 remove outliers: r(all,work,free)=0.1633 0.1629 0.1711 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 0.4046 391.723 359.950 0.635 1.013 0.380 11.894-9.307 99.02 97 4 0.1826 634.141 615.511 0.930 1.013 0.377 9.237-7.194 100.00 213 7 0.2142 518.663 513.062 0.964 1.013 0.345 7.162-5.571 100.00 427 22 0.2299 389.257 376.428 0.927 1.012 0.289 5.546-4.326 100.00 867 58 0.1394 534.388 528.679 0.958 1.010 0.220 4.315-3.360 100.00 1859 96 0.1310 508.208 503.907 1.017 1.006 0.191 3.356-2.611 100.00 3867 181 0.1669 333.864 329.368 1.015 1.000 0.039 2.608-2.000 99.99 8818 434 0.1678 217.622 213.423 1.033 0.988 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4859 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1629 r_free=0.1711 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A A 80 GLN B Total number of N/Q/H flips: 2 r_work=0.1630 r_free=0.1709 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.617527 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.801169 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 0.1350 0.1637 0.0286 0.009 1.0 1.3 0.5 0.0 0 11.809 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.50 16.37 2.86 3.013 18.442 0.801 0.023 12.77 16.55 3.78 3.562 18.709 0.801 0.020 Individual atomic B min max mean iso aniso Overall: 6.57 113.88 19.98 4.02 1785 0 Protein: 6.57 112.85 17.22 4.02 1519 0 Water: 8.59 113.88 36.00 N/A 258 0 Other: 21.62 36.46 26.12 N/A 8 0 Chain A: 6.57 113.88 19.98 N/A 1785 0 Histogram: Values Number of atoms 6.57 - 17.30 1104 17.30 - 28.03 329 28.03 - 38.76 180 38.76 - 49.49 99 49.49 - 60.22 47 60.22 - 70.96 12 70.96 - 81.69 6 81.69 - 92.42 4 92.42 - 103.15 1 103.15 - 113.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1277 r_free=0.1655 r_work=0.1280 r_free=0.1660 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1280 r_free = 0.1660 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 = 0.1657 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.22 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= 0.1657 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020078 | | target function (ls_wunit_k1) not normalized (work): 325.978938 | | target function (ls_wunit_k1) not normalized (free): 26.899570 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1294 0.1276 0.1657 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1905 0.1904 0.1994 n_refl.: 17043 remove outliers: r(all,work,free)=0.1905 0.1904 0.1994 n_refl.: 17043 overall B=-0.40 to atoms: r(all,work,free)=0.1876 0.1874 0.1978 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1295 0.1277 0.1655 n_refl.: 17043 remove outliers: r(all,work,free)=0.1294 0.1276 0.1655 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 0.3483 303.580 277.959 0.611 1.010 0.360 11.894-9.307 99.02 97 4 0.1691 488.261 477.698 0.917 1.010 0.357 9.237-7.194 100.00 213 7 0.1822 399.349 396.298 0.960 1.010 0.351 7.162-5.571 100.00 427 22 0.1857 299.711 294.559 0.933 1.009 0.301 5.546-4.326 100.00 867 58 0.1039 411.456 409.134 0.958 1.007 0.205 4.315-3.360 100.00 1859 96 0.0934 391.298 390.919 1.019 1.005 0.191 3.356-2.611 100.00 3867 181 0.1300 257.061 255.758 1.017 1.000 0.091 2.608-2.000 99.99 8818 434 0.1350 167.560 166.091 1.025 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4365 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1655 