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_6943566.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_6943566.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6943566.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 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.82, per 1000 atoms: 0.54 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: 0.52 Conformation dependent library (CDL) restraints added in 114.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.72 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: 616 0.93 - 1.20: 1079 1.20 - 1.47: 792 1.47 - 1.74: 655 1.74 - 2.01: 11 Bond restraints: 3153 Sorted by residual: bond pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 1.523 1.298 0.226 1.27e-02 6.20e+03 3.16e+02 bond pdb=" N VAL A 177 " pdb=" CA VAL A 177 " ideal model delta sigma weight residual 1.461 1.666 -0.206 1.19e-02 7.06e+03 2.99e+02 bond pdb=" CA VAL A 181 " pdb=" CB VAL A 181 " ideal model delta sigma weight residual 1.540 1.755 -0.215 1.25e-02 6.40e+03 2.96e+02 bond pdb=" N GLU A 147 " pdb=" CA GLU A 147 " ideal model delta sigma weight residual 1.455 1.248 0.207 1.21e-02 6.83e+03 2.93e+02 bond pdb=" N ASP A 60 " pdb=" CA ASP A 60 " ideal model delta sigma weight residual 1.458 1.673 -0.215 1.27e-02 6.20e+03 2.87e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.71: 3185 4.71 - 9.41: 1875 9.41 - 14.12: 592 14.12 - 18.82: 111 18.82 - 23.53: 14 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 108 " pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 121.07 115.47 5.60 3.60e-01 7.72e+00 2.42e+02 angle pdb=" OE1BGLN A 80 " pdb=" CD BGLN A 80 " pdb=" NE2BGLN A 80 " ideal model delta sigma weight residual 122.60 109.44 13.16 1.00e+00 1.00e+00 1.73e+02 angle pdb=" O MET A 17 " pdb=" C MET A 17 " pdb=" N GLU A 18 " ideal model delta sigma weight residual 122.12 135.79 -13.67 1.06e+00 8.90e-01 1.66e+02 angle pdb=" OE1 GLN A 180 " pdb=" CD GLN A 180 " pdb=" NE2 GLN A 180 " ideal model delta sigma weight residual 122.60 109.83 12.77 1.00e+00 1.00e+00 1.63e+02 angle pdb=" CA GLU A 170 " pdb=" C GLU A 170 " pdb=" O GLU A 170 " ideal model delta sigma weight residual 120.90 134.09 -13.19 1.07e+00 8.73e-01 1.52e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 1325 17.65 - 35.30: 103 35.30 - 52.95: 41 52.95 - 70.59: 8 70.59 - 88.24: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C LYS A 188 " pdb=" N LYS A 188 " pdb=" CA LYS A 188 " pdb=" CB LYS A 188 " ideal model delta harmonic sigma weight residual -122.60 -99.14 -23.46 0 2.50e+00 1.60e-01 8.81e+01 dihedral pdb=" N BLYS A 93 " pdb=" C BLYS A 93 " pdb=" CA BLYS A 93 " pdb=" CB BLYS A 93 " ideal model delta harmonic sigma weight residual 122.80 143.61 -20.81 0 2.50e+00 1.60e-01 6.93e+01 dihedral pdb=" C BLYS A 93 " pdb=" N BLYS A 93 " pdb=" CA BLYS A 93 " pdb=" CB BLYS A 93 " ideal model delta harmonic sigma weight residual -122.60 -142.50 19.90 0 2.50e+00 1.60e-01 6.34e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.248: 122 0.248 - 0.495: 81 0.495 - 0.742: 30 0.742 - 0.989: 9 0.989 - 1.237: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.35 -1.24 2.00e-01 2.50e+01 3.82e+01 chirality pdb=" CA BLYS A 93 " pdb=" N BLYS A 93 " pdb=" C BLYS A 93 " pdb=" CB BLYS A 93 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb=" CG ALEU A 153 " pdb=" CB ALEU A 153 " pdb=" CD1ALEU A 153 " pdb=" CD2ALEU A 153 " both_signs ideal model delta sigma weight residual False -2.59 -3.56 0.97 2.00e-01 2.50e+01 2.35e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.017 2.00e-02 2.50e+03 6.32e-02 1.20e+02 pdb=" CG TYR A 141 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.121 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.069 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.071 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.080 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.070 