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_1318715.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_1318715.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1318715.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: 1.54, per 1000 atoms: 0.46 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: 0.45 Conformation dependent library (CDL) restraints added in 166.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.93: 622 0.93 - 1.20: 1046 1.20 - 1.47: 791 1.47 - 1.74: 681 1.74 - 2.01: 13 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 123 " pdb=" O VAL A 123 " ideal model delta sigma weight residual 1.233 1.043 0.190 1.08e-02 8.57e+03 3.09e+02 bond pdb=" N ATYR A 67 " pdb=" CA ATYR A 67 " ideal model delta sigma weight residual 1.456 1.245 0.211 1.21e-02 6.83e+03 3.05e+02 bond pdb=" C ILE A 152 " pdb=" N ALEU A 153 " ideal model delta sigma weight residual 1.331 1.557 -0.227 1.34e-02 5.57e+03 2.87e+02 bond pdb=" C BASN A 97 " pdb=" N ARG A 98 " ideal model delta sigma weight residual 1.331 1.102 0.229 1.43e-02 4.89e+03 2.57e+02 bond pdb=" CG HIS A 126 " pdb=" ND1 HIS A 126 " ideal model delta sigma weight residual 1.378 1.202 0.176 1.10e-02 8.26e+03 2.56e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 3168 4.66 - 9.33: 1865 9.33 - 13.99: 621 13.99 - 18.65: 108 18.65 - 23.31: 15 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH1 ARG A 27 " ideal model delta sigma weight residual 121.50 140.97 -19.47 1.00e+00 1.00e+00 3.79e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N ACYS A 53 " ideal model delta sigma weight residual 123.18 137.62 -14.44 1.08e+00 8.57e-01 1.79e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 131.14 -11.94 9.00e-01 1.23e+00 1.76e+02 angle pdb=" CA GLU A 170 " pdb=" C GLU A 170 " pdb=" O GLU A 170 " ideal model delta sigma weight residual 120.70 107.95 12.75 1.03e+00 9.43e-01 1.53e+02 angle pdb=" O GLU A 170 " pdb=" C GLU A 170 " pdb=" N ALA A 171 " ideal model delta sigma weight residual 122.09 134.96 -12.87 1.08e+00 8.57e-01 1.42e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 1288 16.66 - 33.31: 142 33.31 - 49.97: 37 49.97 - 66.62: 11 66.62 - 83.28: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C LEU A 151 " pdb=" N LEU A 151 " pdb=" CA LEU A 151 " pdb=" CB LEU A 151 " ideal model delta harmonic sigma weight residual -122.60 -143.81 21.21 0 2.50e+00 1.60e-01 7.20e+01 dihedral pdb=" N LEU A 151 " pdb=" C LEU A 151 " pdb=" CA LEU A 151 " pdb=" CB LEU A 151 " ideal model delta harmonic sigma weight residual 122.80 143.54 -20.74 0 2.50e+00 1.60e-01 6.88e+01 dihedral pdb=" C VAL A 71 " pdb=" N VAL A 71 " pdb=" CA VAL A 71 " pdb=" CB VAL A 71 " ideal model delta harmonic sigma weight residual -122.00 -140.09 18.09 0 2.50e+00 1.60e-01 5.23e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.225: 106 0.225 - 0.450: 78 0.450 - 0.675: 39 0.675 - 0.900: 17 0.900 - 1.124: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LEU A 151 " pdb=" N LEU A 151 " pdb=" C LEU A 151 " pdb=" CB LEU A 151 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.48 -1.11 2.00e-01 2.50e+01 3.06e+01 chirality pdb=" CB VAL A 169 " pdb=" CA VAL A 169 " pdb=" CG1 VAL A 169 " pdb=" CG2 VAL A 169 " both_signs ideal model delta sigma weight residual False -2.63 -3.59 0.96 2.00e-01 2.50e+01 2.32e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.110 2.00e-02 2.50e+03 6.74e-02 1.36e+02 pdb=" CG PHE A 119 " -0.090 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.131 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.050 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.015 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.078 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.048 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.014 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.096 2.00e-02 2.50e+03 6.49e-02 1.26e+02 pdb=" CG PHE A 164 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.085 