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_6847832.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6847832.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6847832.pdb" 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 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.61, per 1000 atoms: 0.48 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: 0.54 Conformation dependent library (CDL) restraints added in 202.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.61 - 0.89: 371 0.89 - 1.16: 1258 1.16 - 1.44: 696 1.44 - 1.71: 812 1.71 - 1.99: 16 Bond restraints: 3153 Sorted by residual: bond pdb=" C BGLN A 80 " pdb=" O BGLN A 80 " ideal model delta sigma weight residual 1.236 1.009 0.227 1.15e-02 7.56e+03 3.90e+02 bond pdb=" C ILE A 105 " pdb=" O ILE A 105 " ideal model delta sigma weight residual 1.236 1.430 -0.194 9.90e-03 1.02e+04 3.86e+02 bond pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " ideal model delta sigma weight residual 1.326 1.535 -0.209 1.10e-02 8.26e+03 3.61e+02 bond pdb=" C ALA A 104 " pdb=" O ALA A 104 " ideal model delta sigma weight residual 1.234 1.014 0.220 1.18e-02 7.18e+03 3.47e+02 bond pdb=" C BLYS A 93 " pdb=" O BLYS A 93 " ideal model delta sigma weight residual 1.237 1.457 -0.221 1.19e-02 7.06e+03 3.43e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.45: 3029 4.45 - 8.90: 1892 8.90 - 13.35: 700 13.35 - 17.80: 132 17.80 - 22.26: 24 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 118 " pdb=" C GLY A 118 " pdb=" N PHE A 119 " ideal model delta sigma weight residual 122.54 107.69 14.85 1.02e+00 9.61e-01 2.12e+02 angle pdb=" O ALA A 79 " pdb=" C ALA A 79 " pdb=" N AGLN A 80 " ideal model delta sigma weight residual 122.07 136.61 -14.54 1.03e+00 9.43e-01 1.99e+02 angle pdb=" O BTYR A 67 " pdb=" C BTYR A 67 " pdb=" N ASP A 68 " ideal model delta sigma weight residual 123.24 107.34 15.90 1.23e+00 6.61e-01 1.67e+02 angle pdb=" O VAL A 20 " pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 121.80 107.28 14.52 1.13e+00 7.83e-01 1.65e+02 angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 131.60 -10.37 8.10e-01 1.52e+00 1.64e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 1309 17.65 - 35.29: 115 35.29 - 52.93: 45 52.93 - 70.58: 9 70.58 - 88.22: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C GLN A 95 " pdb=" N GLN A 95 " pdb=" CA GLN A 95 " pdb=" CB GLN A 95 " ideal model delta harmonic sigma weight residual -122.60 -144.23 21.63 0 2.50e+00 1.60e-01 7.48e+01 dihedral pdb=" N GLN A 95 " pdb=" C GLN A 95 " pdb=" CA GLN A 95 " pdb=" CB GLN A 95 " ideal model delta harmonic sigma weight residual 122.80 142.57 -19.77 0 2.50e+00 1.60e-01 6.26e+01 dihedral pdb=" N ARG A 27 " pdb=" C ARG A 27 " pdb=" CA ARG A 27 " pdb=" CB ARG A 27 " ideal model delta harmonic sigma weight residual 122.80 140.06 -17.26 0 2.50e+00 1.60e-01 4.77e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.227: 116 0.227 - 0.453: 75 0.453 - 0.678: 34 0.678 - 0.904: 14 0.904 - 1.129: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ILE A 152 " pdb=" N ILE A 152 " pdb=" C ILE A 152 " pdb=" CB ILE A 152 " both_signs ideal model delta sigma weight residual False 2.43 3.56 -1.13 2.00e-01 2.50e+01 3.19e+01 chirality pdb=" CB THR A 110 " pdb=" CA THR A 110 " pdb=" OG1 THR A 110 " pdb=" CG2 THR A 110 " both_signs ideal model delta sigma weight residual False 2.55 1.53 1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" CA GLN A 95 " pdb=" N GLN A 95 " pdb=" C GLN A 95 " pdb=" CB GLN A 95 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.48e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.135 2.00e-02 2.50e+03 6.68e-02 1.34e+02 pdb=" CG PHE A 164 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.063 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.041 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.112 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.070 