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.092 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.016 2.00e-02 2.50e+03 6.74e-02 1.02e+02 pdb=" CG HIS A 115 " 0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " 0.103 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " -0.053 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " -0.125 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " -0.057 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.012 2.00e-02 2.50e+03 5.62e-02 9.46e+01 pdb=" CG PHE A 162 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.105 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.077 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.032 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.049 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.040 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.063 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.091 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.015 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.050 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 854 2.29 - 2.87: 7943 2.87 - 3.45: 10608 3.45 - 4.02: 15268 4.02 - 4.60: 21947 Nonbonded interactions: 56620 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.715 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.785 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.800 2.270 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.825 2.100 nonbonded pdb="HH22 ARG A 5 " pdb=" O AGLU A 64 " model vdw 1.843 2.450 ... (remaining 56615 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_6943566_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= 0.2781 r_free= 0.1796 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.407216 | | target function (ml) not normalized (work): 71586.401893 | | target function (ml) not normalized (free): 3266.713592 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3179 0.2082 7.5637 5.0322| | 2: 3.63 - 2.88 1.00 2711 122 0.2646 0.1654 4.3238 4.3154| | 3: 2.88 - 2.52 1.00 2682 148 0.2541 0.1715 4.1793 4.1903| | 4: 2.52 - 2.29 1.00 2661 139 0.2532 0.1558 3.4969 3.5681| | 5: 2.29 - 2.13 1.00 2678 122 0.2678 0.1509 3.3996 3.4798| | 6: 2.13 - 2.00 1.00 2692 117 0.2731 0.1894 3.3151 3.4142| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.39 0.77 0.23 1298.69| | 2: 3.63 - 2.88 2711 122 0.83 23.78 1.31 0.23 1298.69| | 3: 2.88 - 2.52 2682 148 0.73 32.69 1.28 0.23 1298.69| | 4: 2.52 - 2.29 2661 139 0.93 11.34 1.29 0.26 134.10| | 5: 2.29 - 2.13 2678 122 0.92 13.42 1.32 0.26 134.10| | 6: 2.13 - 2.00 2692 117 0.90 16.15 1.33 0.26 134.10| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 134.10 max = 1298.69 mean = 722.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.96 mean = 19.13| |phase err.(test): min = 0.00 max = 89.64 mean = 19.34| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.249 1557 Z= 5.539 Angle : 5.281 19.516 2118 Z= 3.691 Chirality : 0.371 1.237 243 Planarity : 0.032 0.103 284 Dihedral : 13.797 88.242 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 27.57 % 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: -2.61 (0.47), residues: 224 helix: -2.85 (0.32), residues: 108 sheet: -1.43 (0.67), residues: 40 loop : 0.44 (0.70), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.107 0.030 ARG A 145 TYR 0.088 0.047 TYR A 141 PHE 0.120 0.035 PHE A 164 HIS 0.065 0.032 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2781 r_free= 0.1796 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.407216 | | target function (ml) not normalized (work): 71586.401893 | | target function (ml) not normalized (free): 3266.713592 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3113 percent. r_work = 0.2912 r_free = 0.1989 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2859 0.2912 0.1989 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2859 0.2912 0.1989 n_refl.: 17050 remove