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.060 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.021 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.128 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.110 2.00e-02 2.50e+03 6.12e-02 1.12e+02 pdb=" CG ATYR A 67 " 0.092 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.033 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.019 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.091 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.008 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.026 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.085 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.005 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.069 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.042 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.32: 1008 2.32 - 2.89: 8110 2.89 - 3.46: 10496 3.46 - 4.03: 15289 4.03 - 4.60: 21737 Nonbonded interactions: 56640 Sorted by model distance: nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.745 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.745 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.767 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.784 2.100 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.832 2.100 ... (remaining 56635 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_1318715_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2793 r_free= 0.1807 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.407463 | | target function (ml) not normalized (work): 71590.424214 | | target function (ml) not normalized (free): 3256.854756 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3194 0.2108 7.5772 5.0288| | 2: 3.63 - 2.88 1.00 2711 122 0.2656 0.1723 4.3244 4.3304| | 3: 2.88 - 2.52 1.00 2682 148 0.2570 0.1735 4.1791 4.1847| | 4: 2.52 - 2.29 1.00 2661 139 0.2525 0.1533 3.5013 3.5695| | 5: 2.29 - 2.13 1.00 2678 122 0.2688 0.1489 3.4054 3.4457| | 6: 2.13 - 2.00 1.00 2692 117 0.2740 0.1792 3.292 3.3598| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.53 0.77 0.23 1295.28| | 2: 3.63 - 2.88 2711 122 0.83 23.74 1.32 0.23 1295.28| | 3: 2.88 - 2.52 2682 148 0.73 32.79 1.28 0.23 1295.28| | 4: 2.52 - 2.29 2661 139 0.94 10.91 1.29 0.26 128.41| | 5: 2.29 - 2.13 2678 122 0.92 13.03 1.32 0.26 128.41| | 6: 2.13 - 2.00 2692 117 0.90 15.78 1.34 0.26 128.41| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 128.41 max = 1295.28 mean = 718.35| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.92 mean = 18.97| |phase err.(test): min = 0.00 max = 89.36 mean = 19.22| |-----------------------------------------------------------------------------| ----------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 0.261 1557 Z= 5.359 Angle : 5.264 19.467 2118 Z= 3.738 Chirality : 0.385 1.124 243 Planarity : 0.031 0.082 284 Dihedral : 13.552 83.279 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 2.48 % Allowed : 2.48 % Favored : 95.03 % 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: -2.42 (0.45), residues: 224 helix: -2.45 (0.36), residues: 108 sheet: -0.48 (0.90), residues: 28 loop : -0.50 (0.54), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.018 ARG A 98 TYR 0.107 0.039 TYR A 141 PHE 0.096 0.035 PHE A 119 HIS 0.067 0.035 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2793 r_free= 0.1807 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.407463 | | target function (ml) not normalized (work): 71590.424214 | | target function (ml) not normalized (free): 3256.854756 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3332 percent. r_work = 0.2926 r_free = 0.1938 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2872 0.2926 0.1938 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2872 0.2926 0.1938 n_refl.: 17050 remove outliers: r(all,work,free)=0.2165 0.2178 0.1938 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2138 