Starting phenix.refine on Sun Dec 29 09:10:02 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3337960.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=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3337960.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3337960.pdb" } 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: 1.35, per 1000 atoms: 0.40 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 113.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.90: 427 0.90 - 1.16: 1204 1.16 - 1.42: 637 1.42 - 1.67: 845 1.67 - 1.93: 40 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLN A 95 " pdb=" O GLN A 95 " ideal model delta sigma weight residual 1.237 1.480 -0.244 1.19e-02 7.06e+03 4.19e+02 bond pdb=" CE1 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 1.321 1.520 -0.199 1.00e-02 1.00e+04 3.95e+02 bond pdb=" CA LEU A 101 " pdb=" C LEU A 101 " ideal model delta sigma weight residual 1.523 1.289 0.234 1.23e-02 6.61e+03 3.61e+02 bond pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta sigma weight residual 1.462 1.319 0.143 7.70e-03 1.69e+04 3.43e+02 bond pdb=" C ILE A 168 " pdb=" O ILE A 168 " ideal model delta sigma weight residual 1.236 1.440 -0.204 1.11e-02 8.12e+03 3.36e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.28: 2930 4.28 - 8.55: 1862 8.55 - 12.83: 781 12.83 - 17.11: 179 17.11 - 21.39: 25 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O LYS A 89 " pdb=" C LYS A 89 " pdb=" N BGLU A 90 " ideal model delta sigma weight residual 122.09 138.18 -16.09 1.04e+00 9.25e-01 2.39e+02 angle pdb=" O LYS A 89 " pdb=" C LYS A 89 " pdb=" N AGLU A 90 " ideal model delta sigma weight residual 122.09 138.01 -15.92 1.04e+00 9.25e-01 2.34e+02 angle pdb=" C ALYS A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta sigma weight residual 122.36 136.29 -13.93 9.70e-01 1.06e+00 2.06e+02 angle pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 110.52 119.67 -9.15 6.70e-01 2.23e+00 1.86e+02 angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.42 112.03 8.39 6.40e-01 2.44e+00 1.72e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.17: 1297 17.17 - 34.33: 131 34.33 - 51.50: 38 51.50 - 68.66: 11 68.66 - 85.82: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ARG A 48 " pdb=" N ARG A 48 " pdb=" CA ARG A 48 " pdb=" CB ARG A 48 " ideal model delta harmonic sigma weight residual -122.60 -143.44 20.84 0 2.50e+00 1.60e-01 6.95e+01 dihedral pdb=" C LEU A 38 " pdb=" N LEU A 38 " pdb=" CA LEU A 38 " pdb=" CB LEU A 38 " ideal model delta harmonic sigma weight residual -122.60 -142.59 19.99 0 2.50e+00 1.60e-01 6.40e+01 dihedral pdb=" N BASN A 97 " pdb=" C BASN A 97 " pdb=" CA BASN A 97 " pdb=" CB BASN A 97 " ideal model delta harmonic sigma weight residual 122.80 103.01 19.79 0 2.50e+00 1.60e-01 6.27e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.204: 87 0.204 - 0.407: 61 0.407 - 0.610: 55 0.610 - 0.813: 33 0.813 - 1.016: 7 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 -1.57 -1.02 2.00e-01 2.50e+01 2.58e+01 chirality pdb=" CA LEU A 38 " pdb=" N LEU A 38 " pdb=" C LEU A 38 " pdb=" CB LEU A 38 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.22e+01 chirality pdb=" CA ARG A 48 " pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CB ARG A 48 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.03e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.071 2.00e-02 2.50e+03 7.77e-02 1.36e+02 pdb=" CG HIS A 115 " 0.129 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " 0.044 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " 0.060 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " 0.037 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " -0.102 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " -0.122 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.050 