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.064 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.026 2.00e-02 2.50e+03 6.56e-02 1.29e+02 pdb=" CG TYR A 139 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.095 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.098 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.061 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.018 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.098 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.104 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.021 2.00e-02 2.50e+03 6.54e-02 1.28e+02 pdb=" CG TYR A 141 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.122 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.077 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.108 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.048 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.089 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.082 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 619 2.25 - 2.84: 7586 2.84 - 3.42: 10750 3.42 - 4.01: 15382 4.01 - 4.60: 22268 Nonbonded interactions: 56605 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.662 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.798 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.821 2.450 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.838 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.865 2.450 ... (remaining 56600 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_6847832_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2786 r_free= 0.1813 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.405922 | | target function (ml) not normalized (work): 71565.395425 | | target function (ml) not normalized (free): 3253.285053 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3197 0.2128 7.5733 5.0247| | 2: 3.63 - 2.88 1.00 2711 122 0.2660 0.1596 4.3253 4.2966| | 3: 2.88 - 2.52 1.00 2682 148 0.2536 0.1808 4.1797 4.1961| | 4: 2.52 - 2.29 1.00 2661 139 0.2565 0.1673 3.5143 3.6166| | 5: 2.29 - 2.13 1.00 2678 122 0.2637 0.1354 3.3806 3.3588| | 6: 2.13 - 2.00 1.00 2692 117 0.2714 0.1892 3.2971 3.3903| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.45 0.77 0.23 1285.90| | 2: 3.63 - 2.88 2711 122 0.83 23.79 1.32 0.23 1285.90| | 3: 2.88 - 2.52 2682 148 0.74 32.52 1.28 0.23 1285.90| | 4: 2.52 - 2.29 2661 139 0.93 11.31 1.30 0.26 132.41| | 5: 2.29 - 2.13 2678 122 0.92 13.31 1.32 0.26 132.41| | 6: 2.13 - 2.00 2692 117 0.90 16.07 1.33 0.26 132.41| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 132.41 max = 1285.90 mean = 715.59| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.93 mean = 19.08| |phase err.(test): min = 0.00 max = 89.80 mean = 19.65| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.227 1557 Z= 5.392 Angle : 5.351 17.239 2118 Z= 3.755 Chirality : 0.369 1.129 243 Planarity : 0.030 0.111 284 Dihedral : 14.223 88.220 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.32 % Favored : 95.14 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 29.73 % 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: -2.74 (0.47), residues: 224 helix: -3.19 (0.35), residues: 102 sheet: -0.39 (0.96), residues: 28 loop : -0.30 (0.55), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.084 0.015 ARG A 98 TYR 0.099 0.044 TYR A 141 PHE 0.104 0.043 PHE A 119 HIS 0.067 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= 0.2786 r_free= 0.1813 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.405922 | | target function (ml) not normalized (work): 71565.395425 | | target function (ml) not normalized (free): 3253.285053 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2656 percent. r_work = 0.2913 r_free = 0.2009 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2861 0.2913 0.2009 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2861 0.2913 0.2009 n_refl.: 17050 remove outliers: r(all,work,free)=0.2154 