0.2151 0.1919 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1618 0.1619 0.1599 n_refl.: 17045 remove outliers: r(all,work,free)=0.1617 0.1618 0.1599 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 0.4055 394.742 359.987 0.636 1.017 0.393 11.894-9.307 99.02 97 4 0.1873 633.572 615.610 0.922 1.018 0.380 9.237-7.194 100.00 213 7 0.2206 518.198 508.338 0.959 1.017 0.365 7.162-5.571 100.00 427 22 0.2339 388.908 375.494 0.914 1.016 0.303 5.546-4.326 100.00 867 58 0.1394 533.909 528.695 0.956 1.013 0.225 4.315-3.360 100.00 1859 96 0.1295 507.752 503.623 1.015 1.008 0.201 3.356-2.611 100.00 3867 181 0.1648 333.564 329.385 1.013 1.000 0.091 2.608-2.000 99.99 8818 434 0.1660 217.427 213.458 1.034 0.985 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4538 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1618 r_free=0.1599 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A A 80 GLN A A 180 GLN Total number of N/Q/H flips: 4 r_work=0.1621 r_free=0.1603 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.458788 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.799881 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1351 0.1619 0.0268 0.008 1.0 1.3 0.5 0.0 0 11.229 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.19 2.68 3.013 18.452 0.800 0.023 12.76 16.46 3.70 3.603 18.741 0.800 0.020 Individual atomic B min max mean iso aniso Overall: 6.32 113.89 20.03 4.03 1785 0 Protein: 6.32 112.14 17.28 4.03 1519 0 Water: 9.01 113.89 35.98 N/A 258 0 Other: 21.94 36.85 26.37 N/A 8 0 Chain A: 6.32 113.89 20.03 N/A 1785 0 Histogram: Values Number of atoms 6.32 - 17.08 1090 17.08 - 27.83 338 27.83 - 38.59 186 38.59 - 49.35 97 49.35 - 60.11 47 60.11 - 70.86 13 70.86 - 81.62 6 81.62 - 92.38 5 92.38 - 103.13 0 103.13 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1276 r_free=0.1646 r_work=0.1280 r_free=0.1655 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1280 r_free = 0.1655 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 = 0.1275 r_free = 0.1654 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.14 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= 0.1275 r_free= 0.1654 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.020042 | | target function (ls_wunit_k1) not normalized (work): 325.420103 | | target function (ls_wunit_k1) not normalized (free): 26.820446 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1275 0.1654 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1918 0.1917 0.1990 n_refl.: 17044 remove outliers: r(all,work,free)=0.1918 0.1917 0.1990 n_refl.: 17044 overall B=-0.41 to atoms: r(all,work,free)=0.1888 0.1887 0.1974 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1275 0.1646 n_refl.: 17044 remove outliers: r(all,work,free)=0.1291 0.1273 0.1646 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 0.3549 302.635 278.955 0.617 1.014 0.368 11.894-9.307 99.02 97 4 0.1687 486.741 476.455 0.912 1.014 0.367 9.237-7.194 100.00 213 7 0.1822 398.105 395.376 0.958 1.014 0.351 7.162-5.571 100.00 427 22 0.1868 298.778 293.346 0.926 1.012 0.311 5.546-4.326 100.00 867 58 0.1040 410.175 407.496 0.955 1.010 0.205 4.315-3.360 100.00 1859 96 0.0926 390.080 389.683 1.017 1.006 0.191 3.356-2.611 100.00 3867 181 0.1297 256.260 255.021 1.017 0.999 0.111 2.608-2.000 99.99 8818 434 0.1347 167.038 165.593 1.031 0.987 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4491 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1646 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A A 80 GLN A A 180 GLN Total number of N/Q/H flips: 4 r_work=0.1277 r_free=0.1652 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1652 | n_water=258 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.1283 r_free=0.1645 | n_water=253 | time (s): 20.140 (total time: 20.830) Filter (q & B) r_work=0.1283 r_free=0.1644 | n_water=251 | time (s): 2.100 (total time: 22.930) Compute maps r_work=0.1283 r_free=0.1644 | n_water=251 | time (s): 0.710 (total time: 23.640) Filter (map) r_work=0.1315 r_free=0.1636 | n_water=214 | time (s): 1.880 (total time: 25.520) Find peaks r_work=0.1315 r_free=0.1636 | n_water=214 | time (s): 0.640 (total time: 26.160) Add new water r_work=0.1542 r_free=0.1839 | n_water=380 | time (s): 1.620 (total time: 27.780) Refine new water occ: r_work=0.1332 r_free=0.1591 adp: r_work=0.1273 r_free=0.1585 occ: r_work=0.1278 r_free=0.1565 adp: r_work=0.1244 r_free=0.1566 occ: r_work=0.1244 r_free=0.1560 adp: r_work=0.1234 r_free=0.1563 ADP+occupancy (water only), MIN, final r_work=0.1234 r_free=0.1563 r_work=0.1234 r_free=0.1563 | n_water=380 | time (s): 19.300 (total time: 47.080) Filter (q & B) r_work=0.1237 r_free=0.1569 | n_water=367 | time (s): 1.780 (total time: 48.860) Filter (dist only) r_work=0.1238 r_free=0.1573 | n_water=366 | time (s): 29.810 (total time: 78.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.389767 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.962841 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 0.1208 0.1633 0.0425 0.008 0.9 2.6 0.5 0.0 0 12.195 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 16.33 4.25 4.147 21.185 0.963 0.018 11.96 16.59 4.63 4.249 21.403 0.963 0.018 Individual atomic B min max mean iso aniso Overall: 6.71 106.73 21.45 4.28 1893 0 Protein: 6.71 106.73 17.76 4.28 1519 0 Water: 8.05 68.15 36.57 N/A 366 0 Other: 23.48 40.54 30.59 N/A 8 0 Chain A: 6.71 106.73 19.50 N/A 1741 0 Chain S: 17.31 66.98 43.83 N/A 152 0 Histogram: Values Number of atoms 6.71 - 16.71 1019 16.71 - 26.71 393 26.71 - 36.72 207 36.72 - 46.72 151 46.72 - 56.72 86 56.72 - 66.72 25 66.72 - 76.73 5 76.73 - 86.73 5 86.73 - 96.73 0 96.73 - 106.73 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1659 r_work=0.1197 r_free=0.1661 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1661 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 = 0.1192 r_free = 0.1665 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.27 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= 0.1192 r_free= 0.1665 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016989 | | target function (ls_wunit_k1) not normalized (work): 275.813255 | | target function (ls_wunit_k1) not normalized (free): 26.520554 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1192 0.1665 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1747 0.1736 0.2001 n_refl.: 17042 remove outliers: r(all,work,free)=0.1747 0.1736 0.2001 n_refl.: 17042 overall B=-0.39 to atoms: r(all,work,free)=0.1721 0.1710 0.1984 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1187 0.1650 n_refl.: 17042 remove outliers: r(all,work,free)=0.1209 0.1187 0.1650 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 0.3412 302.635 281.848 0.599 1.004 0.350 11.894-9.307 99.02 97 4 0.1480 486.741 483.270 0.909 1.005 0.340 9.237-7.194 100.00 213 7 0.1674 398.105 398.134 0.976 1.006 0.290 7.162-5.571 100.00 427 22 0.1570 298.778 294.252 0.935 1.005 0.272 5.546-4.326 100.00 867 58 0.0879 410.175 407.811 0.959 1.005 0.200 4.315-3.360 100.00 1859 96 0.0823 390.080 389.363 1.015 1.003 0.191 3.356-2.611 100.00 3867 181 0.1191 256.260 255.526 1.013 1.001 0.121 2.608-2.000 99.99 8818 434 0.1326 167.038 166.041 1.019 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3975 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1650 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1188 r_free=0.1650 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1650 | n_water=366 | time (s): 0.860 (total time: 0.860) Filter (dist) r_work=0.1191 r_free=0.1655 | n_water=363 | time (s): 30.050 (total time: 30.910) Filter (q & B) r_work=0.1191 r_free=0.1655 | n_water=363 | time (s): 1.270 (total time: 32.180) Compute maps r_work=0.1191 r_free=0.1655 | n_water=363 | time (s): 0.730 (total time: 32.910) Filter (map) r_work=0.1265 r_free=0.1663 | n_water=260 | time (s): 2.100 (total time: 35.010) Find peaks r_work=0.1265 