outliers: r(all,work,free)=0.2148 0.2158 0.1989 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2121 0.2131 0.1970 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1612 0.1610 0.1660 n_refl.: 17045 remove outliers: r(all,work,free)=0.1611 0.1609 0.1660 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 0.4082 395.151 359.341 0.638 1.018 0.387 11.894-9.307 99.02 97 4 0.1899 634.229 613.878 0.925 1.018 0.370 9.237-7.194 100.00 213 7 0.2198 518.735 509.936 0.953 1.018 0.361 7.162-5.571 100.00 427 22 0.2284 389.311 376.493 0.919 1.016 0.286 5.546-4.326 100.00 867 58 0.1362 534.462 528.975 0.954 1.013 0.220 4.315-3.360 100.00 1859 96 0.1282 508.278 504.769 1.015 1.008 0.201 3.356-2.611 100.00 3867 181 0.1648 333.910 329.376 1.013 0.999 0.040 2.608-2.000 99.99 8818 434 0.1655 217.652 213.563 1.036 0.983 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4508 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1609 r_free=0.1660 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1611 r_free=0.1663 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.873744 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.843794 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1350 0.1643 0.0293 0.009 1.0 1.0 0.5 0.0 0 12.437 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.50 16.43 2.93 3.013 18.453 0.844 0.023 12.76 16.60 3.83 3.626 18.728 0.844 0.020 Individual atomic B min max mean iso aniso Overall: 6.13 113.89 20.00 4.07 1785 0 Protein: 6.13 112.87 17.24 4.07 1519 0 Water: 8.56 113.89 36.04 N/A 258 0 Other: 21.95 36.72 26.47 N/A 8 0 Chain A: 6.13 113.89 20.00 N/A 1785 0 Histogram: Values Number of atoms 6.13 - 16.91 1077 16.91 - 27.68 350 27.68 - 38.46 185 38.46 - 49.24 98 49.24 - 60.01 47 60.01 - 70.79 13 70.79 - 81.56 7 81.56 - 92.34 4 92.34 - 103.12 1 103.12 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1276 r_free=0.1660 r_work=0.1280 r_free=0.1666 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1280 r_free = 0.1666 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1275 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= 0.1275 r_free= 0.1660 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020013 | | target function (ls_wunit_k1) not normalized (work): 324.957508 | | target function (ls_wunit_k1) not normalized (free): 27.135165 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1275 0.1660 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1916 0.1914 0.1995 n_refl.: 17044 remove outliers: r(all,work,free)=0.1916 0.1914 0.1995 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1887 0.1885 0.1980 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1295 0.1276 0.1659 n_refl.: 17044 remove outliers: r(all,work,free)=0.1293 0.1275 0.1659 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 0.3538 303.140 278.986 0.626 1.011 0.370 11.894-9.307 99.02 97 4 0.1667 487.553 477.944 0.918 1.011 0.370 9.237-7.194 100.00 213 7 0.1816 398.769 396.134 0.958 1.010 0.351 7.162-5.571 100.00 427 22 0.1835 299.277 294.395 0.931 1.009 0.301 5.546-4.326 100.00 867 58 0.1045 410.859 408.595 0.958 1.008 0.205 4.315-3.360 100.00 1859 96 0.0925 390.731 390.413 1.017 1.005 0.191 3.356-2.611 100.00 3867 181 0.1301 256.688 255.476 1.015 1.000 0.081 2.608-2.000 99.99 8818 434 0.1351 167.317 165.813 1.024 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4066 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1659 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 r_work=0.1277 r_free=0.1663 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1663 | n_water=258 | time (s): 0.830 (total time: 0.830) Filter (dist) r_work=0.1282 r_free=0.1652 | n_water=252 | time (s): 21.250 (total time: 22.080) Filter (q & B) r_work=0.1282 r_free=0.1652 | n_water=250 | time (s): 2.180 (total time: 24.260) Compute maps r_work=0.1282 r_free=0.1652 | n_water=250 | time (s): 0.800 (total time: 25.060) Filter (map) r_work=0.1320 r_free=0.1648 | n_water=211 | time (s): 2.330 (total time: 27.390) Find peaks r_work=0.1320 r_free=0.1648 | n_water=211 | time (s): 0.610 (total time: 28.000) Add new water r_work=0.1545 r_free=0.1879 | n_water=368 | time (s): 2.020 (total time: 30.020) Refine new water occ: r_work=0.1338 r_free=0.1601 adp: r_work=0.1277 r_free=0.1598 occ: r_work=0.1283 r_free=0.1571 adp: r_work=0.1249 r_free=0.1572 occ: r_work=0.1251 r_free=0.1567 adp: r_work=0.1239 r_free=0.1565 ADP+occupancy (water only), MIN, final r_work=0.1239 r_free=0.1565 r_work=0.1239 r_free=0.1565 | n_water=368 | time (s): 25.460 (total time: 55.480) Filter (q & B) r_work=0.1240 r_free=0.1569 | n_water=360 | time (s): 1.800 (total time: 57.280) Filter (dist only) r_work=0.1241 r_free=0.1572 | n_water=359 | time (s): 30.200 (total time: 87.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.857644 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.981061 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1219 0.1609 0.0390 0.008 0.9 2.9 0.5 0.0 0 12.429 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.19 16.09 3.90 4.169 21.055 0.981 0.018 12.00 16.39 4.39 4.162 21.230 0.981 0.018 Individual atomic B min max mean iso aniso Overall: 6.45 107.47 21.15 4.10 1886 0 Protein: 6.45 107.47 17.52 4.09 1519 0 Water: 8.89 65.78 36.22 N/A 359 0 Other: 25.05 47.00 34.36 N/A 8 0 Chain A: 6.45 107.47 19.26 N/A 1738 0 Chain S: 17.19 64.81 43.32 N/A 148 0 Histogram: Values Number of atoms 6.45 - 16.55 1036 16.55 - 26.65 367 26.65 - 36.76 224 36.76 - 46.86 146 46.86 - 56.96 74 56.96 - 67.06 29 67.06 - 77.17 3 77.17 - 87.27 4 87.27 - 97.37 1 97.37 - 107.47 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1639 r_work=0.1200 r_free=0.1639 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1639 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1634 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1197 r_free= 0.1634 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016987 | | target function (ls_wunit_k1) not normalized (work): 275.784297 | | target function (ls_wunit_k1) not normalized (free): 24.904499 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1197 0.1634 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1756 0.1748 0.1956 n_refl.: 17042 remove outliers: r(all,work,free)=0.1756 0.1748 0.1956 n_refl.: 17042 overall B=-0.47 to atoms: r(all,work,free)=0.1727 0.1718 0.1938 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1191 0.1628 n_refl.: 17042 remove outliers: r(all,work,free)=0.1211 0.1190 0.1628 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 0.3189 299.981 286.266 0.610 1.006 0.350 11.894-9.307 99.02 97 4 0.1505 487.553 484.601 0.916 1.007 0.350 9.237-7.194 100.00 213 7 0.1649 398.769 400.335 0.975 1.006 0.301 7.162-5.571 100.00 427 22 0.1553 299.277 296.062 0.940 1.006 0.271 5.546-4.326 100.00 867 58 0.0882 410.859 407.920 0.958 1.005 0.216 4.315-3.360 100.00 1859 96 0.0836 390.731 389.898 1.015 1.004 0.212 3.356-2.611 100.00 3867 181 0.1201 256.688 255.790 1.009 1.001 0.101 2.608-2.000 99.99 8818 434 0.1329 167.317 166.282 1.011 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1677 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1628 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=0.1190 r_free=0.1630 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1630 | n_water=359 | time (s): 0.930 (total time: 0.930) Filter (dist) r_work=0.1191 r_free=0.1632 | n_water=357 | time (s): 28.610 (total time: 29.540) Filter (q & B) r_work=0.1191 r_free=0.1632 | n_water=357 | time (s): 0.800 (total time: 30.340) Compute maps r_work=0.1191 r_free=0.1632 | n_water=357 | time (s): 0.560 (total time: 30.900) Filter (map) r_work=0.1256 r_free=0.1624 | n_water=261 | time (s): 1.940 (total time: 32.840) Find peaks r_work=0.1256 r_free=0.1624 | n_water=261 | time (s): 0.460 (total time: 33.300) Add new water r_work=0.1449 