0.2164 0.2009 n_refl.: 17045 overall B=-0.39 to atoms: r(all,work,free)=0.2128 0.2137 0.1993 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1609 0.1605 0.1691 n_refl.: 17045 remove outliers: r(all,work,free)=0.1608 0.1604 0.1691 n_refl.: 17044 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.4060 394.745 364.206 0.650 1.018 0.403 11.894-9.307 99.02 97 4 0.1872 633.578 611.186 0.924 1.018 0.385 9.237-7.194 100.00 213 7 0.2159 518.203 508.566 0.945 1.018 0.381 7.162-5.571 100.00 427 22 0.2282 388.912 376.127 0.916 1.016 0.284 5.546-4.326 100.00 867 58 0.1399 533.913 528.941 0.956 1.013 0.220 4.315-3.360 100.00 1859 96 0.1297 507.757 503.227 1.016 1.008 0.191 3.356-2.611 100.00 3867 181 0.1652 333.567 329.067 1.012 0.999 0.091 2.608-2.000 99.99 8818 434 0.1628 217.429 213.438 1.035 0.983 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4093 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1604 r_free=0.1691 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1606 r_free=0.1691 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.278459 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.901890 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1353 0.1639 0.0286 0.009 1.0 1.0 0.5 0.0 0 11.139 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.53 16.39 2.86 3.013 18.464 0.902 0.023 12.80 16.62 3.83 3.597 18.684 0.902 0.021 Individual atomic B min max mean iso aniso Overall: 5.93 113.90 19.91 4.10 1785 0 Protein: 5.93 113.00 17.13 4.10 1519 0 Water: 8.59 113.90 36.08 N/A 258 0 Other: 21.75 37.33 26.33 N/A 8 0 Chain A: 5.93 113.90 19.91 N/A 1785 0 Histogram: Values Number of atoms 5.93 - 16.73 1075 16.73 - 27.53 348 27.53 - 38.33 187 38.33 - 49.12 95 49.12 - 59.92 53 59.92 - 70.72 12 70.72 - 81.51 7 81.51 - 92.31 4 92.31 - 103.11 1 103.11 - 113.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1280 r_free=0.1662 r_work=0.1283 r_free=0.1670 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1283 r_free = 0.1670 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1278 r_free = 0.1660 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1278 r_free= 0.1660 coordinate error (max.-lik. estimate): 0.12 A | | | | normalized target function (ls_wunit_k1) (work): 0.020084 | | target function (ls_wunit_k1) not normalized (work): 326.103162 | | target function (ls_wunit_k1) not normalized (free): 27.315512 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1296 0.1278 0.1660 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1909 0.1908 0.1984 n_refl.: 17044 remove outliers: r(all,work,free)=0.1909 0.1908 0.1984 n_refl.: 17044 overall B=-0.51 to atoms: r(all,work,free)=0.1872 0.1871 0.1963 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1294 0.1276 0.1651 n_refl.: 17044 remove outliers: r(all,work,free)=0.1292 0.1275 0.1651 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 0.3552 303.687 279.287 0.623 1.007 0.368 11.894-9.307 99.02 97 4 0.1700 488.433 476.738 0.917 1.007 0.367 9.237-7.194 100.00 213 7 0.1813 399.489 395.977 0.960 1.007 0.351 7.162-5.571 100.00 427 22 0.1829 299.817 294.613 0.931 1.007 0.291 5.546-4.326 100.00 867 58 0.1046 411.600 409.147 0.958 1.006 0.201 4.315-3.360 100.00 1859 96 0.0925 391.436 390.942 1.016 1.004 0.192 3.356-2.611 100.00 3867 181 0.1296 257.151 255.773 1.009 1.001 0.091 2.608-2.000 99.99 8818 434 0.1354 167.618 166.290 1.011 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9583 b_overall=-1.1478 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1651 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1277 r_free=0.1653 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1653 | n_water=258 | time (s): 0.770 (total time: 0.770) Filter (dist) r_work=0.1285 r_free=0.1643 | n_water=253 | time (s): 20.370 (total time: 21.140) Filter (q & B) r_work=0.1285 r_free=0.1642 | n_water=251 | time (s): 1.410 (total time: 22.550) Compute maps r_work=0.1285 r_free=0.1642 | n_water=251 | time (s): 0.590 (total time: 23.140) Filter (map) r_work=0.1324 r_free=0.1631 | n_water=207 | time (s): 1.780 (total time: 24.920) Find peaks r_work=0.1324 r_free=0.1631 | n_water=207 | time (s): 0.680 (total time: 25.600) Add new water r_work=0.1553 r_free=0.1863 | n_water=368 | time (s): 2.100 (total time: 27.700) Refine new water occ: r_work=0.1332 r_free=0.1563 adp: r_work=0.1275 r_free=0.1555 occ: r_work=0.1280 r_free=0.1533 adp: r_work=0.1248 r_free=0.1539 occ: r_work=0.1250 r_free=0.1532 adp: r_work=0.1238 r_free=0.1534 ADP+occupancy (water only), MIN, final r_work=0.1238 r_free=0.1534 r_work=0.1238 r_free=0.1534 | n_water=368 | time (s): 21.810 (total time: 49.510) Filter (q & B) r_work=0.1239 r_free=0.1537 | n_water=360 | time (s): 1.450 (total time: 50.960) Filter (dist only) r_work=0.1239 r_free=0.1537 | n_water=359 | time (s): 27.370 (total time: 78.330) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.965897 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.968851 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 0.1209 0.1582 0.0373 0.008 0.9 2.2 0.5 0.0 0 11.983 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 15.82 3.73 4.175 20.852 0.969 0.018 11.94 16.12 4.18 4.266 21.150 0.969 0.018 Individual atomic B min max mean iso aniso Overall: 6.66 107.49 21.21 4.33 1886 0 Protein: 6.66 107.49 17.62 4.31 1519 0 Water: 8.14 65.68 36.09 N/A 359 0 Other: 25.21 45.94 35.79 N/A 8 0 Chain A: 6.66 107.49 19.28 N/A 1734 0 Chain S: 18.20 64.02 43.30 N/A 152 0 Histogram: Values Number of atoms 6.66 - 16.74 1033 16.74 - 26.83 370 26.83 - 36.91 225 36.91 - 46.99 157 46.99 - 57.08 65 57.08 - 67.16 25 67.16 - 77.24 4 77.24 - 87.32 3 87.32 - 97.41 2 97.41 - 107.49 2 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1612 r_work=0.1196 r_free=0.1615 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1615 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1610 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1190 r_free= 0.1610 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.016947 | | target function (ls_wunit_k1) not normalized (work): 275.139979 | | target function (ls_wunit_k1) not normalized (free): 25.014669 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1190 0.1610 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1743 0.1733 0.1968 n_refl.: 17042 remove outliers: r(all,work,free)=0.1743 0.1733 0.1968 n_refl.: 17042 overall B=-0.46 to atoms: r(all,work,free)=0.1714 0.1704 0.1948 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1187 0.1605 n_refl.: 17042 remove outliers: r(all,work,free)=0.1206 0.1186 0.1605 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 0.3251 300.522 284.755 0.592 1.002 0.340 11.894-9.307 99.02 97 4 0.1497 488.433 487.942 0.922 1.003 0.335 9.237-7.194 100.00 213 7 0.1675 399.489 399.596 0.976 1.003 0.284 7.162-5.571 100.00 427 22 0.1548 299.817 296.158 0.940 1.003 0.251 5.546-4.326 100.00 867 58 0.0856 411.600 409.956 0.964 1.003 0.206 4.315-3.360 100.00 1859 96 0.0833 391.436 390.565 1.017 1.002 0.202 3.356-2.611 100.00 3867 181 0.1190 257.151 256.379 1.009 1.001 0.132 2.608-2.000 99.99 8818 434 0.1330 167.618 166.472 1.008 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1430 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1186 r_free=0.1605 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B Total number of N/Q/H flips: 1 r_work=0.1186 r_free=0.1607 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1186 r_free=0.1607 | n_water=359 | time (s): 0.870 (total time: 0.870) Filter (dist) r_work=0.1187 r_free=0.1609 | n_water=357 | time (s): 32.160 (total time: 33.030) Filter (q & B) r_work=0.1187 r_free=0.1609 | n_water=357 | time (s): 0.770 (total time: 33.800) Compute maps r_work=0.1187 r_free=0.1609 | n_water=357 | time (s): 0.560 (total time: 34.360) Filter (map) r_work=0.1254 r_free=0.1622 | n_water=264 | time (s): 1.910 (total time: 36.270) Find peaks