2.00e-02 2.50e+03 6.28e-02 1.18e+02 pdb=" CG TYR A 139 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.112 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.090 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.068 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.046 2.00e-02 2.50e+03 6.45e-02 9.35e+01 pdb=" CG HIS A 126 " -0.156 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.060 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.054 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.016 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.018 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 1380 2.37 - 2.92: 8342 2.92 - 3.48: 10421 3.48 - 4.04: 15124 4.04 - 4.60: 21393 Nonbonded interactions: 56660 Sorted by model distance: nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.808 2.100 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.822 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.832 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.832 2.270 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.837 2.100 ... (remaining 56655 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 1 N 265 6.97 1 C 957 5.97 2 H 1596 1.00 1 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_3337960_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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3611 r_free= 0.1982 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.459364 | | target function (ml) not normalized (work): 21984.662329 | | target function (ml) not normalized (free): 1148.798715 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.79 1.00 2500 142 0.3802 0.2206 4.8463 4.9064| | 2: 3.78 - 3.00 1.00 2430 110 0.3377 0.1603 4.0613 4.1099| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.79 2500 142 0.50 48.78 0.83 0.13 6598.73| | 2: 3.78 - 3.00 2430 110 0.94 11.03 1.48 0.26 434.28| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 366.74 max = 12064.85 mean = 3560.27| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.17| |phase err.(test): min = 0.00 max = 89.95 mean = 33.07| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.267 1557 Z= 5.518 Angle : 5.435 18.859 2118 Z= 3.876 Chirality : 0.419 1.016 243 Planarity : 0.033 0.105 284 Dihedral : 14.574 85.823 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 34.05 % 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: -2.55 (0.48), residues: 224 helix: -2.75 (0.40), residues: 103 sheet: 0.14 (1.08), residues: 28 loop : -0.72 (0.50), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.081 0.021 ARG A 27 TYR 0.063 0.022 TYR A 139 PHE 0.072 0.032 PHE A 164 HIS 0.109 0.042 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3611 r_free= 0.1982 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.459364 | | target function (ml) not normalized (work): 21984.662329 | | target function (ml) not normalized (free): 1148.798715 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3566 0.3646 0.2084 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3566 0.3646 0.2084 n_refl.: 5182 remove outliers: r(all,work,free)=0.2516 0.2542 0.2084 n_refl.: 5178 overall B=-2.86 to atoms: r(all,work,free)=0.2406 0.2429 0.2045 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1555 0.1554 0.1575 n_refl.: 5178 remove outliers: r(all,work,free)=0.1551 0.1549 0.1575 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3860 449.690 407.005 0.655 1.073 0.398 11.894-9.307 99.02 97 4 0.1889 714.369 693.539 0.937 1.069 0.383 9.237-7.194 100.00 213 7 0.2200 584.212 572.359 0.974 1.061 0.384 7.162-5.571 100.00 427 22 0.2346 438.380 423.782 0.936 1.048 0.346 5.546-4.326 100.00 867 58 0.1385 601.833 594.282 0.978 1.025 0.226 4.315-3.360 100.00 1859 96 0.1292 572.350 566.972 1.055 0.988 0.200 3.356-3.002 100.00 1373 60 0.1572 440.848 433.782 