r_free=0.1814 | n_water=408 | time (s): 1.500 (total time: 34.800) Refine new water occ: r_work=0.1247 r_free=0.1580 adp: r_work=0.1237 r_free=0.1585 occ: r_work=0.1223 r_free=0.1551 adp: r_work=0.1209 r_free=0.1557 occ: r_work=0.1205 r_free=0.1540 adp: r_work=0.1193 r_free=0.1541 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1541 r_work=0.1193 r_free=0.1541 | n_water=408 | time (s): 28.650 (total time: 63.450) Filter (q & B) r_work=0.1195 r_free=0.1547 | n_water=403 | time (s): 1.620 (total time: 65.070) Filter (dist only) r_work=0.1195 r_free=0.1547 | n_water=403 | time (s): 30.310 (total time: 95.380) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.890897 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.148732 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 0.1171 0.1549 0.0377 0.009 1.0 5.4 0.5 0.0 0 0.945 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.71 15.49 3.77 4.223 21.181 0.149 4.995 11.51 15.66 4.15 4.756 21.128 0.149 4.974 Individual atomic B min max mean iso aniso Overall: 6.18 103.86 20.65 4.58 1930 0 Protein: 6.18 103.86 16.78 4.58 1519 0 Water: 8.93 62.39 34.96 N/A 403 0 Other: 25.39 44.42 33.14 N/A 8 0 Chain A: 6.18 103.86 18.51 N/A 1734 0 Chain S: 15.86 62.39 39.52 N/A 196 0 Histogram: Values Number of atoms 6.18 - 15.95 1065 15.95 - 25.72 350 25.72 - 35.48 226 35.48 - 45.25 172 45.25 - 55.02 75 55.02 - 64.79 29 64.79 - 74.56 4 74.56 - 84.32 4 84.32 - 94.09 3 94.09 - 103.86 2 =========================== Idealize ADP of riding H ========================== r_work=0.1151 r_free=0.1566 r_work=0.1152 r_free=0.1568 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1152 r_free = 0.1568 target_work(ml) = 4.974 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1146 r_free = 0.1561 target_work(ml) = 4.967 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1146 r_free= 0.1561 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.967023 | | target function (ml) not normalized (work): 80634.644950 | | target function (ml) not normalized (free): 4193.151837 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1166 0.1146 0.1561 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1673 0.1665 0.1863 n_refl.: 17041 remove outliers: r(all,work,free)=0.1673 0.1665 0.1863 n_refl.: 17041 overall B=-0.34 to atoms: r(all,work,free)=0.1650 0.1642 0.1851 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1165 0.1144 0.1562 n_refl.: 17041 remove outliers: r(all,work,free)=0.1165 0.1144 0.1562 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 0.3423 299.981 280.325 0.579 1.007 0.350 11.894-9.307 99.02 97 4 0.1753 487.553 480.938 0.913 1.008 0.340 9.237-7.194 100.00 213 7 0.1829 398.769 399.924 0.983 1.007 0.244 7.162-5.571 100.00 427 22 0.1647 299.277 294.335 0.945 1.007 0.241 5.546-4.326 100.00 867 58 0.0964 410.859 407.235 0.964 1.006 0.216 4.315-3.360 100.00 1859 96 0.0883 390.731 388.679 1.011 1.004 0.211 3.356-2.611 100.00 3867 181 0.1267 256.688 254.504 1.010 1.000 0.131 2.608-2.000 99.99 8818 434 0.1091 167.317 165.896 1.013 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1679 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1144 r_free=0.1562 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=0.1558 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1558 | n_water=403 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.1146 r_free=0.1558 | n_water=403 | time (s): 31.360 (total time: 31.980) Filter (q & B) r_work=0.1147 r_free=0.1562 | n_water=401 | time (s): 2.220 (total time: 34.200) Compute maps r_work=0.1147 r_free=0.1562 | n_water=401 | time (s): 0.610 (total time: 34.810) Filter (map) r_work=0.1190 r_free=0.1602 | n_water=320 | time (s): 2.180 (total time: 36.990) Find peaks r_work=0.1190 r_free=0.1602 | n_water=320 | time (s): 0.640 (total time: 37.630) Add new water r_work=0.1335 r_free=0.1708 | n_water=456 | time (s): 1.800 (total time: 39.430) Refine new water occ: r_work=0.1177 r_free=0.1539 adp: r_work=0.1170 r_free=0.1544 occ: r_work=0.1157 r_free=0.1525 adp: r_work=0.1148 r_free=0.1527 occ: r_work=0.1143 r_free=0.1513 adp: r_work=0.1135 r_free=0.1514 ADP+occupancy (water only), MIN, final r_work=0.1135 r_free=0.1514 r_work=0.1135 r_free=0.1514 | n_water=456 | time (s): 22.820 (total time: 62.250) Filter (q & B) r_work=0.1138 r_free=0.1517 | n_water=448 | time (s): 1.930 (total time: 64.180) Filter (dist only) r_work=0.1138 r_free=0.1517 | n_water=448 | time (s): 32.850 (total time: 97.