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_1617309.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1617309.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1617309.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 1.34, 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: 0.55 Conformation dependent library (CDL) restraints added in 195.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 550 0.91 - 1.17: 1095 1.17 - 1.42: 641 1.42 - 1.67: 828 1.67 - 1.93: 39 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.537 1.400 0.137 5.00e-03 4.00e+04 7.49e+02 bond pdb=" CA TYR A 141 " pdb=" C TYR A 141 " ideal model delta sigma weight residual 1.524 1.275 0.249 1.31e-02 5.83e+03 3.61e+02 bond pdb=" C BGLN A 80 " pdb=" O BGLN A 80 " ideal model delta sigma weight residual 1.236 1.020 0.216 1.15e-02 7.56e+03 3.53e+02 bond pdb=" C GLN A 180 " pdb=" N VAL A 181 " ideal model delta sigma weight residual 1.334 1.563 -0.229 1.25e-02 6.40e+03 3.35e+02 bond pdb=" N ILE A 31 " pdb=" CA ILE A 31 " ideal model delta sigma weight residual 1.458 1.671 -0.213 1.17e-02 7.31e+03 3.32e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.34: 3470 5.34 - 10.68: 1850 10.68 - 16.02: 409 16.02 - 21.36: 45 21.36 - 26.71: 3 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 119.20 104.35 14.85 9.00e-01 1.23e+00 2.72e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N ACYS A 53 " ideal model delta sigma weight residual 123.18 138.56 -15.38 1.05e+00 9.07e-01 2.15e+02 angle pdb=" CA GLU A 170 " pdb=" C GLU A 170 " pdb=" O GLU A 170 " ideal model delta sigma weight residual 120.63 134.55 -13.92 1.08e+00 8.57e-01 1.66e+02 angle pdb=" OE1AGLN A 80 " pdb=" CD AGLN A 80 " pdb=" NE2AGLN A 80 " ideal model delta sigma weight residual 122.60 109.84 12.76 1.00e+00 1.00e+00 1.63e+02 angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.42 128.37 -7.95 6.40e-01 2.44e+00 1.54e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.45: 1299 17.45 - 34.89: 126 34.89 - 52.33: 39 52.33 - 69.78: 15 69.78 - 87.22: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ALYS A 99 " pdb=" N ALYS A 99 " pdb=" CA ALYS A 99 " pdb=" CB ALYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -145.87 23.27 0 2.50e+00 1.60e-01 8.66e+01 dihedral pdb=" C ARG A 48 " pdb=" N ARG A 48 " pdb=" CA ARG A 48 " pdb=" CB ARG A 48 " ideal model delta harmonic sigma weight residual -122.60 -143.97 21.37 0 2.50e+00 1.60e-01 7.31e+01 dihedral pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CA ARG A 48 " pdb=" CB ARG A 48 " ideal model delta harmonic sigma weight residual 122.80 143.75 -20.95 0 2.50e+00 1.60e-01 7.02e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.211: 98 0.211 - 0.419: 75 0.419 - 0.628: 53 0.628 - 0.837: 12 0.837 - 1.046: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ARG A 48 " pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CB ARG A 48 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.73e+01 chirality pdb=" CA ALYS A 99 " pdb=" N ALYS A 99 " pdb=" C ALYS A 99 " pdb=" CB ALYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.65e+01 chirality pdb=" CA BTYR A 67 " pdb=" N BTYR A 67 " pdb=" C BTYR A 67 " pdb=" CB BTYR A 67 " both_signs ideal model delta sigma weight residual False 2.51 3.44 -0.93 2.00e-01 2.50e+01 2.15e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.102 2.00e-02 2.50e+03 7.42e-02 1.65e+02 pdb=" CG PHE A 164 " 0.119 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.092 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.101 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.094 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.040 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.087 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.023 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.006 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.048 2.00e-02 2.50e+03 6.66e-02 1.33e+02 pdb=" CG PHE A 