r_free=0.1663 | n_water=260 | time (s): 0.670 (total time: 35.680) Add new water r_work=0.1439 r_free=0.1817 | n_water=417 | time (s): 2.000 (total time: 37.680) Refine new water occ: r_work=0.1233 r_free=0.1585 adp: r_work=0.1226 r_free=0.1591 occ: r_work=0.1208 r_free=0.1567 adp: r_work=0.1199 r_free=0.1573 occ: r_work=0.1191 r_free=0.1564 adp: r_work=0.1183 r_free=0.1565 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1565 r_work=0.1183 r_free=0.1565 | n_water=417 | time (s): 30.420 (total time: 68.100) Filter (q & B) r_work=0.1186 r_free=0.1575 | n_water=403 | time (s): 1.710 (total time: 69.810) Filter (dist only) r_work=0.1186 r_free=0.1575 | n_water=403 | time (s): 33.110 (total time: 102.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.852967 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.177789 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 0.1177 0.1559 0.0381 0.009 0.9 4.8 0.5 0.0 0 0.926 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.77 15.59 3.81 4.339 21.504 0.178 4.997 11.56 15.70 4.14 4.864 21.434 0.178 4.976 Individual atomic B min max mean iso aniso Overall: 5.82 105.44 20.88 4.71 1930 0 Protein: 5.82 105.44 17.07 4.71 1519 0 Water: 8.49 63.07 35.05 N/A 403 0 Other: 23.09 41.45 30.13 N/A 8 0 Chain A: 5.82 105.44 18.76 N/A 1734 0 Chain S: 18.31 63.07 39.61 N/A 196 0 Histogram: Values Number of atoms 5.82 - 15.78 1023 15.78 - 25.74 381 25.74 - 35.71 235 35.71 - 45.67 171 45.67 - 55.63 77 55.63 - 65.59 30 65.59 - 75.55 5 75.55 - 85.52 3 85.52 - 95.48 3 95.48 - 105.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1156 r_free=0.1570 r_work=0.1156 r_free=0.1571 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1156 r_free = 0.1571 target_work(ml) = 4.976 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1150 r_free = 0.1581 target_work(ml) = 4.974 | | 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.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1150 r_free= 0.1581 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.974351 | | target function (ml) not normalized (work): 80758.585353 | | target function (ml) not normalized (free): 4197.791053 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1171 0.1150 0.1581 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1677 0.1669 0.1888 n_refl.: 17042 remove outliers: r(all,work,free)=0.1677 0.1669 0.1888 n_refl.: 17042 overall B=-0.40 to atoms: r(all,work,free)=0.1649 0.1640 0.1876 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1167 0.1146 0.1578 n_refl.: 17042 remove outliers: r(all,work,free)=0.1166 0.1145 0.1578 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 0.3585 299.153 281.331 0.563 1.006 0.338 11.894-9.307 99.02 97 4 0.1703 486.741 481.100 0.903 1.007 0.336 9.237-7.194 100.00 213 7 0.1816 398.105 399.124 0.985 1.007 0.260 7.162-5.571 100.00 427 22 0.1718 298.778 292.003 0.937 1.006 0.231 5.546-4.326 100.00 867 58 0.0974 410.175 405.930 0.963 1.005 0.200 4.315-3.360 100.00 1859 96 0.0895 390.080 387.370 1.013 1.004 0.191 3.356-2.611 100.00 3867 181 0.1263 256.260 254.068 1.014 1.001 0.142 2.608-2.000 99.99 8818 434 0.1081 167.038 165.652 1.021 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4129 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1145 r_free=0.1578 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1146 r_free=0.1576 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1576 | n_water=403 | time (s): 0.770 (total time: 0.770) Filter (dist) r_work=0.1146 r_free=0.1582 | n_water=402 | time (s): 31.850 (total time: 32.620) Filter (q & B) r_work=0.1146 r_free=0.1582 | n_water=402 | time (s): 0.950 (total time: 33.570) Compute maps r_work=0.1146 r_free=0.1582 | n_water=402 | time (s): 0.850 (total time: 34.420) Filter (map) r_work=0.1195 r_free=0.1598 | n_water=319 | time (s): 1.990 (total time: 36.410) Find peaks r_work=0.1195 r_free=0.1598 | n_water=319 | time (s): 0.560 (total time: 36.970) Add