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.933346 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.159709 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1123 0.1560 0.0437 0.009 1.0 4.2 0.5 0.0 0 0.967 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.23 15.60 4.37 4.416 20.929 0.160 4.962 11.11 15.54 4.43 4.618 20.984 0.160 4.953 Individual atomic B min max mean iso aniso Overall: 5.78 100.74 20.96 4.81 1975 0 Protein: 5.78 100.74 16.37 4.81 1519 0 Water: 8.34 65.13 36.28 N/A 448 0 Other: 25.34 43.37 33.13 N/A 8 0 Chain A: 5.78 100.74 18.05 N/A 1733 0 Chain S: 16.72 65.13 41.78 N/A 242 0 Histogram: Values Number of atoms 5.78 - 15.27 1033 15.27 - 24.77 372 24.77 - 34.26 206 34.26 - 43.76 189 43.76 - 53.26 120 53.26 - 62.75 38 62.75 - 72.25 6 72.25 - 81.74 5 81.74 - 91.24 4 91.24 - 100.74 2 =========================== Idealize ADP of riding H ========================== r_work=0.1111 r_free=0.1554 r_work=0.1111 r_free=0.1555 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1111 r_free = 0.1555 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1103 r_free = 0.1550 target_work(ml) = 4.947 | | occupancies: max = 1.00 min = 0.19 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= 0.1103 r_free= 0.1550 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.946554 | | target function (ml) not normalized (work): 80302.359154 | | target function (ml) not normalized (free): 4190.120166 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1125 0.1103 0.1550 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1590 0.1577 0.1879 n_refl.: 17041 remove outliers: r(all,work,free)=0.1590 0.1577 0.1879 n_refl.: 17041 overall B=-0.26 to atoms: r(all,work,free)=0.1574 0.1560 0.1869 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1122 0.1101 0.1547 n_refl.: 17041 remove outliers: r(all,work,free)=0.1122 0.1100 0.1547 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 0.3658 296.419 277.278 0.555 1.003 0.340 11.894-9.307 99.02 97 4 0.1710 487.553 480.753 0.913 1.004 0.334 9.237-7.194 100.00 213 7 0.1731 398.769 399.542 0.983 1.004 0.220 7.162-5.571 100.00 427 22 0.1552 299.277 293.868 0.943 1.004 0.215 5.546-4.326 100.00 867 58 0.0917 410.859 407.857 0.964 1.003 0.205 4.315-3.360 100.00 1859 96 0.0849 390.731 388.550 1.006 1.002 0.201 3.356-2.611 100.00 3867 181 0.1236 256.688 254.498 1.003 1.001 0.141 2.608-2.000 99.99 8818 434 0.1038 167.317 166.057 0.997 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.9081 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1100 r_free=0.1547 After: r_work=0.1102 r_free=0.1546 ================================== NQH flips ================================== r_work=0.1102 r_free=0.1546 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1102 r_free=0.1546 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1102 r_free=0.1546 | n_water=448 | time (s): 0.840 (total time: 0.840) Filter (dist) r_work=0.1108 r_free=0.1547 | n_water=446 | time (s): 38.280 (total time: 39.120) Filter (q & B) r_work=0.1108 r_free=0.1547 | n_water=446 | time (s): 1.120 (total time: 40.240) Compute maps r_work=0.1108 r_free=0.1547 | n_water=446 | time (s): 0.540 (total time: 40.780) Filter (map) r_work=0.1176 r_free=0.1566 | n_water=343 | time (s): 1.650 (total time: 42.430) Find peaks r_work=0.1176 r_free=0.1566 | n_water=343 | time (s): 0.570 (total