162 " -0.103 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.086 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.091 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.080 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.064 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.069 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.047 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.034 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.070 2.00e-02 2.50e+03 6.43e-02 1.24e+02 pdb=" CG BTYR A 67 " -0.051 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.048 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.090 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.016 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.044 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.109 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.048 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.055 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.34: 1240 2.34 - 2.91: 8270 2.91 - 3.47: 10441 3.47 - 4.04: 15154 4.04 - 4.60: 21532 Nonbonded interactions: 56637 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.781 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.810 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.811 2.450 nonbonded pdb=" O GLN A 95 " pdb=" H BGLY A 100 " model vdw 1.826 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.840 2.450 ... (remaining 56632 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_1617309_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2791 r_free= 0.1801 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.421810 | | target function (ml) not normalized (work): 71823.453949 | | target function (ml) not normalized (free): 3269.249575 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3191 0.2063 7.6246 5.0202| | 2: 3.63 - 2.88 1.00 2711 122 0.2659 0.1771 4.3239 4.321| | 3: 2.88 - 2.52 1.00 2682 148 0.2566 0.1798 4.1755 4.1984| | 4: 2.52 - 2.29 1.00 2661 139 0.2556 0.1533 3.5039 3.5895| | 5: 2.29 - 2.13 1.00 2678 122 0.2617 0.1419 3.4007 3.4758| | 6: 2.13 - 2.00 1.00 2692 117 0.2769 0.1764 3.3352 3.4149| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.40 0.77 0.23 1279.88| | 2: 3.63 - 2.88 2711 122 0.83 23.62 1.31 0.23 1279.88| | 3: 2.88 - 2.52 2682 148 0.73 32.55 1.29 0.23 1279.88| | 4: 2.52 - 2.29 2661 139 0.93 11.84 1.30 0.26 143.27| | 5: 2.29 - 2.13 2678 122 0.92 14.03 1.31 0.26 143.27| | 6: 2.13 - 2.00 2692 117 0.89 16.85 1.34 0.26 143.27| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 143.27 max = 1279.88 mean = 717.91| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.97 mean = 19.38| |phase err.(test): min = 0.00 max = 89.83 mean = 19.67| |-----------------------------------------------------------------------------| ----------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 0.249 1557 Z= 5.572 Angle : 5.349 20.777 2118 Z= 3.757 Chirality : 0.370 1.046 243 Planarity : 0.033 0.089 284 Dihedral : 13.847 87.219 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 31.89 % 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: -1.93 (0.51), residues: 224 helix: -2.69 (0.40), residues: 101 sheet: 0.90 (0.96), residues: 28 loop : -0.02 (0.61), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.065 0.021 ARG A 27 TYR 0.102 0.046 TYR A 139 PHE 0.115 0.051 PHE A 164 HIS 0.086 0.045 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2791 r_free= 0.1801 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.421810 | | target function (ml) not normalized (work): 71823.453949 | | target function (ml) not normalized (free): 3269.249575 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2864 percent. r_work = 0.2919 r_free = 0.1976 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2865 0.2919 0.1976 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2865 0.2919 0.1976 n_refl.: 17050 remove outliers: r(all,work,free)=0.2161 