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=0.1277 r_free=0.1655 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1655 | n_water=258 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.1284 r_free=0.1642 | n_water=253 | time (s): 19.660 (total time: 20.380) Filter (q & B) r_work=0.1284 r_free=0.1643 | n_water=251 | time (s): 1.700 (total time: 22.080) Compute maps r_work=0.1284 r_free=0.1643 | n_water=251 | time (s): 0.580 (total time: 22.660) Filter (map) r_work=0.1319 r_free=0.1635 | n_water=216 | time (s): 1.540 (total time: 24.200) Find peaks r_work=0.1319 r_free=0.1635 | n_water=216 | time (s): 0.500 (total time: 24.700) Add new water r_work=0.1524 r_free=0.1848 | n_water=373 | time (s): 1.540 (total time: 26.240) Refine new water occ: r_work=0.1332 r_free=0.1588 adp: r_work=0.1275 r_free=0.1585 occ: r_work=0.1281 r_free=0.1550 adp: r_work=0.1249 r_free=0.1557 occ: r_work=0.1252 r_free=0.1547 adp: r_work=0.1240 r_free=0.1549 ADP+occupancy (water only), MIN, final r_work=0.1240 r_free=0.1549 r_work=0.1240 r_free=0.1549 | n_water=373 | time (s): 19.170 (total time: 45.410) Filter (q & B) r_work=0.1242 r_free=0.1551 | n_water=362 | time (s): 1.430 (total time: 46.840) Filter (dist only) r_work=0.1242 r_free=0.1553 | n_water=361 | time (s): 28.650 (total time: 75.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.075391 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.022676 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 0.1219 0.1601 0.0382 0.008 0.9 2.6 0.5 0.0 0 12.038 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.19 16.01 3.82 4.142 21.055 1.023 0.018 12.00 16.16 4.16 4.222 21.365 1.023 0.018 Individual atomic B min max mean iso aniso Overall: 7.11 107.45 21.43 4.35 1888 0 Protein: 7.11 107.45 17.80 4.34 1519 0 Water: 8.57 68.14 36.46 N/A 361 0 Other: 24.65 41.83 33.34 N/A 8 0 Chain A: 7.11 107.45 19.63 N/A 1743 0 Chain S: 18.25 64.35 43.15 N/A 145 0 Histogram: Values Number of atoms 7.11 - 17.14 1048 17.14 - 27.18 357 27.18 - 37.21 215 37.21 - 47.24 162 47.24 - 57.28 65 57.28 - 67.31 30 67.31 - 77.35 4 77.35 - 87.38 3 87.38 - 97.41 2 97.41 - 107.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1616 r_work=0.1202 r_free=0.1618 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1618 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1630 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1199 r_free= 0.1630 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017156 | | target function (ls_wunit_k1) not normalized (work): 278.529111 | | target function (ls_wunit_k1) not normalized (free): 25.168243 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1199 0.1630 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1768 0.1758 0.1991 n_refl.: 17042 remove outliers: r(all,work,free)=0.1768 0.1758 0.1991 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1743 0.1733 0.1973 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1194 0.1625 n_refl.: 17042 remove outliers: r(all,work,free)=0.1214 0.1194 0.1625 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 0.3244 303.580 286.031 0.607 1.003 0.350 11.894-9.307 99.02 97 4 0.1537 488.261 483.938 0.919 1.003 0.350 9.237-7.194 100.00 213 7 0.1657 399.349 399.646 0.978 1.003 0.310 7.162-5.571 100.00 427 22 0.1570 299.711 295.741 0.935 1.003 0.281 5.546-4.326 100.00 867 58 0.0895 411.456 408.889 0.961 