r_work=0.1254 r_free=0.1622 | n_water=264 | time (s): 0.450 (total time: 36.720) Add new water r_work=0.1443 r_free=0.1792 | n_water=416 | time (s): 1.410 (total time: 38.130) Refine new water occ: r_work=0.1237 r_free=0.1542 adp: r_work=0.1229 r_free=0.1553 occ: r_work=0.1210 r_free=0.1517 adp: r_work=0.1200 r_free=0.1526 occ: r_work=0.1191 r_free=0.1508 adp: r_work=0.1183 r_free=0.1514 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1514 r_work=0.1183 r_free=0.1514 | n_water=416 | time (s): 43.070 (total time: 81.200) Filter (q & B) r_work=0.1186 r_free=0.1518 | n_water=404 | time (s): 2.070 (total time: 83.270) Filter (dist only) r_work=0.1186 r_free=0.1518 | n_water=404 | time (s): 30.030 (total time: 113.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.882230 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.141754 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 0.1161 0.1544 0.0383 0.009 1.0 2.6 0.5 0.0 0 0.941 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.61 15.44 3.83 4.358 21.339 0.142 4.995 11.42 15.48 4.06 4.937 21.254 0.142 4.972 Individual atomic B min max mean iso aniso Overall: 6.17 104.92 20.70 4.65 1931 0 Protein: 6.17 104.92 16.78 4.64 1519 0 Water: 8.57 64.86 35.18 N/A 404 0 Other: 24.66 43.98 32.75 N/A 8 0 Chain A: 6.17 104.92 18.45 N/A 1731 0 Chain S: 17.84 64.86 40.09 N/A 200 0 Histogram: Values Number of atoms 6.17 - 16.05 1071 16.05 - 25.92 349 25.92 - 35.80 225 35.80 - 45.67 169 45.67 - 55.55 79 55.55 - 65.42 25 65.42 - 75.30 4 75.30 - 85.17 5 85.17 - 95.05 2 95.05 - 104.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1142 r_free=0.1548 r_work=0.1143 r_free=0.1548 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1143 r_free = 0.1548 target_work(ml) = 4.972 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1137 r_free = 0.1559 target_work(ml) = 4.968 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1137 r_free= 0.1559 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.968248 | | target function (ml) not normalized (work): 80654.533933 | | target function (ml) not normalized (free): 4195.762745 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1158 0.1137 0.1559 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1648 0.1639 0.1875 n_refl.: 17041 remove outliers: r(all,work,free)=0.1648 0.1639 0.1875 n_refl.: 17041 overall B=-0.34 to atoms: r(all,work,free)=0.1626 0.1616 0.1865 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1157 0.1136 0.1559 n_refl.: 17041 remove outliers: r(all,work,free)=0.1156 0.1135 0.1559 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 0.3403 296.954 278.633 0.571 1.006 0.340 11.894-9.307 99.02 97 4 0.1727 488.433 481.276 0.914 1.008 0.324 9.237-7.194 100.00 213 7 0.1796 399.489 399.125 0.984 1.008 0.254 7.162-5.571 100.00 427 22 0.1625 299.817 294.651 0.939 1.007 0.220 5.546-4.326 100.00 867 58 0.0918 411.600 408.364 0.966 1.006 0.211 4.315-3.360 100.00 1859 96 0.0879 391.436 389.648 1.011 1.004 0.201 3.356-2.611 100.00 3867 181 0.1261 257.151 255.070 1.010 1.001 0.131 2.608-2.000 99.99 8818 434 0.1091 167.618 166.168 1.013 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1633 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1135 r_free=0.1559 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1135 r_free=0.1559 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1135 r_free=0.1559 | n_water=404 | time (s): 0.700 (total time: 0.700) Filter (dist) r_work=0.1135 r_free=0.1559 | n_water=404 | time (s): 34.050 (total time: 34.750) Filter (q & B) r_work=0.1135 r_free=0.1559 | n_water=404 | time (s): 0.980 (total time: 35.730) Compute maps r_work=0.1135 r_free=0.1559 | n_water=404 | time (s): 0.650 (total time: 36.380) Filter (map) r_work=0.1185 r_free=0.1564 | n_water=316 | time (s): 1.600 (total time: 37.980) Find peaks r_work=0.1185 r_free=0.1564 | n_water=316 | time (s): 0.470 (total time: 38.450) Add new water r_work=0.1337 