1.074 0.951 0.075 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-3.6594 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1549 r_free=0.1575 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.1549 r_free=0.1576 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 20.243008 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.866277 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.1167 0.1809 0.0643 0.010 1.0 2.2 0.5 0.0 0 10.122 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.67 18.09 6.43 3.013 15.997 1.866 0.018 10.26 18.19 7.94 4.899 16.187 1.866 0.015 Individual atomic B min max mean iso aniso Overall: 2.15 111.74 17.38 5.27 1785 0 Protein: 2.15 111.74 14.70 5.27 1519 0 Water: 4.00 111.44 32.97 N/A 258 0 Other: 16.00 36.41 23.82 N/A 8 0 Chain A: 2.15 111.74 17.38 N/A 1785 0 Histogram: Values Number of atoms 2.15 - 13.11 918 13.11 - 24.07 487 24.07 - 35.03 185 35.03 - 45.99 107 45.99 - 56.95 55 56.95 - 67.91 17 67.91 - 78.87 7 78.87 - 89.82 5 89.82 - 100.78 1 100.78 - 111.74 3 =========================== Idealize ADP of riding H ========================== r_work=0.1026 r_free=0.1819 r_work=0.1020 r_free=0.1826 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1020 r_free = 0.1826 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1012 r_free = 0.1812 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1012 r_free= 0.1812 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013965 | | target function (ls_wunit_k1) not normalized (work): 68.766110 | | target function (ls_wunit_k1) not normalized (free): 10.531529 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1053 0.1012 0.1812 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2095 0.2093 0.2243 n_refl.: 5176 remove outliers: r(all,work,free)=0.2095 0.2093 0.2243 n_refl.: 5176 overall B=-0.93 to atoms: r(all,work,free)=0.2056 0.2052 0.2232 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1052 0.1011 0.1809 n_refl.: 5176 remove outliers: r(all,work,free)=0.1052 0.1011 0.1809 n_refl.: 5176 ======================== 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 96.88 88 5 0.3330 330.718 313.028 0.670 1.023 0.385 11.894-9.307 99.02 97 4 0.1487 525.372 517.486 0.975 1.023 0.359 9.237-7.194 100.00 213 7 0.1651 429.650 429.682 1.011 1.021 0.336 7.162-5.571 100.00 427 22 0.1604 322.400 319.071 0.972 1.016 0.322 5.546-4.326 100.00 867 58 0.0911 442.610 439.566 0.990 1.009 0.206 4.315-3.360 100.00 1859 96 0.0767 420.927 421.079 1.042 0.996 0.201 3.356-3.002 100.00 1373 60 0.1005 324.216 322.626 1.025 0.983 0.061 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.3281 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1011 r_free=0.1809 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A A 80 GLN B Total number of N/Q/H flips: 2 r_work=0.1012 r_free=0.1809 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1012 r_free=0.1809 | n_water=258 | time (s): 0.450 (total time: 0.450) Filter (dist) r_work=0.1035 r_free=0.1806 | n_water=248 | time (s): 21.920 (total time: 22.370) Filter (q & B) r_work=0.1035 r_free=0.1807 | n_water=245 | time (s): 1.330 (total time: 23.700) Compute maps r_work=0.1035 r_free=0.1807 | n_water=245 | time (s): 0.430 (total time: 24.130) Filter (map) r_work=0.1326 r_free=0.1853 | n_water=146 | time (s): 1.750 (total time: 25.880) Find peaks r_work=0.1326 r_free=0.1853 | n_water=146 | time (s): 0.560 (total time: 26.440) Add new water r_work=0.1670 r_free=0.2113 | n_water=232 | time (s): 1.710 (total time: 28.150) Refine new water occ: r_work=0.1150 r_free=0.1734 adp: r_work=0.1125 r_free=0.1747 occ: r_work=0.1121 r_free=0.1715 adp: r_work=0.1111 r_free=0.1724 occ: r_work=0.1109 r_free=0.1710 adp: r_work=0.1107 r_free=0.1711 ADP+occupancy (water only), MIN, final r_work=0.1107 r_free=0.1711 r_work=0.1107 r_free=0.1711 | n_water=232 | time (s): 9.370 (total time: 37.520) Filter (q & B) r_work=0.1107 r_free=0.1711 | n_water=232 | time (s): 0.970 (total time: 38.490) Filter (dist only) r_work=0.1119 r_free=0.1713 | n_water=227 | time (s): 16.730 (total time: 55.