1.003 0.211 4.315-3.360 100.00 1859 96 0.0821 391.298 390.404 1.016 1.002 0.201 3.356-2.611 100.00 3867 181 0.1211 257.061 256.115 1.012 1.001 0.053 2.608-2.000 99.99 8818 434 0.1330 167.560 166.439 1.014 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3646 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1625 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1194 r_free=0.1625 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1625 | n_water=361 | time (s): 0.630 (total time: 0.630) Filter (dist) r_work=0.1194 r_free=0.1627 | n_water=359 | time (s): 29.590 (total time: 30.220) Filter (q & B) r_work=0.1194 r_free=0.1627 | n_water=359 | time (s): 1.200 (total time: 31.420) Compute maps r_work=0.1194 r_free=0.1627 | n_water=359 | time (s): 0.760 (total time: 32.180) Filter (map) r_work=0.1256 r_free=0.1623 | n_water=262 | time (s): 1.830 (total time: 34.010) Find peaks r_work=0.1256 r_free=0.1623 | n_water=262 | time (s): 0.530 (total time: 34.540) Add new water r_work=0.1442 r_free=0.1753 | n_water=404 | time (s): 1.450 (total time: 35.990) Refine new water occ: r_work=0.1250 r_free=0.1579 adp: r_work=0.1241 r_free=0.1584 occ: r_work=0.1224 r_free=0.1565 adp: r_work=0.1212 r_free=0.1567 occ: r_work=0.1206 r_free=0.1559 adp: r_work=0.1195 r_free=0.1561 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1561 r_work=0.1195 r_free=0.1561 | n_water=404 | time (s): 26.440 (total time: 62.430) Filter (q & B) r_work=0.1197 r_free=0.1560 | n_water=396 | time (s): 2.080 (total time: 64.510) Filter (dist only) r_work=0.1197 r_free=0.1560 | n_water=396 | time (s): 31.180 (total time: 95.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.854724 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.143912 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 0.1180 0.1551 0.0371 0.009 0.9 3.5 0.5 0.0 0 0.927 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.80 15.51 3.71 4.387 21.588 0.144 4.999 11.64 15.58 3.95 4.898 21.484 0.144 4.977 Individual atomic B min max mean iso aniso Overall: 5.99 105.31 20.89 4.64 1923 0 Protein: 5.99 105.31 17.02 4.64 1519 0 Water: 8.84 63.45 35.45 N/A 396 0 Other: 26.16 45.10 33.84 N/A 8 0 Chain A: 5.99 105.31 18.81 N/A 1738 0 Chain S: 19.42 63.45 40.41 N/A 185 0 Histogram: Values Number of atoms 5.99 - 15.92 1045 15.92 - 25.85 357 25.85 - 35.78 227 35.78 - 45.71 179 45.71 - 55.65 75 55.65 - 65.58 28 65.58 - 75.51 4 75.51 - 85.44 3 85.44 - 95.38 3 95.38 - 105.31 2 =========================== Idealize ADP of riding H ========================== r_work=0.1164 r_free=0.1558 r_work=0.1164 r_free=0.1561 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1164 r_free = 0.1561 target_work(ml) = 4.978 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1159 r_free = 0.1558 target_work(ml) = 4.974 | | occupancies: max = 1.00 min = 0.21 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= 0.1159 r_free= 0.1558 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.973891 | | target function (ml) not normalized (work): 80751.121745 | | target function (ml) not normalized (free): 4188.553842 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1178 0.1159 0.1558 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1696 0.1688 0.1900 n_refl.: 17042 remove outliers: r(all,work,free)=0.1696 0.1688 0.1900 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1670 