r_free=0.1696 | n_water=459 | time (s): 1.950 (total time: 40.400) Refine new water occ: r_work=0.1170 r_free=0.1539 adp: r_work=0.1159 r_free=0.1540 occ: r_work=0.1146 r_free=0.1529 adp: r_work=0.1134 r_free=0.1525 occ: r_work=0.1129 r_free=0.1525 adp: r_work=0.1119 r_free=0.1521 ADP+occupancy (water only), MIN, final r_work=0.1119 r_free=0.1521 r_work=0.1119 r_free=0.1521 | n_water=459 | time (s): 34.210 (total time: 74.610) Filter (q & B) r_work=0.1121 r_free=0.1528 | n_water=450 | time (s): 1.930 (total time: 76.540) Filter (dist only) r_work=0.1121 r_free=0.1530 | n_water=449 | time (s): 36.970 (total time: 113.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.030009 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.169972 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 0.1111 0.1568 0.0456 0.010 1.0 2.9 0.5 0.0 0 1.015 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.11 15.68 4.56 4.458 20.950 0.170 4.957 11.02 15.65 4.64 4.665 20.996 0.170 4.950 Individual atomic B min max mean iso aniso Overall: 5.44 102.13 20.94 4.91 1976 0 Protein: 5.44 102.13 16.39 4.90 1519 0 Water: 8.37 66.36 36.11 N/A 449 0 Other: 25.96 45.68 33.78 N/A 8 0 Chain A: 5.44 102.13 18.02 N/A 1730 0 Chain S: 15.49 66.36 41.50 N/A 246 0 Histogram: Values Number of atoms 5.44 - 15.11 1012 15.11 - 24.77 393 24.77 - 34.44 219 34.44 - 44.11 188 44.11 - 53.78 109 53.78 - 63.45 37 63.45 - 73.12 9 73.12 - 82.79 4 82.79 - 92.46 3 92.46 - 102.13 2 =========================== Idealize ADP of riding H ========================== r_work=0.1102 r_free=0.1565 r_work=0.1102 r_free=0.1565 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1102 r_free = 0.1565 target_work(ml) = 4.950 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1096 r_free = 0.1572 target_work(ml) = 4.948 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1096 r_free= 0.1572 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.947584 | | target function (ml) not normalized (work): 80314.136155 | | target function (ml) not normalized (free): 4194.457606 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1119 0.1096 0.1572 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1574 0.1561 0.1865 n_refl.: 17040 remove outliers: r(all,work,free)=0.1574 0.1561 0.1865 n_refl.: 17040 overall B=-0.26 to atoms: r(all,work,free)=0.1558 0.1544 0.1856 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1117 0.1094 0.1570 n_refl.: 17040 remove outliers: r(all,work,free)=0.1117 0.1094 0.1570 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 0.3515 296.954 275.373 0.557 1.004 0.340 11.894-9.307 99.02 97 4 0.1707 488.433 481.215 0.917 1.005 0.330 9.237-7.194 100.00 213 7 0.1692 399.489 400.560 0.986 1.005 0.230 7.162-5.571 100.00 427 22 0.1534 299.817 294.335 0.938 1.004 0.212 5.546-4.326 100.00 867 58 0.0895 411.600 408.237 0.967 1.004 0.208 4.315-3.360 100.00 1859 96 0.0847 391.436 389.104 1.004 1.003 0.201 3.356-2.611 100.00 3867 181 0.1230 257.151 254.768 1.002 1.001 0.151 2.608-2.000 99.99 8818 434 0.1038 167.618 166.391 0.997 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9049 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1094 r_free=0.1570 After: r_work=0.1096 r_free=0.1569 ================================== NQH flips ================================== r_work=0.1096 r_free=0.1569 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1096 r_free=0.1569 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1096 r_free=0.1569 | n_water=449 | time (s): 0.810 (total time: 0.810) Filter (dist) r_work=0.1102 r_free=0.1562 | n_water=447 | time (s): 40.920 (total time: 41.730) Filter (q & B) r_work=0.1102 r_free=0.1562 | n_water=447 | time (s): 0.890 (total time: 42.620) Compute maps r_work=0.1102 r_free=0.1562 | n_water=447 | time (s): 0.590 (total time: 43.210) Filter (map) r_work=0.1165 r_free=0.1556 | n_water=343 | time (s): 1.870 (total time: 45.080) Find peaks r_work=0.1165 