new water r_work=0.1336 r_free=0.1712 | n_water=468 | time (s): 2.050 (total time: 39.020) Refine new water occ: r_work=0.1178 r_free=0.1546 adp: r_work=0.1168 r_free=0.1546 occ: r_work=0.1155 r_free=0.1526 adp: r_work=0.1144 r_free=0.1524 occ: r_work=0.1138 r_free=0.1515 adp: r_work=0.1129 r_free=0.1515 ADP+occupancy (water only), MIN, final r_work=0.1129 r_free=0.1515 r_work=0.1129 r_free=0.1515 | n_water=468 | time (s): 20.250 (total time: 59.270) Filter (q & B) r_work=0.1134 r_free=0.1518 | n_water=457 | time (s): 2.010 (total time: 61.280) Filter (dist only) r_work=0.1136 r_free=0.1523 | n_water=454 | time (s): 37.760 (total time: 99.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.116936 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.165709 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1116 0.1572 0.0456 0.010 1.0 4.2 0.5 0.0 0 1.058 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.16 15.72 4.56 4.507 21.179 0.166 4.959 11.03 15.59 4.56 4.618 21.200 0.166 4.948 Individual atomic B min max mean iso aniso Overall: 5.95 103.37 21.13 4.78 1981 0 Protein: 5.95 103.37 16.60 4.78 1519 0 Water: 8.45 67.65 36.12 N/A 454 0 Other: 23.32 42.02 30.24 N/A 8 0 Chain A: 5.95 103.37 18.25 N/A 1733 0 Chain S: 15.59 67.65 41.26 N/A 248 0 Histogram: Values Number of atoms 5.95 - 15.69 1051 15.69 - 25.43 363 25.43 - 35.17 222 35.17 - 44.92 197 44.92 - 54.66 93 54.66 - 64.40 40 64.40 - 74.14 8 74.14 - 83.89 2 83.89 - 93.63 3 93.63 - 103.37 2 =========================== Idealize ADP of riding H ========================== r_work=0.1103 r_free=0.1559 r_work=0.1103 r_free=0.1559 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1103 r_free = 0.1559 target_work(ml) = 4.948 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1093 r_free = 0.1559 target_work(ml) = 4.944 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1093 r_free= 0.1559 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.944345 | | target function (ml) not normalized (work): 80266.489184 | | target function (ml) not normalized (free): 4178.829993 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1115 0.1093 0.1559 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1591 0.1578 0.1885 n_refl.: 17041 remove outliers: r(all,work,free)=0.1591 0.1578 0.1885 n_refl.: 17041 overall B=-0.32 to atoms: r(all,work,free)=0.1570 0.1557 0.1873 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1114 0.1091 0.1560 n_refl.: 17041 remove outliers: r(all,work,free)=0.1114 0.1091 0.1560 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 0.3730 299.153 277.116 0.552 1.002 0.330 11.894-9.307 99.02 97 4 0.1717 486.741 480.643 0.915 1.002 0.330 9.237-7.194 100.00 213 7 0.1660 398.105 399.813 0.997 1.002 0.240 7.162-5.571 100.00 427 22 0.1535 298.778 293.595 0.943 1.002 0.200 5.546-4.326 100.00 867 58 0.0900 410.175 406.894 0.966 1.002 0.191 4.315-3.360 100.00 1859 96 0.0842 390.080 387.740 1.010 1.002 0.191 3.356-2.611 100.00 3867 181 0.1220 256.260 253.955 1.006 1.001 0.141 2.608-2.000 99.99 8818 434 0.1034 167.038 165.779 1.005 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1015 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1091 r_free=0.1560 After: r_work=0.1093 r_free=0.1559 ================================== NQH flips ================================== r_work=0.1093 r_free=0.1559 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1093 r_free=0.1559 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1093 r_free=0.1559 | n_water=454 | time (s): 0.770 (total time: 0.770) Filter (dist) r_work=0.1093 r_free=0.1559 | n_water=453 | time (s): 37.200 (total time: 37.970) Filter (q & B) r_work=0.1093 r_free=0.1559 | n_water=453 | time (s): 1.250 (total time: 39.220) Compute maps r_work=0.1093 r_free=0.1559 | n_water=453 | time (s): 0.610 (total time: 39.830) Filter (map) r_work=0.1172 r_free=0.1576 | n_water=334 | time (s): 1.880 (total time: 41.710) Find peaks r_work=0.1172 