0.2173 0.1976 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2135 0.2146 0.1962 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1621 0.1618 0.1693 n_refl.: 17045 remove outliers: r(all,work,free)=0.1619 0.1616 0.1693 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 0.3906 398.709 361.627 0.657 1.013 0.407 11.894-9.307 99.02 97 4 0.1890 633.244 613.457 0.926 1.014 0.378 9.237-7.194 100.00 213 7 0.2127 517.930 509.262 0.960 1.013 0.361 7.162-5.571 100.00 427 22 0.2273 388.707 375.724 0.924 1.012 0.288 5.546-4.326 100.00 867 58 0.1396 533.632 528.739 0.957 1.010 0.233 4.315-3.360 100.00 1859 96 0.1305 507.489 502.434 1.017 1.006 0.201 3.356-2.611 100.00 3867 181 0.1666 333.392 328.853 1.012 1.000 0.044 2.608-2.000 99.99 8818 434 0.1651 217.314 213.493 1.029 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4272 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1616 r_free=0.1693 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.1621 r_free=0.1705 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.023909 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.851698 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 0.1349 0.1635 0.0286 0.009 1.0 1.3 0.5 0.0 0 12.012 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.49 16.35 2.86 3.013 18.458 0.852 0.023 12.77 16.58 3.80 3.578 18.726 0.852 0.020 Individual atomic B min max mean iso aniso Overall: 6.63 113.90 19.99 4.04 1785 0 Protein: 6.63 112.88 17.24 4.04 1519 0 Water: 8.90 113.90 36.02 N/A 258 0 Other: 21.99 36.36 26.42 N/A 8 0 Chain A: 6.63 113.90 19.99 N/A 1785 0 Histogram: Values Number of atoms 6.63 - 17.35 1107 17.35 - 28.08 328 28.08 - 38.81 179 38.81 - 49.53 99 49.53 - 60.26 47 60.26 - 70.99 11 70.99 - 81.72 6 81.72 - 92.44 4 92.44 - 103.17 1 103.17 - 113.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1277 r_free=0.1658 r_work=0.1280 r_free=0.1666 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1280 r_free = 0.1666 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 = 0.1274 r_free = 0.1652 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.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1274 r_free= 0.1652 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019882 | | target function (ls_wunit_k1) not normalized (work): 322.808690 | | target function (ls_wunit_k1) not normalized (free): 27.252325 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1292 0.1274 0.1652 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1907 0.1906 0.1989 n_refl.: 17043 remove outliers: r(all,work,free)=0.1907 0.1906 0.1989 n_refl.: 17043 overall B=-0.38 to atoms: r(all,work,free)=0.1880 0.1878 0.1974 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1292 0.1275 0.1638 n_refl.: 17043 remove outliers: r(all,work,free)=0.1291 0.1274 0.1638 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 0.3568 304.005 284.391 0.650 1.000 0.380 11.894-9.307 99.02 97 4 0.1701 486.935 477.217 0.927 0.999 0.367 9.237-7.194 100.00 213 7 0.1835 398.264 396.525 0.969 0.998 0.340 7.162-5.571 100.00 427 22 0.1827 298.897 294.543 0.943 0.997 0.301 5.546-4.326 100.00 867 58 0.1050 410.338 408.533 0.968 0.995 0.210 4.315-3.360 100.00 1859 96 0.0930 390.235 390.132 1.030 0.992 0.191 3.356-2.611 100.00 3867 181 0.1296 256.362 254.970 1.027 0.986 0.101 2.608-2.000 99.99 8818 434 0.1345 167.104 165.309 1.036 0.977 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3420 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1638 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1276 r_free=0.1638 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1638 | n_water=258 | time (s): 0.590 (total time: 0.590) Filter (dist) r_work=0.1283 r_free=0.1626 | n_water=252 | time (s): 20.070 (total time: 20.660) Filter (q & B) r_work=0.1284 r_free=0.1627 | n_water=250 | time (s): 1.680 (total time: 22.340) Compute maps r_work=0.1284 r_free=0.1627 | n_water=250 | time (s): 0.580 (total