r_free=0.1556 | n_water=343 | time (s): 0.560 (total time: 45.640) Add new water r_work=0.1291 r_free=0.1661 | n_water=475 | time (s): 1.610 (total time: 47.250) Refine new water occ: r_work=0.1141 r_free=0.1506 adp: r_work=0.1132 r_free=0.1508 occ: r_work=0.1122 r_free=0.1500 adp: r_work=0.1112 r_free=0.1499 occ: r_work=0.1108 r_free=0.1498 adp: r_work=0.1101 r_free=0.1496 ADP+occupancy (water only), MIN, final r_work=0.1101 r_free=0.1496 r_work=0.1101 r_free=0.1496 | n_water=475 | time (s): 27.590 (total time: 74.840) Filter (q & B) r_work=0.1105 r_free=0.1504 | n_water=462 | time (s): 1.650 (total time: 76.490) Filter (dist only) r_work=0.1105 r_free=0.1506 | n_water=461 | time (s): 40.100 (total time: 116.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.945730 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.158211 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 0.1126 0.1529 0.0403 0.010 1.1 5.8 0.5 0.0 0 0.973 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 15.29 4.03 4.568 20.735 0.158 4.953 11.17 15.12 3.95 4.642 20.790 0.158 4.941 Individual atomic B min max mean iso aniso Overall: 5.08 101.33 20.87 4.99 1988 0 Protein: 5.08 101.33 16.13 4.97 1519 0 Water: 7.79 63.97 36.28 N/A 461 0 Other: 25.51 44.72 33.30 N/A 8 0 Chain A: 5.08 101.33 17.71 N/A 1729 0 Chain S: 16.56 63.97 42.00 N/A 259 0 Histogram: Values Number of atoms 5.08 - 14.70 1010 14.70 - 24.33 393 24.33 - 33.95 207 33.95 - 43.58 200 43.58 - 53.20 121 53.20 - 62.83 36 62.83 - 72.45 12 72.45 - 82.08 3 82.08 - 91.70 2 91.70 - 101.33 4 =========================== Idealize ADP of riding H ========================== r_work=0.1117 r_free=0.1512 r_work=0.1117 r_free=0.1512 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1117 r_free = 0.1512 target_work(ml) = 4.942 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1111 r_free = 0.1517 target_work(ml) = 4.937 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1111 r_free= 0.1517 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.937255 | | target function (ml) not normalized (work): 80146.460583 | | target function (ml) not normalized (free): 4172.268244 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1127 0.1418 5.46 5.6677| | 2: 3.63 - 2.88 1.00 2711 122 0.1103 0.1536 5.2349 5.3655| | 3: 2.88 - 2.52 1.00 2681 148 0.1364 0.1624 5.1444 5.217| | 4: 2.52 - 2.29 1.00 2661 139 0.0927 0.1498 4.6171 4.9673| | 5: 2.29 - 2.13 1.00 2678 122 0.0960 0.1461 4.5727 4.8596| | 6: 2.13 - 2.00 1.00 2692 117 0.1114 0.1771 4.5648 4.7955| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.94 9.34 1.00 0.96 6679.43| | 2: 3.63 - 2.88 2711 122 0.92 13.28 1.01 0.96 6679.43| | 3: 2.88 - 2.52 2681 148 0.87 19.41 0.99 0.96 6679.43| | 4: 2.52 - 2.29 2661 139 0.93 11.97 1.01 0.97 2078.04| | 5: 2.29 - 2.13 2678 122 0.92 13.91 1.00 0.97 2078.04| | 6: 2.13 - 2.00 2692 117 0.90 16.68 0.99 0.97 2078.04| |alpha: min = 0.96 max = 0.97 mean = 0.97| |beta: min = 2078.04 max = 6679.43 mean = 4402.97| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.96 mean = 14.06| |phase err.(test): min = 0.00 max = 88.89 mean = 13.72| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1131 0.1111 0.1517 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1565 0.1552 0.1851 n_refl.: 17040 remove outliers: r(all,work,free)=0.1565 0.1552 0.1851 n_refl.: 17040 overall B=-0.23 to atoms: r(all,work,free)=0.1552 0.1538 0.1842 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1131 0.1112 0.1515 n_refl.: 17040 remove outliers: r(all,work,free)=0.1131 0.1112 0.1515 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 0.3506 296.954 276.712 0.546 1.005 0.330 11.894-9.307 99.02 97 4 0.1679 488.433 482.035 0.914 1.006 0.330 9.237-7.194 100.00 213 7 0.1800 399.489 399.707 0.985 1.006 0.230 7.162-5.571 100.00 427 22 0.1595 299.817 293.118 0.930 1.005 0.193 5.546-4.326 100.00 867 58 0.0923 411.600 408.171 0.966 1.004 0.183 4.315-3.360 100.00 1859 96 