r_free=0.1576 | n_water=334 | time (s): 0.420 (total time: 42.130) Add new water r_work=0.1291 r_free=0.1674 | n_water=463 | time (s): 1.370 (total time: 43.500) Refine new water occ: r_work=0.1136 r_free=0.1540 adp: r_work=0.1128 r_free=0.1538 occ: r_work=0.1116 r_free=0.1531 adp: r_work=0.1107 r_free=0.1529 occ: r_work=0.1101 r_free=0.1524 adp: r_work=0.1095 r_free=0.1523 ADP+occupancy (water only), MIN, final r_work=0.1095 r_free=0.1523 r_work=0.1095 r_free=0.1523 | n_water=463 | time (s): 36.210 (total time: 79.710) Filter (q & B) r_work=0.1098 r_free=0.1527 | n_water=454 | time (s): 2.100 (total time: 81.810) Filter (dist only) r_work=0.1098 r_free=0.1528 | n_water=453 | time (s): 36.970 (total time: 118.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.028198 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.156117 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1116 0.1538 0.0422 0.011 1.1 5.8 0.5 0.0 0 1.014 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.16 15.38 4.22 4.514 20.792 0.156 4.946 11.06 15.30 4.23 4.602 20.834 0.156 4.939 Individual atomic B min max mean iso aniso Overall: 5.75 102.10 20.84 4.92 1980 0 Protein: 5.75 102.10 16.29 4.91 1519 0 Water: 8.21 64.26 35.95 N/A 453 0 Other: 22.40 37.23 28.58 N/A 8 0 Chain A: 5.75 102.10 17.89 N/A 1733 0 Chain S: 14.99 64.26 41.50 N/A 247 0 Histogram: Values Number of atoms 5.75 - 15.38 1054 15.38 - 25.02 362 25.02 - 34.65 214 34.65 - 44.29 185 44.29 - 53.92 116 53.92 - 63.56 32 63.56 - 73.19 8 73.19 - 82.83 3 82.83 - 92.46 2 92.46 - 102.10 4 =========================== Idealize ADP of riding H ========================== r_work=0.1106 r_free=0.1530 r_work=0.1106 r_free=0.1530 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1106 r_free = 0.1530 target_work(ml) = 4.939 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1101 r_free = 0.1541 target_work(ml) = 4.936 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1101 r_free= 0.1541 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.936252 | | target function (ml) not normalized (work): 80135.107001 | | target function (ml) not normalized (free): 4163.862699 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2811 159 0.1115 0.1469 5.454 5.6506| | 2: 3.63 - 2.88 1.00 2711 122 0.1073 0.1522 5.2188 5.3663| | 3: 2.88 - 2.52 1.00 2681 148 0.1355 0.1698 5.1286 5.2025| | 4: 2.52 - 2.29 1.00 2661 139 0.0931 0.1498 4.6299 4.9429| | 5: 2.29 - 2.13 1.00 2678 122 0.0960 0.1457 4.5821 4.863| | 6: 2.13 - 2.00 1.00 2692 117 0.1117 0.1755 4.5746 4.7898| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2811 159 0.94 9.12 1.00 0.95 6402.74| | 2: 3.63 - 2.88 2711 122 0.92 12.92 1.01 0.95 6402.74| | 3: 2.88 - 2.52 2681 148 0.87 19.05 0.99 0.95 6402.74| | 4: 2.52 - 2.29 2661 139 0.93 12.19 1.01 0.97 2147.85| | 5: 2.29 - 2.13 2678 122 0.91 14.30 1.00 0.97 2147.85| | 6: 2.13 - 2.00 2692 117 0.89 17.01 0.99 0.97 2147.85| |alpha: min = 0.95 max = 0.97 mean = 0.96| |beta: min = 2147.85 max = 6402.74 mean = 4297.84| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.97 mean = 14.06| |phase err.(test): min = 0.00 max = 89.68 mean = 13.83| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1122 0.1101 0.1541 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1576 0.1563 0.1857 n_refl.: 17041 remove outliers: r(all,work,free)=0.1576 0.1563 0.1857 n_refl.: 17041 overall B=-0.25 to atoms: r(all,work,free)=0.1561 0.1547 0.1848 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1123 0.1102 0.1541 n_refl.: 17041 remove outliers: r(all,work,free)=0.1123 0.1102 0.1541 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 0.3641 299.153 279.081 0.550 1.004 0.330 11.894-9.307 99.02 97 4 0.1764 486.741 479.890 0.911 1.005 0.307 9.237-7.194 100.00 213 7 0.1720 398.105 398.991 0.996 1.005 0.240 7.162-5.571 100.00 427 22 0.1533 298.778 293.643 0.936 1.005 0.200 5.546-4.326 100.00 867 58 0.0926 410.175 407.156 0.964 1.004 0.191 4.315-3.360 100.00 