time: 22.920) Filter (map) r_work=0.1320 r_free=0.1623 | n_water=210 | time (s): 1.470 (total time: 24.390) Find peaks r_work=0.1320 r_free=0.1623 | n_water=210 | time (s): 0.430 (total time: 24.820) Add new water r_work=0.1540 r_free=0.1887 | n_water=371 | time (s): 1.540 (total time: 26.360) Refine new water occ: r_work=0.1328 r_free=0.1616 adp: r_work=0.1272 r_free=0.1610 occ: r_work=0.1278 r_free=0.1583 adp: r_work=0.1246 r_free=0.1585 occ: r_work=0.1248 r_free=0.1577 adp: r_work=0.1235 r_free=0.1579 ADP+occupancy (water only), MIN, final r_work=0.1235 r_free=0.1579 r_work=0.1235 r_free=0.1579 | n_water=371 | time (s): 26.180 (total time: 52.540) Filter (q & B) r_work=0.1238 r_free=0.1586 | n_water=361 | time (s): 1.510 (total time: 54.050) Filter (dist only) r_work=0.1239 r_free=0.1588 | n_water=360 | time (s): 28.990 (total time: 83.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.891000 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.005771 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 0.1205 0.1595 0.0390 0.008 0.9 3.5 0.5 0.0 0 11.945 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 15.95 3.90 4.152 21.065 1.006 0.018 11.89 16.24 4.35 4.218 21.312 1.006 0.017 Individual atomic B min max mean iso aniso Overall: 6.83 107.50 21.29 4.31 1887 0 Protein: 6.83 107.50 17.75 4.31 1519 0 Water: 8.36 68.18 35.93 N/A 360 0 Other: 24.57 43.41 33.78 N/A 8 0 Chain A: 6.83 107.50 19.45 N/A 1737 0 Chain S: 19.53 62.70 42.51 N/A 150 0 Histogram: Values Number of atoms 6.83 - 16.90 1041 16.90 - 26.97 368 26.97 - 37.03 221 37.03 - 47.10 148 47.10 - 57.17 70 57.17 - 67.24 27 67.24 - 77.30 5 77.30 - 87.37 4 87.37 - 97.44 1 97.44 - 107.50 2 =========================== Idealize ADP of riding H ========================== r_work=0.1189 r_free=0.1624 r_work=0.1191 r_free=0.1626 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1626 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1187 r_free = 0.1622 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= 0.1187 r_free= 0.1622 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016820 | | target function (ls_wunit_k1) not normalized (work): 273.071352 | | target function (ls_wunit_k1) not normalized (free): 25.317718 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1187 0.1622 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1807 0.1804 0.1942 n_refl.: 17042 remove outliers: r(all,work,free)=0.1807 0.1804 0.1942 n_refl.: 17042 overall B=-0.46 to atoms: r(all,work,free)=0.1776 0.1771 0.1922 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1182 0.1617 n_refl.: 17042 remove outliers: r(all,work,free)=0.1203 0.1182 0.1617 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 0.3371 304.005 283.003 0.627 1.007 0.380 11.894-9.307 99.02 97 4 0.1430 486.935 483.156 0.919 1.007 0.360 9.237-7.194 100.00 213 7 0.1607 398.264 398.991 0.974 1.007 0.311 7.162-5.571 100.00 427 22 0.1535 298.897 295.484 0.937 1.006 0.281 5.546-4.326 100.00 867 58 0.0887 410.338 407.869 0.959 1.005 0.211 4.315-3.360 100.00 1859 96 0.0812 390.235 389.097 1.013 1.004 0.202 3.356-2.611 100.00 3867 181 0.1187 256.362 255.663 1.008 1.001 0.132 2.608-2.000 99.99 8818 434 0.1330 167.104 166.157 1.010 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1615 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1182 r_free=0.1617 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1182 r_free=0.1617 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1182 r_free=0.1617 | n_water=360 | time (s): 0.580 (total time: 0.580) Filter (dist) r_work=0.1182 r_free=0.1620 | n_water=358 | time (s): 28.510 (total time: 29.090) Filter (q & B) r_work=0.1182 r_free=0.1620 | n_water=358 | time (s): 1.210 (total time: 30.300) Compute maps r_work=0.1182 r_free=0.1620 | n_water=358 | time (s): 0.750 (total time: 31.050) Filter (map) r_work=0.1253 r_free=0.1633 | n_water=261 | time (s): 2.290 (total time: 33.340) Find peaks