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.345296 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.980374 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.1011 0.1831 0.0821 0.009 1.0 5.1 0.5 0.0 0 11.173 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.11 18.31 8.21 4.654 16.770 2.980 0.014 9.42 18.69 9.27 5.488 17.140 2.980 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 108.39 16.51 6.53 1754 0 Protein: 0.00 108.39 14.99 6.51 1519 0 Water: 0.00 62.79 26.42 N/A 227 0 Other: 10.79 36.96 24.32 N/A 8 0 Chain A: 0.00 108.39 15.71 N/A 1669 0 Chain S: 3.78 59.68 32.12 N/A 85 0 Histogram: Values Number of atoms 0.00 - 10.84 697 10.84 - 21.68 652 21.68 - 32.52 212 32.52 - 43.36 115 43.36 - 54.19 38 54.19 - 65.03 26 65.03 - 75.87 7 75.87 - 86.71 4 86.71 - 97.55 1 97.55 - 108.39 2 =========================== Idealize ADP of riding H ========================== r_work=0.0942 r_free=0.1869 r_work=0.0939 r_free=0.1871 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0939 r_free = 0.1871 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0933 r_free = 0.1829 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0933 r_free= 0.1829 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.011903 | | target function (ls_wunit_k1) not normalized (work): 58.610403 | | target function (ls_wunit_k1) not normalized (free): 10.416914 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0980 0.0933 0.1829 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2131 0.2137 0.2179 n_refl.: 5176 remove outliers: r(all,work,free)=0.2131 0.2137 0.2179 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2131 0.2137 0.2179 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0982 0.0937 0.1837 n_refl.: 5176 remove outliers: r(all,work,free)=0.0980 0.0934 0.1837 n_refl.: 5175 ======================== 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 0.3275 327.933 309.502 0.671 1.014 0.370 11.894-9.307 99.02 97 4 0.1384 525.372 521.150 0.983 1.015 0.350 9.237-7.194 100.00 213 7 0.1477 429.650 429.976 1.012 1.014 0.325 7.162-5.571 100.00 427 22 0.1423 322.400 320.364 0.988 1.011 0.320 5.546-4.326 100.00 867 58 0.0785 442.610 440.183 1.000 1.006 0.240 4.315-3.360 100.00 1859 96 0.0729 420.927 420.659 1.048 0.998 0.200 3.356-3.002 100.00 1373 60 0.0956 324.216 322.571 1.030 0.990 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.8256 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0934 r_free=0.1837 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.0935 r_free=0.1839 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0935 r_free=0.1839 | n_water=227 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.0958 r_free=0.1852 | n_water=220 | time (s): 18.720 (total time: 19.330) Filter (q & B) r_work=0.1018 r_free=0.1840 | n_water=218 | time (s): 1.470 (total time: 20.800) Compute maps r_work=0.1018 r_free=0.1840 | n_water=218 | time (s): 0.440 (total time: 21.240) Filter (map) r_work=0.1286 r_free=0.1885 | n_water=147 | time (s): 1.230 (total time: 22.470) Find peaks r_work=0.1286 r_free=0.1885 | n_water=147 | time (s): 0.380 (total time: 22.850) Add new water r_work=0.1699 r_free=0.2246 | n_water=239 | time (s): 1.460 (total time: 24.310) Refine new water occ: r_work=0.1064 r_free=0.1759 adp: r_work=0.1058 r_free=0.1773 occ: r_work=0.1045 r_free=0.1754 adp: r_work=0.1045 r_free=0.1763 occ: r_work=0.1034 r_free=0.1746 adp: r_work=0.1034 r_free=0.1746 ADP+occupancy (water only), MIN, final r_work=0.1034 r_free=0.1746 r_work=0.1034 r_free=0.1746 | n_water=239 | time (s): 8.930 (total time: 33.240) Filter (q & B) r_work=0.1034 r_free=0.1746 | n_water=239 | time (s): 0.740 (total time: 33.980) Filter (dist only) r_work=0.1034 r_free=0.1749 | n_water=238 | time (s): 19.540 (total time: 53.