1859 96 0.0872 390.080 387.640 1.004 1.003 0.181 3.356-2.611 100.00 3867 181 0.1226 256.260 254.286 1.002 1.000 0.067 2.608-2.000 99.99 8818 434 0.1035 167.038 165.659 0.997 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8712 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2793 0.1807 0.081 5.264 8.8 119.3 19.9 258 0.000 1_bss: 0.1618 0.1599 0.081 5.264 8.4 118.9 19.5 258 0.000 1_settarget: 0.1618 0.1599 0.081 5.264 8.4 118.9 19.5 258 0.000 1_nqh: 0.1621 0.1603 0.081 5.264 8.4 118.9 19.5 258 0.013 1_weight: 0.1621 0.1603 0.081 5.264 8.4 118.9 19.5 258 0.013 1_xyzrec: 0.1351 0.1619 0.008 0.955 8.4 118.9 19.5 258 0.157 1_adp: 0.1276 0.1646 0.008 0.955 6.3 113.9 20.0 258 0.157 1_regHadp: 0.1280 0.1655 0.008 0.955 6.3 113.9 20.0 258 0.157 1_occ: 0.1275 0.1654 0.008 0.955 6.3 113.9 20.0 258 0.157 2_bss: 0.1273 0.1646 0.008 0.955 5.9 113.5 19.6 258 0.157 2_settarget: 0.1273 0.1646 0.008 0.955 5.9 113.5 19.6 258 0.157 2_updatecdl: 0.1273 0.1646 0.009 0.985 5.9 113.5 19.6 258 0.157 2_nqh: 0.1277 0.1652 0.009 0.985 5.9 113.5 19.6 258 0.145 2_sol: 0.1238 0.1573 0.009 0.985 5.9 111.7 21.1 366 n/a 2_weight: 0.1238 0.1573 0.009 0.985 5.9 111.7 21.1 366 n/a 2_xyzrec: 0.1208 0.1633 0.008 0.932 5.9 111.7 21.1 366 n/a 2_adp: 0.1196 0.1659 0.008 0.932 6.7 106.7 21.5 366 n/a 2_regHadp: 0.1197 0.1661 0.008 0.932 6.7 106.7 21.5 366 n/a 2_occ: 0.1192 0.1665 0.008 0.932 6.7 106.7 21.5 366 n/a 3_bss: 0.1187 0.1650 0.008 0.932 6.3 106.3 21.1 366 n/a 3_settarget: 0.1187 0.1650 0.008 0.932 6.3 106.3 21.1 366 n/a 3_updatecdl: 0.1187 0.1650 0.008 0.931 6.3 106.3 21.1 366 n/a 3_nqh: 0.1188 0.1650 0.008 0.931 6.3 106.3 21.1 366 n/a 3_sol: 0.1186 0.1575 0.008 0.931 6.3 106.3 21.0 403 n/a 3_weight: 0.1186 0.1575 0.008 0.931 6.3 106.3 21.0 403 n/a 3_xyzrec: 0.1177 0.1559 0.009 0.931 6.3 106.3 21.0 403 n/a 3_adp: 0.1156 0.1570 0.009 0.931 5.8 105.4 20.9 403 n/a 3_regHadp: 0.1156 0.1571 0.009 0.931 5.8 105.4 20.9 403 n/a 3_occ: 0.1150 0.1581 0.009 0.931 5.8 105.4 20.9 403 n/a 4_bss: 0.1145 0.1578 0.009 0.931 5.4 105.0 20.5 403 n/a 4_settarget: 0.1145 0.1578 0.009 0.931 5.4 105.0 20.5 403 n/a 4_updatecdl: 0.1145 0.1578 0.009 0.931 5.4 105.0 20.5 403 n/a 4_nqh: 0.1146 0.1576 0.009 0.931 5.4 105.0 20.5 403 n/a 4_sol: 0.1136 0.1523 0.009 0.931 5.4 105.0 21.1 454 n/a 4_weight: 0.1136 0.1523 0.009 0.931 5.4 105.0 21.1 454 n/a 4_xyzrec: 0.1116 0.1572 0.010 1.000 5.4 105.0 21.1 454 n/a 4_adp: 0.1103 0.1559 0.010 1.000 5.9 103.4 21.1 454 n/a 4_regHadp: 0.1103 0.1559 0.010 1.000 5.9 103.4 21.1 454 n/a 4_occ: 0.1093 0.1559 0.010 1.000 5.9 103.4 21.1 454 n/a 5_bss: 0.1091 0.1560 0.010 1.000 5.6 103.1 20.8 454 n/a 5_settarget: 0.1091 0.1560 0.010 1.000 5.6 103.1 20.8 454 n/a 5_updatecdl: 0.1091 0.1560 0.010 1.002 5.6 103.1 20.8 454 n/a 5_setrh: 0.1093 0.1559 0.010 1.002 5.6 103.1 20.8 454 n/a 5_nqh: 0.1093 0.1559 0.010 1.002 5.6 103.1 20.8 454 n/a 5_sol: 0.1098 0.1528 0.010 1.002 5.6 103.1 20.8 453 n/a 5_weight: 0.1098 0.1528 0.010 1.002 5.6 103.1 20.8 453 n/a 5_xyzrec: 0.1116 0.1538 0.011 1.061 5.6 103.1 20.8 453 n/a 5_adp: 0.1106 0.1530 0.011 1.061 5.7 102.1 20.8 453 n/a 5_regHadp: 0.1106 0.1530 0.011 1.061 5.7 102.1 20.8 453 n/a 5_occ: 0.1101 0.1541 0.011 1.061 5.7 102.1 20.8 453 n/a end: 0.1102 0.1541 0.011 1.061 5.5 101.8 20.6 453 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_1318715_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_1318715_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.2100 Refinement macro-cycles (run) : 926.5500 Write final files (write_after_run_outputs) : 21.0400 Total : 951.8000 Total CPU time: 16.26 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:16 PST -0800 (1735494076.89 s) Start R-work = 0.1618, R-free = 0.1599 Final R-work = 0.1102, R-free = 0.1541 =============================================================================== Job complete usr+sys time: 996.81 seconds wall clock time: 17 minutes 0.01 seconds (1020.01 seconds total)