r_work=0.1253 r_free=0.1633 | n_water=261 | time (s): 0.620 (total time: 33.960) Add new water r_work=0.1451 r_free=0.1866 | n_water=408 | time (s): 2.020 (total time: 35.980) Refine new water occ: r_work=0.1256 r_free=0.1629 adp: r_work=0.1249 r_free=0.1631 occ: r_work=0.1226 r_free=0.1591 adp: r_work=0.1215 r_free=0.1593 occ: r_work=0.1205 r_free=0.1568 adp: r_work=0.1193 r_free=0.1568 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1568 r_work=0.1193 r_free=0.1568 | n_water=408 | time (s): 33.770 (total time: 69.750) Filter (q & B) r_work=0.1195 r_free=0.1566 | n_water=399 | time (s): 2.030 (total time: 71.780) Filter (dist only) r_work=0.1195 r_free=0.1566 | n_water=399 | time (s): 30.530 (total time: 102.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.881643 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.160598 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 0.1176 0.1573 0.0397 0.009 1.0 4.5 0.5 0.0 0 0.941 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.76 15.73 3.97 4.363 21.455 0.161 4.997 11.58 15.82 4.24 4.908 21.303 0.161 4.978 Individual atomic B min max mean iso aniso Overall: 6.48 105.62 20.66 4.62 1926 0 Protein: 6.48 105.62 16.86 4.61 1519 0 Water: 8.12 62.43 34.92 N/A 399 0 Other: 25.24 44.66 32.67 N/A 8 0 Chain A: 6.48 105.62 18.57 N/A 1733 0 Chain S: 13.36 62.43 39.43 N/A 193 0 Histogram: Values Number of atoms 6.48 - 16.39 1080 16.39 - 26.30 336 26.30 - 36.22 234 36.22 - 46.13 168 46.13 - 56.05 72 56.05 - 65.96 24 65.96 - 75.88 4 75.88 - 85.79 4 85.79 - 95.70 2 95.70 - 105.62 2 =========================== Idealize ADP of riding H ========================== r_work=0.1158 r_free=0.1582 r_work=0.1157 r_free=0.1582 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1157 r_free = 0.1582 target_work(ml) = 4.978 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1146 r_free = 0.1586 target_work(ml) = 4.971 | | 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= 0.1146 r_free= 0.1586 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.970633 | | target function (ml) not normalized (work): 80698.231304 | | target function (ml) not normalized (free): 4195.016256 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1168 0.1146 0.1586 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1723 0.1719 0.1873 n_refl.: 17042 remove outliers: r(all,work,free)=0.1723 0.1719 0.1873 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1696 0.1691 0.1864 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1165 0.1143 0.1585 n_refl.: 17042 remove outliers: r(all,work,free)=0.1164 0.1142 0.1585 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 0.3540 306.027 275.703 0.592 1.008 0.358 11.894-9.307 99.02 97 4 0.1618 486.935 481.116 0.915 1.008 0.350 9.237-7.194 100.00 213 7 0.1751 398.264 399.081 0.993 1.008 0.269 7.162-5.571 100.00 427 22 0.1569 298.897 293.797 0.941 1.007 0.241 5.546-4.326 100.00 867 58 0.0930 410.338 407.077 0.964 1.006 0.211 4.315-3.360 100.00 1859 96 0.0891 390.235 387.976 1.010 1.004 0.201 3.356-2.611 100.00 3867 181 0.1284 256.362 254.185 1.008 1.001 0.152 2.608-2.000 99.99 8818 434 0.1091 167.104 165.749 1.012 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1658 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1142 r_free=0.1585 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1142 r_free=0.1585 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1142 r_free=0.1585 | n_water=399 | time (s): 0.810 (total time: 0.810) Filter (dist) r_work=0.1142 r_free=0.1585 | n_water=399 | time (s): 31.890 (total time: 32.700) Filter (q & B) r_work=0.1143 r_free=0.1587 | n_water=398 | time (s): 1.940 (total time: 34.640) Compute maps r_work=0.1143 r_free=0.1587 | n_water=398 | time (s): 0.680 (total time: 35.320) Filter (map) r_work=0.1207 r_free=0.1564 | n_water=311 | time (s): 1.960 (total time: 37.280) Find peaks r_work=0.1207 r_free=0.1564 | n_water=311 | time (s): 0.650 (total time: 