0.1661 0.1886 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1175 0.1156 0.1558 n_refl.: 17042 remove outliers: r(all,work,free)=0.1174 0.1155 0.1558 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 0.3500 300.088 280.948 0.570 1.005 0.331 11.894-9.307 99.02 97 4 0.1694 488.261 479.025 0.910 1.006 0.325 9.237-7.194 100.00 213 7 0.1818 399.349 400.306 0.982 1.006 0.290 7.162-5.571 100.00 427 22 0.1642 299.711 294.139 0.935 1.006 0.251 5.546-4.326 100.00 867 58 0.0972 411.456 407.461 0.964 1.005 0.221 4.315-3.360 100.00 1859 96 0.0901 391.298 389.015 1.012 1.004 0.201 3.356-2.611 100.00 3867 181 0.1294 257.061 254.755 1.013 1.001 0.131 2.608-2.000 99.99 8818 434 0.1092 167.560 166.152 1.018 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3628 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1155 r_free=0.1558 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1155 r_free=0.1558 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1155 r_free=0.1558 | n_water=396 | time (s): 0.900 (total time: 0.900) Filter (dist) r_work=0.1155 r_free=0.1558 | n_water=396 | time (s): 28.520 (total time: 29.420) Filter (q & B) r_work=0.1155 r_free=0.1558 | n_water=396 | time (s): 1.090 (total time: 30.510) Compute maps r_work=0.1155 r_free=0.1558 | n_water=396 | time (s): 0.590 (total time: 31.100) Filter (map) r_work=0.1210 r_free=0.1572 | n_water=308 | time (s): 1.450 (total time: 32.550) Find peaks r_work=0.1210 r_free=0.1572 | n_water=308 | time (s): 0.410 (total time: 32.960) Add new water r_work=0.1359 r_free=0.1696 | n_water=448 | time (s): 1.500 (total time: 34.460) Refine new water occ: r_work=0.1192 r_free=0.1517 adp: r_work=0.1183 r_free=0.1523 occ: r_work=0.1167 r_free=0.1499 adp: r_work=0.1157 r_free=0.1503 occ: r_work=0.1149 r_free=0.1493 adp: r_work=0.1141 r_free=0.1493 ADP+occupancy (water only), MIN, final r_work=0.1141 r_free=0.1493 r_work=0.1141 r_free=0.1493 | n_water=448 | time (s): 23.630 (total time: 58.090) Filter (q & B) r_work=0.1144 r_free=0.1498 | n_water=436 | time (s): 2.130 (total time: 60.220) Filter (dist only) r_work=0.1144 r_free=0.1501 | n_water=435 | time (s): 36.200 (total time: 96.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.980832 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.165707 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 0.1122 0.1553 0.0430 0.010 1.0 4.2 0.5 0.0 0 0.990 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.22 15.53 4.30 4.474 21.108 0.166 4.954 11.11 15.60 4.49 4.622 21.124 0.166 4.952 Individual atomic B min max mean iso aniso Overall: 5.82 103.01 20.98 4.84 1962 0 Protein: 5.82 103.01 16.62 4.83 1519 0 Water: 8.19 63.13 35.99 N/A 435 0 Other: 26.91 46.05 34.57 N/A 8 0 Chain A: 5.82 103.01 18.37 N/A 1738 0 Chain S: 16.62 63.13 41.28 N/A 224 0 Histogram: Values Number of atoms 5.82 - 15.54 1037 15.54 - 25.26 370 25.26 - 34.98 211 34.98 - 44.69 200 44.69 - 54.41 94 54.41 - 64.13 35 64.13 - 73.85 8 73.85 - 83.57 2 83.57 - 93.29 3 93.29 - 103.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1111 r_free=0.1560 r_work=0.1111 r_free=0.1560 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1111 r_free = 0.1560 target_work(ml) = 4.952 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1102 r_free = 0.1579 target_work(ml) = 4.952 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1102 r_free= 0.1579 coordinate error (max.