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.096416 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.185950 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.0926 0.1851 0.0925 0.010 1.0 4.8 0.5 0.0 0 0.548 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.26 18.51 9.25 5.445 17.738 0.186 5.138 8.83 18.70 9.87 7.161 17.715 0.186 5.041 Individual atomic B min max mean iso aniso Overall: 0.00 106.36 16.19 8.76 1765 0 Protein: 0.00 106.36 15.05 8.73 1519 0 Water: 0.00 57.79 23.21 N/A 238 0 Other: 9.30 44.16 25.64 N/A 8 0 Chain A: 0.00 106.36 15.69 N/A 1654 0 Chain S: 0.00 53.97 23.67 N/A 111 0 Histogram: Values Number of atoms 0.00 - 10.64 684 10.64 - 21.27 660 21.27 - 31.91 237 31.91 - 42.55 115 42.55 - 53.18 34 53.18 - 63.82 16 63.82 - 74.45 10 74.45 - 85.09 4 85.09 - 95.73 4 95.73 - 106.36 1 =========================== Idealize ADP of riding H ========================== r_work=0.0883 r_free=0.1870 r_work=0.0888 r_free=0.1876 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0888 r_free = 0.1876 target_work(ml) = 5.045 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0877 r_free = 0.1872 target_work(ml) = 5.038 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0877 r_free= 0.1872 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.037828 | | target function (ml) not normalized (work): 24801.224921 | | target function (ml) not normalized (free): 1886.526083 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0926 0.0877 0.1872 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2135 0.2141 0.2199 n_refl.: 5175 remove outliers: r(all,work,free)=0.2135 0.2141 0.2199 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2135 0.2141 0.2199 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0914 0.0866 0.1854 n_refl.: 5175 remove outliers: r(all,work,free)=0.0912 0.0863 0.1854 n_refl.: 5174 ======================== 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 0.3591 330.114 295.563 0.597 0.994 0.340 11.894-9.307 99.02 97 4 0.1789 525.372 511.865 0.948 0.999 0.325 9.237-7.194 100.00 213 7 0.1841 429.650 421.530 1.006 1.000 0.310 7.162-5.571 100.00 427 22 0.1813 322.400 313.079 0.976 1.001 0.300 5.546-4.326 100.00 867 58 0.0883 442.610 437.466 0.997 1.002 0.260 4.315-3.360 100.00 1859 96 0.0570 420.927 420.400 1.050 1.003 0.220 3.356-3.002 100.00 1373 60 0.0586 324.216 323.430 1.029 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.1860 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0863 r_free=0.1854 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0864 r_free=0.1851 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0864 r_free=0.1851 | n_water=238 | time (s): 0.590 (total time: 0.590) Filter (dist) r_work=0.0896 r_free=0.1864 | n_water=232 | time (s): 20.570 (total time: 21.160) Filter (q & B) r_work=0.0976 r_free=0.1889 | n_water=228 | time (s): 1.920 (total time: 23.080) Compute maps r_work=0.0976 r_free=0.1889 | n_water=228 | time (s): 0.680 (total time: 23.760) Filter (map) r_work=0.1274 r_free=0.1919 | n_water=149 | time (s): 1.510 (total time: 25.270) Find peaks r_work=0.1274 r_free=0.1919 | n_water=149 | time (s): 0.590 (total time: 25.860) Add new water r_work=0.1608 r_free=0.2229 | n_water=232 | time (s): 1.820 (total time: 27.680) Refine new water occ: r_work=0.1043 r_free=0.1789 adp: r_work=0.1037 r_free=0.1805 occ: r_work=0.1027 r_free=0.1781 adp: r_work=0.1026 r_free=0.1798 occ: r_work=0.1017 r_free=0.1768 adp: r_work=0.1016 r_free=0.1785 ADP+occupancy (water only), MIN, final r_work=0.1016 r_free=0.1785 r_work=0.1016 r_free=0.1785 | n_water=232 | time (s): 10.980 (total time: 38.660) Filter (q & B) r_work=0.1016 r_free=0.1793 | n_water=230 | time (s): 1.300 (total time: 39.960) Filter (dist only) r_work=0.1041 r_free=0.1781 | n_water=227 | time (s): 18.540 (total time: 58.