37.930) Add new water r_work=0.1360 r_free=0.1718 | n_water=456 | time (s): 1.940 (total time: 39.870) Refine new water occ: r_work=0.1189 r_free=0.1538 adp: r_work=0.1179 r_free=0.1548 occ: r_work=0.1163 r_free=0.1507 adp: r_work=0.1152 r_free=0.1520 occ: r_work=0.1145 r_free=0.1492 adp: r_work=0.1136 r_free=0.1504 ADP+occupancy (water only), MIN, final r_work=0.1136 r_free=0.1504 r_work=0.1136 r_free=0.1504 | n_water=456 | time (s): 34.620 (total time: 74.490) Filter (q & B) r_work=0.1140 r_free=0.1510 | n_water=445 | time (s): 1.570 (total time: 76.060) Filter (dist only) r_work=0.1143 r_free=0.1511 | n_water=444 | time (s): 34.860 (total time: 110.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.956950 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.169798 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 0.1123 0.1567 0.0443 0.009 1.0 3.8 0.5 0.0 0 0.978 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.23 15.67 4.43 4.440 20.957 0.170 4.964 11.10 15.62 4.52 4.655 20.980 0.170 4.954 Individual atomic B min max mean iso aniso Overall: 5.76 104.06 20.91 4.82 1971 0 Protein: 5.76 104.06 16.38 4.81 1519 0 Water: 8.18 64.09 36.19 N/A 444 0 Other: 24.74 44.70 32.26 N/A 8 0 Chain A: 5.76 104.06 18.08 N/A 1732 0 Chain S: 14.40 64.09 41.42 N/A 239 0 Histogram: Values Number of atoms 5.76 - 15.59 1062 15.59 - 25.42 357 25.42 - 35.25 211 35.25 - 45.08 198 45.08 - 54.91 101 54.91 - 64.74 29 64.74 - 74.57 6 74.57 - 84.40 3 84.40 - 94.23 2 94.23 - 104.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.1110 r_free=0.1562 r_work=0.1110 r_free=0.1563 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1110 r_free = 0.1563 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1104 r_free = 0.1555 target_work(ml) = 4.950 | | occupancies: max = 1.00 min = 0.20 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= 0.1104 r_free= 0.1555 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.949607 | | target function (ml) not normalized (work): 80351.921609 | | target function (ml) not normalized (free): 4188.425920 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1126 0.1104 0.1555 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1576 0.1566 0.1819 n_refl.: 17041 remove outliers: r(all,work,free)=0.1576 0.1566 0.1819 n_refl.: 17041 overall B=-0.26 to atoms: r(all,work,free)=0.1560 0.1549 0.1811 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1122 0.1101 0.1544 n_refl.: 17041 remove outliers: r(all,work,free)=0.1122 0.1100 0.1544 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3614 302.541 280.735 0.578 1.005 0.350 11.894-9.307 99.02 97 4 0.1715 486.935 479.236 0.914 1.005 0.330 9.237-7.194 100.00 213 7 0.1687 398.264 400.071 0.997 1.005 0.250 7.162-5.571 100.00 427 22 0.1560 298.897 292.643 0.937 1.005 0.220 5.546-4.326 100.00 867 58 0.0913 410.338 406.847 0.963 1.004 0.190 4.315-3.360 100.00 1859 96 0.0853 390.235 387.708 1.003 1.003 0.177 3.356-2.611 100.00 3867 181 0.1236 256.362 254.159 1.001 1.001 0.141 2.608-2.000 99.99 8818 434 0.1037 167.104 165.881 0.997 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.8994 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1100 r_free=0.1544 After: r_work=0.1102 r_free=0.1543 ================================== NQH flips ================================== r_work=0.1102 r_free=0.1543 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1102 r_free=0.1543 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1102 r_free=0.1543 | n_water=444 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.1102 r_free=0.1543 | n_water=444 | time (s): 36.750 (total time: 37.420) Filter (q & B) r_work=0.1102 r_free=0.1543 | n_water=444 | time (s): 0.970 (total time: 38.390) Compute maps r_work=0.1102 r_free=0.1543 | n_water=444 | time (s): 0.610 (total time: 39.000) Filter (map) r_work=0.1182 r_free=0.1569 | n_water=334 | time (s): 1.670 (total time: 40.670) Find peaks r_work=0.1182 