0.0897 391.436 389.219 1.003 1.003 0.167 3.356-2.611 100.00 3867 181 0.1243 257.151 254.632 1.001 1.000 0.121 2.608-2.000 99.99 8818 434 0.1034 167.618 166.329 0.993 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7803 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2786 0.1813 0.081 5.351 8.8 119.3 19.9 258 0.000 1_bss: 0.1604 0.1691 0.081 5.351 8.5 118.9 19.5 258 0.000 1_settarget: 0.1604 0.1691 0.081 5.351 8.5 118.9 19.5 258 0.000 1_nqh: 0.1606 0.1691 0.081 5.351 8.5 118.9 19.5 258 0.003 1_weight: 0.1606 0.1691 0.081 5.351 8.5 118.9 19.5 258 0.003 1_xyzrec: 0.1353 0.1639 0.009 0.956 8.5 118.9 19.5 258 0.154 1_adp: 0.1280 0.1662 0.009 0.956 5.9 113.9 19.9 258 0.154 1_regHadp: 0.1283 0.1670 0.009 0.956 5.9 113.9 19.9 258 0.154 1_occ: 0.1278 0.1660 0.009 0.956 5.9 113.9 19.9 258 0.154 2_bss: 0.1275 0.1651 0.009 0.956 5.4 113.4 19.4 258 0.154 2_settarget: 0.1275 0.1651 0.009 0.956 5.4 113.4 19.4 258 0.154 2_updatecdl: 0.1275 0.1651 0.009 0.972 5.4 113.4 19.4 258 0.154 2_nqh: 0.1277 0.1653 0.009 0.972 5.4 113.4 19.4 258 0.151 2_sol: 0.1239 0.1537 0.009 0.972 5.4 112.5 20.7 359 n/a 2_weight: 0.1239 0.1537 0.009 0.972 5.4 112.5 20.7 359 n/a 2_xyzrec: 0.1209 0.1582 0.008 0.914 5.4 112.5 20.7 359 n/a 2_adp: 0.1194 0.1612 0.008 0.914 6.7 107.5 21.2 359 n/a 2_regHadp: 0.1196 0.1615 0.008 0.914 6.7 107.5 21.2 359 n/a 2_occ: 0.1190 0.1610 0.008 0.914 6.7 107.5 21.2 359 n/a 3_bss: 0.1186 0.1605 0.008 0.914 6.2 107.0 20.8 359 n/a 3_settarget: 0.1186 0.1605 0.008 0.914 6.2 107.0 20.8 359 n/a 3_updatecdl: 0.1186 0.1605 0.008 0.914 6.2 107.0 20.8 359 n/a 3_nqh: 0.1186 0.1607 0.008 0.914 6.2 107.0 20.8 359 n/a 3_sol: 0.1186 0.1518 0.008 0.914 6.2 107.0 20.9 404 n/a 3_weight: 0.1186 0.1518 0.008 0.914 6.2 107.0 20.9 404 n/a 3_xyzrec: 0.1161 0.1544 0.009 0.967 6.2 107.0 20.9 404 n/a 3_adp: 0.1142 0.1548 0.009 0.967 6.2 104.9 20.7 404 n/a 3_regHadp: 0.1143 0.1548 0.009 0.967 6.2 104.9 20.7 404 n/a 3_occ: 0.1137 0.1559 0.009 0.967 6.2 104.9 20.7 404 n/a 4_bss: 0.1135 0.1559 0.009 0.967 5.8 104.6 20.4 404 n/a 4_settarget: 0.1135 0.1559 0.009 0.967 5.8 104.6 20.4 404 n/a 4_updatecdl: 0.1135 0.1559 0.009 0.967 5.8 104.6 20.4 404 n/a 4_nqh: 0.1135 0.1559 0.009 0.967 5.8 104.6 20.4 404 n/a 4_sol: 0.1121 0.1530 0.009 0.967 5.8 104.6 20.9 449 n/a 4_weight: 0.1121 0.1530 0.009 0.967 5.8 104.6 20.9 449 n/a 4_xyzrec: 0.1111 0.1568 0.010 0.997 5.8 104.6 20.9 449 n/a 4_adp: 0.1102 0.1565 0.010 0.997 5.4 102.1 20.9 449 n/a 4_regHadp: 0.1102 0.1565 0.010 0.997 5.4 102.1 20.9 449 n/a 4_occ: 0.1096 0.1572 0.010 0.997 5.4 102.1 20.9 449 n/a 5_bss: 0.1094 0.1570 0.010 0.997 5.2 101.9 20.7 449 n/a 5_settarget: 0.1094 0.1570 0.010 0.997 5.2 101.9 20.7 449 n/a 5_updatecdl: 0.1094 0.1570 0.010 0.998 5.2 101.9 20.7 449 n/a 5_setrh: 0.1096 0.1569 0.010 0.998 5.2 101.9 20.7 449 n/a 5_nqh: 0.1096 0.1569 0.010 0.998 5.2 101.9 20.7 449 n/a 5_sol: 0.1105 0.1506 0.010 0.998 5.2 101.9 20.8 461 n/a 5_weight: 0.1105 0.1506 0.010 0.998 5.2 101.9 20.8 461 n/a 5_xyzrec: 0.1126 0.1529 0.010 1.061 5.2 101.9 20.8 461 n/a 5_adp: 0.1117 0.1512 0.010 1.061 5.1 101.3 20.9 461 n/a 5_regHadp: 0.1117 0.1512 0.010 1.061 5.1 101.3 20.9 461 n/a 5_occ: 0.1111 0.1517 0.010 1.061 5.1 101.3 20.9 461 n/a end: 0.1112 0.1515 0.010 1.061 4.9 101.1 20.6 461 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6847832_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6847832_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8600 Refinement macro-cycles (run) : 952.4100 Write final files (write_after_run_outputs) : 17.2500 Total : 973.5200 Total CPU time: 16.62 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:38 PST -0800 (1735494098.98 s) Start R-work = 0.1604, R-free = 0.1691 Final R-work = 0.1112, R-free = 0.1515 =============================================================================== Job complete usr+sys time: 1017.34 seconds wall clock time: 17 minutes 20.56 seconds (1040.56 seconds total)