time: 43.000) Add new water r_work=0.1303 r_free=0.1653 | n_water=482 | time (s): 1.890 (total time: 44.890) Refine new water occ: r_work=0.1146 r_free=0.1511 adp: r_work=0.1139 r_free=0.1514 occ: r_work=0.1125 r_free=0.1497 adp: r_work=0.1117 r_free=0.1496 occ: r_work=0.1110 r_free=0.1490 adp: r_work=0.1103 r_free=0.1487 ADP+occupancy (water only), MIN, final r_work=0.1103 r_free=0.1487 r_work=0.1103 r_free=0.1487 | n_water=482 | time (s): 51.420 (total time: 96.310) Filter (q & B) r_work=0.1107 r_free=0.1504 | n_water=470 | time (s): 1.610 (total time: 97.920) Filter (dist only) r_work=0.1107 r_free=0.1506 | n_water=469 | time (s): 37.930 (total time: 135.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.019097 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.158331 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 0.1125 0.1535 0.0410 0.010 1.1 4.5 0.5 0.0 0 1.010 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.25 15.35 4.10 4.503 20.803 0.158 4.953 11.13 15.34 4.21 4.568 20.875 0.158 4.946 Individual atomic B min max mean iso aniso Overall: 5.21 99.78 21.07 4.94 1996 0 Protein: 5.21 99.78 16.13 4.94 1519 0 Water: 7.94 66.81 36.89 N/A 469 0 Other: 24.68 40.83 31.58 N/A 8 0 Chain A: 5.21 99.78 17.78 N/A 1732 0 Chain S: 18.48 66.81 42.65 N/A 264 0 Histogram: Values Number of atoms 5.21 - 14.67 1003 14.67 - 24.13 395 24.13 - 33.58 202 33.58 - 43.04 188 43.04 - 52.50 137 52.50 - 61.95 48 61.95 - 71.41 13 71.41 - 80.87 3 80.87 - 90.32 4 90.32 - 99.78 3 =========================== Idealize ADP of riding H ========================== r_work=0.1113 r_free=0.1534 r_work=0.1113 r_free=0.1534 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1113 r_free = 0.1534 target_work(ml) = 4.946 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1108 r_free = 0.1538 target_work(ml) = 4.943 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1108 r_free= 0.1538 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.942588 | | target function (ml) not normalized (work): 80233.030750 | | target function (ml) not normalized (free): 4180.672100 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1102 0.1445 5.4484 5.7027| | 2: 3.63 - 2.88 1.00 2711 122 0.1104 0.1444 5.2371 5.3574| | 3: 2.88 - 2.52 1.00 2681 148 0.1379 0.1758 5.1533 5.2482| | 4: 2.52 - 2.29 1.00 2661 139 0.0935 0.1584 4.6285 4.9777| | 5: 2.29 - 2.13 1.00 2678 122 0.0956 0.1483 4.582 4.8635| | 6: 2.13 - 2.00 1.00 2692 117 0.1122 0.1698 4.5774 4.7723| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.41 1.00 0.96 6827.31| | 2: 3.63 - 2.88 2711 122 0.92 13.42 1.01 0.96 6827.31| | 3: 2.88 - 2.52 2681 148 0.87 19.66 0.99 0.96 6827.31| | 4: 2.52 - 2.29 2661 139 0.93 12.21 1.01 0.97 2153.42| | 5: 2.29 - 2.13 2678 122 0.91 14.28 1.00 0.97 2153.42| | 6: 2.13 - 2.00 2692 117 0.89 17.00 0.99 0.97 2153.42| |alpha: min = 0.96 max = 0.97 mean = 0.97| |beta: min = 2153.42 max = 6827.31 mean = 4514.98| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.88 mean = 14.29| |phase err.(test): min = 0.00 max = 89.28 mean = 13.94| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1129 0.1108 0.1538 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1582 0.1566 0.1906 n_refl.: 17040 remove outliers: r(all,work,free)=0.1582 0.1566 0.1906 n_refl.: 17040 overall B=-0.22 to atoms: r(all,work,free)=0.1568 0.1553 0.1898 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1129 0.1108 0.1538 n_refl.: 17040 remove outliers: r(all,work,free)=0.1129 0.1108 0.1538 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 0.3697 296.419 275.016 0.535 1.002 0.324 11.894-9.307 99.02 97 4 0.1690 487.553 482.887 0.923 1.003 0.320 9.237-7.194 100.00 213 7 0.1718 398.769 399.493 0.986 1.003 0.230 7.162-5.571 100.00 427 22 0.1517 299.277 293.947 0.942 1.003 0.230 5.546-4.326 100.00 867 58 0.0902 410.859 408.342 0.964 1.003 0.200 4.315-3.360 100.00 1859 96 0.0878 390.731 388.639 1.005 1.002 0.191 