r_free=0.1569 | n_water=334 | time (s): 0.430 (total time: 41.100) Add new water r_work=0.1295 r_free=0.1662 | n_water=478 | time (s): 1.580 (total time: 42.680) Refine new water occ: r_work=0.1134 r_free=0.1520 adp: r_work=0.1128 r_free=0.1519 occ: r_work=0.1115 r_free=0.1499 adp: r_work=0.1107 r_free=0.1499 occ: r_work=0.1101 r_free=0.1486 adp: r_work=0.1095 r_free=0.1487 ADP+occupancy (water only), MIN, final r_work=0.1095 r_free=0.1487 r_work=0.1095 r_free=0.1487 | n_water=478 | time (s): 30.100 (total time: 72.780) Filter (q & B) r_work=0.1101 r_free=0.1502 | n_water=460 | time (s): 2.200 (total time: 74.980) Filter (dist only) r_work=0.1101 r_free=0.1502 | n_water=459 | time (s): 38.720 (total time: 113.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.962761 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.194433 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1117 0.1518 0.0402 0.009 1.0 5.4 0.5 0.0 0 0.981 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.17 15.18 4.02 4.509 20.683 0.194 4.945 11.05 15.09 4.04 4.570 20.755 0.194 4.936 Individual atomic B min max mean iso aniso Overall: 5.52 103.94 20.87 5.02 1986 0 Protein: 5.52 103.94 16.16 5.02 1519 0 Water: 7.93 66.26 36.25 N/A 459 0 Other: 24.99 43.88 32.45 N/A 8 0 Chain A: 5.52 103.94 17.85 N/A 1732 0 Chain S: 16.29 66.26 41.45 N/A 254 0 Histogram: Values Number of atoms 5.52 - 15.36 1067 15.36 - 25.21 348 25.21 - 35.05 218 35.05 - 44.89 188 44.89 - 54.73 119 54.73 - 64.58 29 64.58 - 74.42 8 74.42 - 84.26 4 84.26 - 94.10 2 94.10 - 103.94 3 =========================== Idealize ADP of riding H ========================== r_work=0.1105 r_free=0.1509 r_work=0.1105 r_free=0.1509 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1105 r_free = 0.1509 target_work(ml) = 4.936 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1099 r_free = 0.1507 target_work(ml) = 4.931 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1099 r_free= 0.1507 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.931442 | | target function (ml) not normalized (work): 80052.105729 | | target function (ml) not normalized (free): 4162.766896 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1111 0.1391 5.4411 5.6705| | 2: 3.63 - 2.88 1.00 2711 122 0.1073 0.1465 5.2112 5.3421| | 3: 2.88 - 2.52 1.00 2681 148 0.1357 0.1724 5.1258 5.1998| | 4: 2.52 - 2.29 1.00 2661 139 0.0915 0.1493 4.6226 4.9226| | 5: 2.29 - 2.13 1.00 2678 122 0.0967 0.1477 4.5835 4.8886| | 6: 2.13 - 2.00 1.00 2692 117 0.1121 0.1717 4.5755 4.7793| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2810 159 0.95 9.03 1.00 0.96 6316.47| | 2: 3.63 - 2.88 2711 122 0.92 12.82 1.01 0.96 6316.47| | 3: 2.88 - 2.52 2681 148 0.88 18.91 0.99 0.96 6316.47| | 4: 2.52 - 2.29 2661 139 0.93 12.34 1.01 0.97 2146.14| | 5: 2.29 - 2.13 2678 122 0.91 14.31 1.00 0.97 2146.14| | 6: 2.13 - 2.00 2692 117 0.89 17.02 0.99 0.97 2146.14| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2146.14 max = 6316.47 mean = 4253.27| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.91 mean = 14.03| |phase err.(test): min = 0.00 max = 88.32 mean = 13.62| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1119 0.1099 0.1507 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1559 0.1550 0.1768 n_refl.: 17040 remove outliers: r(all,work,free)=0.1559 0.1550 0.1768 n_refl.: 17040 overall B=-0.19 to atoms: r(all,work,free)=0.1548 0.1539 0.1763 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1119 0.1100 0.1506 n_refl.: 17040 remove outliers: r(all,work,free)=0.1119 0.1100 0.1506 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3618 302.541 278.256 0.577 1.006 0.360 11.894-9.307 99.02 97 4 0.1702 486.935 481.785 0.924 1.006 0.327 9.237-7.194 100.00 213 7 0.1726 398.264 400.314 0.999 1.006 0.230 7.162-5.571 100.00 427 22 0.1609 298.897 292.831 0.941 1.005 0.230 5.546-4.326 100.00 867 58 0.0922 410.338 406.788 0.967 1.005 0.186 4.315-3.360 100.00 1859 96 