-lik. estimate): 0.12 A | | | | normalized target function (ml) (work): 4.951871 | | target function (ml) not normalized (work): 80388.669895 | | target function (ml) not normalized (free): 4193.880498 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1125 0.1102 0.1579 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1598 0.1584 0.1896 n_refl.: 17041 remove outliers: r(all,work,free)=0.1598 0.1584 0.1896 n_refl.: 17041 overall B=-0.29 to atoms: r(all,work,free)=0.1580 0.1565 0.1887 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1123 0.1100 0.1575 n_refl.: 17041 remove outliers: r(all,work,free)=0.1123 0.1100 0.1575 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 0.3705 300.088 278.091 0.556 1.001 0.324 11.894-9.307 99.02 97 4 0.1702 488.261 480.858 0.924 1.002 0.320 9.237-7.194 100.00 213 7 0.1671 399.349 400.991 0.986 1.002 0.270 7.162-5.571 100.00 427 22 0.1525 299.711 294.832 0.941 1.003 0.240 5.546-4.326 100.00 867 58 0.0926 411.456 408.108 0.966 1.003 0.201 4.315-3.360 100.00 1859 96 0.0851 391.298 389.058 1.008 1.002 0.201 3.356-2.611 100.00 3867 181 0.1233 257.061 254.813 1.005 1.001 0.111 2.608-2.000 99.99 8818 434 0.1040 167.560 166.397 1.000 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.0133 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1100 r_free=0.1575 After: r_work=0.1102 r_free=0.1573 ================================== NQH flips ================================== r_work=0.1102 r_free=0.1573 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1102 r_free=0.1573 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1102 r_free=0.1573 | n_water=435 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.1102 r_free=0.1573 | n_water=435 | time (s): 34.780 (total time: 35.400) Filter (q & B) r_work=0.1102 r_free=0.1573 | n_water=435 | time (s): 0.890 (total time: 36.290) Compute maps r_work=0.1102 r_free=0.1573 | n_water=435 | time (s): 0.590 (total time: 36.880) Filter (map) r_work=0.1185 r_free=0.1570 | n_water=325 | time (s): 1.600 (total time: 38.480) Find peaks r_work=0.1185 r_free=0.1570 | n_water=325 | time (s): 0.480 (total time: 38.960) Add new water r_work=0.1304 r_free=0.1682 | n_water=456 | time (s): 1.500 (total time: 40.460) Refine new water occ: r_work=0.1150 r_free=0.1519 adp: r_work=0.1142 r_free=0.1519 occ: r_work=0.1131 r_free=0.1501 adp: r_work=0.1121 r_free=0.1502 occ: r_work=0.1118 r_free=0.1494 adp: r_work=0.1109 r_free=0.1493 ADP+occupancy (water only), MIN, final r_work=0.1109 r_free=0.1493 r_work=0.1109 r_free=0.1493 | n_water=456 | time (s): 23.190 (total time: 63.650) Filter (q & B) r_work=0.1111 r_free=0.1507 | n_water=446 | time (s): 1.630 (total time: 65.280) Filter (dist only) r_work=0.1111 r_free=0.1507 | n_water=445 | time (s): 37.910 (total time: 103.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.885654 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.143074 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 0.1132 0.1531 0.0399 0.010 1.1 6.4 0.5 0.0 0 0.943 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.32 15.31 3.99 4.558 20.843 0.143 4.958 11.23 15.13 3.90 4.643 20.795 0.143 4.948 Individual atomic B min max mean iso aniso Overall: 5.33 101.70 20.67 4.85 1972 0 Protein: 5.33 101.70 16.20 4.84 1519 0 Water: 7.93 63.22 35.71 