3.356-2.611 100.00 3867 181 0.1255 256.688 254.246 1.000 1.001 0.151 2.608-2.000 99.99 8818 434 0.1038 167.317 165.953 0.989 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7772 ================= 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 : 0.2781 0.1796 0.083 5.281 8.8 119.3 19.9 258 0.000 1_bss: 0.1609 0.1660 0.083 5.281 8.4 118.9 19.5 258 0.000 1_settarget: 0.1609 0.1660 0.083 5.281 8.4 118.9 19.5 258 0.000 1_nqh: 0.1611 0.1663 0.083 5.281 8.4 118.9 19.5 258 0.006 1_weight: 0.1611 0.1663 0.083 5.281 8.4 118.9 19.5 258 0.006 1_xyzrec: 0.1350 0.1643 0.009 1.004 8.4 118.9 19.5 258 0.148 1_adp: 0.1276 0.1660 0.009 1.004 6.1 113.9 20.0 258 0.148 1_regHadp: 0.1280 0.1666 0.009 1.004 6.1 113.9 20.0 258 0.148 1_occ: 0.1275 0.1660 0.009 1.004 6.1 113.9 20.0 258 0.148 2_bss: 0.1275 0.1659 0.009 1.004 5.7 113.5 19.6 258 0.148 2_settarget: 0.1275 0.1659 0.009 1.004 5.7 113.5 19.6 258 0.148 2_updatecdl: 0.1275 0.1659 0.009 1.009 5.7 113.5 19.6 258 0.148 2_nqh: 0.1277 0.1663 0.009 1.009 5.7 113.5 19.6 258 0.145 2_sol: 0.1241 0.1572 0.009 1.009 5.7 112.5 20.8 359 n/a 2_weight: 0.1241 0.1572 0.009 1.009 5.7 112.5 20.8 359 n/a 2_xyzrec: 0.1219 0.1609 0.008 0.940 5.7 112.5 20.8 359 n/a 2_adp: 0.1200 0.1639 0.008 0.940 6.4 107.5 21.2 359 n/a 2_regHadp: 0.1200 0.1639 0.008 0.940 6.4 107.5 21.2 359 n/a 2_occ: 0.1197 0.1634 0.008 0.940 6.4 107.5 21.2 359 n/a 3_bss: 0.1190 0.1628 0.008 0.940 6.0 107.0 20.7 359 n/a 3_settarget: 0.1190 0.1628 0.008 0.940 6.0 107.0 20.7 359 n/a 3_updatecdl: 0.1190 0.1628 0.008 0.942 6.0 107.0 20.7 359 n/a 3_nqh: 0.1190 0.1630 0.008 0.942 6.0 107.0 20.7 359 n/a 3_sol: 0.1195 0.1547 0.008 0.942 6.0 107.0 20.7 403 n/a 3_weight: 0.1195 0.1547 0.008 0.942 6.0 107.0 20.7 403 n/a 3_xyzrec: 0.1171 0.1549 0.009 0.954 6.0 107.0 20.7 403 n/a 3_adp: 0.1151 0.1566 0.009 0.954 6.2 103.9 20.6 403 n/a 3_regHadp: 0.1152 0.1568 0.009 0.954 6.2 103.9 20.6 403 n/a 3_occ: 0.1146 0.1561 0.009 0.954 6.2 103.9 20.6 403 n/a 4_bss: 0.1144 0.1562 0.009 0.954 5.8 103.5 20.3 403 n/a 4_settarget: 0.1144 0.1562 0.009 0.954 5.8 103.5 20.3 403 n/a 4_updatecdl: 0.1144 0.1562 0.009 0.954 5.8 103.5 20.3 403 n/a 4_nqh: 0.1146 0.1558 0.009 0.954 5.8 103.5 20.3 403 n/a 4_sol: 0.1138 0.1517 0.009 0.954 5.8 103.5 20.9 448 n/a 4_weight: 0.1138 0.1517 0.009 0.954 5.8 103.5 20.9 448 n/a 4_xyzrec: 0.1123 0.1560 0.009 0.973 5.8 103.5 20.9 448 n/a 4_adp: 0.1111 0.1554 0.009 0.973 5.8 100.7 21.0 448 n/a 4_regHadp: 0.1111 0.1555 0.009 0.973 5.8 100.7 21.0 448 n/a 4_occ: 0.1103 0.1550 0.009 0.973 5.8 100.7 21.0 448 n/a 5_bss: 0.1100 0.1547 0.009 0.973 5.5 100.5 20.7 448 n/a 5_settarget: 0.1100 0.1547 0.009 0.973 5.5 100.5 20.7 448 n/a 5_updatecdl: 0.1100 0.1547 0.009 0.974 5.5 100.5 20.7 448 n/a 5_setrh: 0.1102 0.1546 0.009 0.974 5.5 100.5 20.7 448 n/a 5_nqh: 0.1102 0.1546 0.009 0.974 5.5 100.5 20.7 448 n/a 5_sol: 0.1107 0.1506 0.009 0.974 5.5 100.5 20.9 469 n/a 5_weight: 0.1107 0.1506 0.009 0.974 5.5 100.5 20.9 469 n/a 5_xyzrec: 0.1125 0.1535 0.010 1.052 5.5 100.5 20.9 469 n/a 5_adp: 0.1113 0.1534 0.010 1.052 5.2 99.8 21.1 469 n/a 5_regHadp: 0.1113 0.1534 0.010 1.052 5.2 99.8 21.1 469 n/a 5_occ: 0.1108 0.1538 0.010 1.052 5.2 99.8 21.1 469 n/a end: 0.1108 0.1538 0.010 1.052 5.0 99.6 20.8 469 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6943566_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6943566_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.9900 Refinement macro-cycles (run) : 943.6100 Write final files (write_after_run_outputs) : 19.2600 Total : 966.8600 Total CPU time: 16.48 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:30 PST -0800 (1735494090.95 s) Start R-work = 0.1609, R-free = 0.1660 Final R-work = 0.1108, R-free = 0.1538 =============================================================================== Job complete usr+sys time: 1008.02 seconds wall clock time: 17 minutes 11.98 seconds (1031.98 seconds total)