0.0849 390.235 387.810 1.005 1.003 0.167 3.356-2.611 100.00 3867 181 0.1235 256.362 254.039 1.004 1.000 0.111 2.608-2.000 99.99 8818 434 0.1031 167.104 165.810 0.994 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.6795 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2791 0.1801 0.082 5.349 8.8 119.3 19.9 258 0.000 1_bss: 0.1616 0.1693 0.082 5.349 8.4 118.9 19.5 258 0.000 1_settarget: 0.1616 0.1693 0.082 5.349 8.4 118.9 19.5 258 0.000 1_nqh: 0.1621 0.1705 0.082 5.349 8.4 118.9 19.5 258 0.006 1_weight: 0.1621 0.1705 0.082 5.349 8.4 118.9 19.5 258 0.006 1_xyzrec: 0.1349 0.1635 0.009 0.993 8.4 118.9 19.5 258 0.149 1_adp: 0.1277 0.1658 0.009 0.993 6.6 113.9 20.0 258 0.149 1_regHadp: 0.1280 0.1666 0.009 0.993 6.6 113.9 20.0 258 0.149 1_occ: 0.1274 0.1652 0.009 0.993 6.6 113.9 20.0 258 0.149 2_bss: 0.1274 0.1638 0.009 0.993 6.2 113.5 19.6 258 0.149 2_settarget: 0.1274 0.1638 0.009 0.993 6.2 113.5 19.6 258 0.149 2_updatecdl: 0.1274 0.1638 0.009 1.012 6.2 113.5 19.6 258 0.149 2_nqh: 0.1276 0.1638 0.009 1.012 6.2 113.5 19.6 258 0.146 2_sol: 0.1239 0.1588 0.009 1.012 6.2 112.5 20.8 360 n/a 2_weight: 0.1239 0.1588 0.009 1.012 6.2 112.5 20.8 360 n/a 2_xyzrec: 0.1205 0.1595 0.008 0.926 6.2 112.5 20.8 360 n/a 2_adp: 0.1189 0.1624 0.008 0.926 6.8 107.5 21.3 360 n/a 2_regHadp: 0.1191 0.1626 0.008 0.926 6.8 107.5 21.3 360 n/a 2_occ: 0.1187 0.1622 0.008 0.926 6.8 107.5 21.3 360 n/a 3_bss: 0.1182 0.1617 0.008 0.926 6.4 107.0 20.8 360 n/a 3_settarget: 0.1182 0.1617 0.008 0.926 6.4 107.0 20.8 360 n/a 3_updatecdl: 0.1182 0.1617 0.008 0.921 6.4 107.0 20.8 360 n/a 3_nqh: 0.1182 0.1617 0.008 0.921 6.4 107.0 20.8 360 n/a 3_sol: 0.1195 0.1566 0.008 0.921 6.4 107.0 20.9 399 n/a 3_weight: 0.1195 0.1566 0.008 0.921 6.4 107.0 20.9 399 n/a 3_xyzrec: 0.1176 0.1573 0.009 0.952 6.4 107.0 20.9 399 n/a 3_adp: 0.1158 0.1582 0.009 0.952 6.5 105.6 20.7 399 n/a 3_regHadp: 0.1157 0.1582 0.009 0.952 6.5 105.6 20.7 399 n/a 3_occ: 0.1146 0.1586 0.009 0.952 6.5 105.6 20.7 399 n/a 4_bss: 0.1142 0.1585 0.009 0.952 6.1 105.2 20.3 399 n/a 4_settarget: 0.1142 0.1585 0.009 0.952 6.1 105.2 20.3 399 n/a 4_updatecdl: 0.1142 0.1585 0.009 0.951 6.1 105.2 20.3 399 n/a 4_nqh: 0.1142 0.1585 0.009 0.951 6.1 105.2 20.3 399 n/a 4_sol: 0.1143 0.1511 0.009 0.951 6.1 105.2 20.9 444 n/a 4_weight: 0.1143 0.1511 0.009 0.951 6.1 105.2 20.9 444 n/a 4_xyzrec: 0.1123 0.1567 0.009 0.963 6.1 105.2 20.9 444 n/a 4_adp: 0.1110 0.1562 0.009 0.963 5.8 104.1 20.9 444 n/a 4_regHadp: 0.1110 0.1563 0.009 0.963 5.8 104.1 20.9 444 n/a 4_occ: 0.1104 0.1555 0.009 0.963 5.8 104.1 20.9 444 n/a 5_bss: 0.1100 0.1544 0.009 0.963 5.5 103.8 20.6 444 n/a 5_settarget: 0.1100 0.1544 0.009 0.963 5.5 103.8 20.6 444 n/a 5_updatecdl: 0.1100 0.1544 0.009 0.964 5.5 103.8 20.6 444 n/a 5_setrh: 0.1102 0.1543 0.009 0.964 5.5 103.8 20.6 444 n/a 5_nqh: 0.1102 0.1543 0.009 0.964 5.5 103.8 20.6 444 n/a 5_sol: 0.1101 0.1502 0.009 0.964 5.5 103.8 20.7 459 n/a 5_weight: 0.1101 0.1502 0.009 0.964 5.5 103.8 20.7 459 n/a 5_xyzrec: 0.1117 0.1518 0.009 1.002 5.5 103.8 20.7 459 n/a 5_adp: 0.1105 0.1509 0.009 1.002 5.5 103.9 20.9 459 n/a 5_regHadp: 0.1105 0.1509 0.009 1.002 5.5 103.9 20.9 459 n/a 5_occ: 0.1099 0.1507 0.009 1.002 5.5 103.9 20.9 459 n/a end: 0.1100 0.1506 0.009 1.002 5.3 103.8 20.7 459 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_1617309_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_1617309_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.2200 Refinement macro-cycles (run) : 932.1900 Write final files (write_after_run_outputs) : 20.7900 Total : 957.2000 Total CPU time: 16.31 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:20 PST -0800 (1735494080.41 s) Start R-work = 0.1616, R-free = 0.1693 Final R-work = 0.1100, R-free = 0.1506 =============================================================================== Job complete usr+sys time: 1000.29 seconds wall clock time: 17 minutes 3.22 seconds (1023.22 seconds total)