N/A 445 0 Other: 25.58 43.32 32.52 N/A 8 0 Chain A: 5.33 101.70 17.88 N/A 1737 0 Chain S: 19.16 63.22 41.31 N/A 235 0 Histogram: Values Number of atoms 5.33 - 14.97 1022 14.97 - 24.61 379 24.61 - 34.24 215 34.24 - 43.88 189 43.88 - 53.52 119 53.52 - 63.15 31 63.15 - 72.79 8 72.79 - 82.43 2 82.43 - 92.06 3 92.06 - 101.70 4 =========================== Idealize ADP of riding H ========================== r_work=0.1123 r_free=0.1513 r_work=0.1123 r_free=0.1513 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1123 r_free = 0.1513 target_work(ml) = 4.948 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1116 r_free = 0.1517 target_work(ml) = 4.943 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1116 r_free= 0.1517 coordinate error (max.-lik. estimate): 0.12 A | | | | normalized target function (ml) (work): 4.943259 | | target function (ml) not normalized (work): 80248.872635 | | target function (ml) not normalized (free): 4169.137956 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1135 0.1381 5.4621 5.6636| | 2: 3.63 - 2.88 1.00 2711 122 0.1088 0.1488 5.2081 5.3515| | 3: 2.88 - 2.52 1.00 2681 148 0.1366 0.1689 5.1274 5.1945| | 4: 2.52 - 2.29 1.00 2661 139 0.0948 0.1482 4.6495 4.9238| | 5: 2.29 - 2.13 1.00 2678 122 0.0971 0.1532 4.5975 4.9188| | 6: 2.13 - 2.00 1.00 2692 117 0.1126 0.1829 4.5857 4.8074| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.75 1.00 0.96 6250.96| | 2: 3.63 - 2.88 2711 122 0.92 12.74 1.01 0.96 6250.96| | 3: 2.88 - 2.52 2681 148 0.88 18.70 0.99 0.96 6250.96| | 4: 2.52 - 2.29 2661 139 0.93 12.47 1.01 0.96 2215.65| | 5: 2.29 - 2.13 2678 122 0.91 14.53 1.00 0.96 2215.65| | 6: 2.13 - 2.00 2692 117 0.89 17.29 0.99 0.96 2215.65| |alpha: min = 0.96 max = 0.96 mean = 0.96| |beta: min = 2215.65 max = 6250.96 mean = 4254.69| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.97 mean = 14.04| |phase err.(test): min = 0.00 max = 87.42 mean = 13.53| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1135 0.1116 0.1517 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1580 0.1570 0.1806 n_refl.: 17041 remove outliers: r(all,work,free)=0.1580 0.1570 0.1806 n_refl.: 17041 overall B=-0.21 to atoms: r(all,work,free)=0.1567 0.1557 0.1801 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1135 0.1116 0.1517 n_refl.: 17041 remove outliers: r(all,work,free)=0.1135 0.1116 0.1517 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 0.3700 300.088 280.810 0.554 1.005 0.330 11.894-9.307 99.02 97 4 0.1720 488.261 480.099 0.921 1.006 0.290 9.237-7.194 100.00 213 7 0.1758 399.349 402.455 0.980 1.006 0.260 7.162-5.571 100.00 427 22 0.1600 299.711 294.979 0.934 1.006 0.240 5.546-4.326 100.00 867 58 0.0933 411.456 408.438 0.961 1.005 0.207 4.315-3.360 100.00 1859 96 0.0876 391.298 388.878 1.002 1.003 0.201 3.356-2.611 100.00 3867 181 0.1248 257.061 254.781 0.999 1.001 0.111 2.608-2.000 99.99 8818 434 0.1046 167.560 166.264 0.990 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7303 ================= 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 : 0.2793 0.1865 0.082 5.278 8.8 119.3 19.9 258 0.000 1_bss: 0.1629 0.1711 0.082 5.278 8.4 118.9 19.5 258 0.000 1_settarget: 0.1629 0.1711 0.082 5.278 8.4 118.9 19.5 258 0.000 1_nqh: 0.1630 0.1709 0.082 5.278 8.4 118.9 19.5 258 0.007 1_weight: 0.1630 0.1709 0.082 5.278 8.4 118.9 19.5 258 0.007 1_xyzrec: 0.1350 0.1637 0.009 0.985 8.4 118.9 19.5 258 0.149 1_adp: 0.1277 0.1655 0.009 0.985 6.6 113.9 20.0 258 0.149 1_regHadp: 0.1280 0.1660 0.009 0.985 6.6 113.9 20.0 258 0.149 1_occ: 0.1276 0.1657 0.009 0.985 6.6 113.9 20.0 258 0.149 2_bss: 0.1276 0.1655 0.009 0.985 6.2 113.5 19.6 258 0.149 2_settarget: 0.1276 0.1655 0.009 0.985 6.2 113.5 19.6 258 0.149 2_updatecdl: 0.1276 0.1655 0.009 1.001 6.2 113.5 19.6 258 0.149 2_nqh: 0.1277 0.1655 0.009 1.001 6.2 113.5 19.6 258 0.152 2_sol: 0.1242 0.1553 0.009 1.001 6.2 112.4 20.9 361 n/a 2_weight: 0.1242 0.1553 0.009 1.001 6.2 112.4 20.9 361 n/a 2_xyzrec: 0.1219 0.1601 0.008 0.931 6.2 112.4 20.9 361 n/a 2_adp: 0.1200 0.1616 0.008 0.931 7.1 107.4 21.4 361 n/a 2_regHadp: 0.1202 0.1618 0.008 0.931 7.1 107.4 21.4 361 n/a 2_occ: 0.1199 0.1630 0.008 0.931 7.1 107.4 21.4 361 n/a 3_bss: 0.1194 0.1625 0.008 0.931 6.7 107.1 21.1 361 n/a 3_settarget: 0.1194 0.1625 0.008 0.931 6.7 107.1 21.1 361 n/a 3_updatecdl: 0.1194 0.1625 0.008 0.928 6.7 107.1 21.1 361 n/a 3_nqh: 0.1194 0.1625 0.008 0.928 6.7 107.1 21.1 361 n/a 3_sol: 0.1197 0.1560 0.008 0.928 6.7 107.1 21.1 396 n/a 3_weight: 0.1197 0.1560 0.008 0.928 6.7 107.1 21.1 396 n/a 3_xyzrec: 0.1180 0.1551 0.009 0.938 6.7 107.1 21.1 396 n/a 3_adp: 0.1164 0.1558 0.009 0.938 6.0 105.3 20.9 396 n/a 3_regHadp: 0.1164 0.1561 0.009 0.938 6.0 105.3 20.9 396 n/a 3_occ: 0.1159 0.1558 0.009 0.938 6.0 105.3 20.9 396 n/a 4_bss: 0.1155 0.1558 0.009 0.938 5.6 104.9 20.5 396 n/a 4_settarget: 0.1155 0.1558 0.009 0.938 5.6 104.9 20.5 396 n/a 4_updatecdl: 0.1155 0.1558 0.009 0.938 5.6 104.9 20.5 396 n/a 4_nqh: 0.1155 0.1558 0.009 0.938 5.6 104.9 20.5 396 n/a 4_sol: 0.1144 0.1501 0.009 0.938 5.6 104.9 21.0 435 n/a 4_weight: 0.1144 0.1501 0.009 0.938 5.6 104.9 21.0 435 n/a 4_xyzrec: 0.1122 0.1553 0.010 0.978 5.6 104.9 21.0 435 n/a 4_adp: 0.1111 0.1560 0.010 0.978 5.8 103.0 21.0 435 n/a 4_regHadp: 0.1111 0.1560 0.010 0.978 5.8 103.0 21.0 435 n/a 4_occ: 0.1102 0.1579 0.010 0.978 5.8 103.0 21.0 435 n/a 5_bss: 0.1100 0.1575 0.010 0.978 5.5 102.7 20.7 435 n/a 5_settarget: 0.1100 0.1575 0.010 0.978 5.5 102.7 20.7 435 n/a 5_updatecdl: 0.1100 0.1575 0.010 0.980 5.5 102.7 20.7 435 n/a 5_setrh: 0.1102 0.1573 0.010 0.980 5.5 102.7 20.7 435 n/a 5_nqh: 0.1102 0.1573 0.010 0.980 5.5 102.7 20.7 435 n/a 5_sol: 0.1111 0.1507 0.010 0.980 5.5 102.7 20.8 445 n/a 5_weight: 0.1111 0.1507 0.010 0.980 5.5 102.7 20.8 445 n/a 5_xyzrec: 0.1132 0.1531 0.010 1.055 5.5 102.7 20.8 445 n/a 5_adp: 0.1123 0.1513 0.010 1.055 5.3 101.7 20.7 445 n/a 5_regHadp: 0.1123 0.1513 0.010 1.055 5.3 101.7 20.7 445 n/a 5_occ: 0.1116 0.1517 0.010 1.055 5.3 101.7 20.7 445 n/a end: 0.1116 0.1517 0.010 1.055 5.1 101.5 20.5 445 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_5352376_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_5352376_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.9700 Refinement macro-cycles (run) : 890.5400 Write final files (write_after_run_outputs) : 22.5600 Total : 917.0700 Total CPU time: 15.68 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:40:42 PST -0800 (1735494042.38 s) Start R-work = 0.1629, R-free = 0.1711 Final R-work = 0.1116, R-free = 0.1517 =============================================================================== Job complete usr+sys time: 966.29 seconds wall clock time: 16 minutes 29.51 seconds (989.51 seconds total)