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.045531 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.200822 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.0927 0.1832 0.0905 0.010 1.0 3.5 0.5 0.0 0 0.523 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.27 18.32 9.05 6.849 17.819 0.201 5.093 8.97 18.58 9.62 7.967 17.928 0.201 5.024 Individual atomic B min max mean iso aniso Overall: 0.00 105.67 16.54 10.26 1754 0 Protein: 0.00 105.67 15.45 10.21 1519 0 Water: 0.00 60.65 23.54 N/A 227 0 Other: 8.23 46.25 26.63 N/A 8 0 Chain A: 0.00 105.67 15.95 N/A 1637 0 Chain S: 0.00 60.65 24.87 N/A 117 0 Histogram: Values Number of atoms 0.00 - 10.57 653 10.57 - 21.13 660 21.13 - 31.70 247 31.70 - 42.27 112 42.27 - 52.83 45 52.83 - 63.40 17 63.40 - 73.97 8 73.97 - 84.53 8 84.53 - 95.10 2 95.10 - 105.67 2 =========================== Idealize ADP of riding H ========================== r_work=0.0897 r_free=0.1858 r_work=0.0901 r_free=0.1866 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0901 r_free = 0.1866 target_work(ml) = 5.028 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0890 r_free = 0.1855 target_work(ml) = 5.021 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0890 r_free= 0.1855 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.021044 | | target function (ml) not normalized (work): 24713.579570 | | target function (ml) not normalized (free): 1980.959850 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0938 0.0890 0.1855 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2115 0.2116 0.2255 n_refl.: 5174 remove outliers: r(all,work,free)=0.2115 0.2116 0.2255 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2115 0.2116 0.2255 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0938 0.0889 0.1859 n_refl.: 5174 remove outliers: r(all,work,free)=0.0938 0.0889 0.1859 n_refl.: 5174 ======================== 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 0.3910 330.114 299.515 0.596 0.987 0.330 11.894-9.307 99.02 97 4 0.1846 525.372 509.424 0.954 0.993 0.320 9.237-7.194 100.00 213 7 0.2027 429.650 420.090 1.005 0.996 0.310 7.162-5.571 100.00 427 22 0.2012 322.400 312.444 0.985 0.998 0.300 5.546-4.326 100.00 867 58 0.0953 442.610 436.950 1.011 1.000 0.260 4.315-3.360 100.00 1859 96 0.0568 420.927 420.587 1.067 1.003 0.220 3.356-3.002 100.00 1373 60 0.0518 324.216 323.675 1.051 1.005 0.078 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.1028 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0889 r_free=0.1859 After: r_work=0.0892 r_free=0.1860 ================================== NQH flips ================================== r_work=0.0892 r_free=0.1860 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.0894 r_free=0.1863 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0894 r_free=0.1863 | n_water=227 | time (s): 0.470 (total time: 0.470) Filter (dist) r_work=0.0910 r_free=0.1873 | n_water=223 | time (s): 16.740 (total time: 17.210) Filter (q & B) r_work=0.0989 r_free=0.1854 | n_water=220 | time (s): 1.570 (total time: 18.780) Compute maps r_work=0.0989 r_free=0.1854 | n_water=220 | time (s): 0.540 (total time: 19.320) Filter (map) r_work=0.1231 r_free=0.1874 | n_water=150 | time (s): 1.270 (total time: 20.590) Find peaks r_work=0.1231 r_free=0.1874 | n_water=150 | time (s): 0.410 (total time: 21.000) Add new water r_work=0.1531 r_free=0.2176 | n_water=216 | time (s): 1.520 (total time: 22.520) Refine new water occ: r_work=0.1010 r_free=0.1842 adp: r_work=0.1002 r_free=0.1857 occ: r_work=0.0997 r_free=0.1834 adp: r_work=0.0996 r_free=0.1845 occ: r_work=0.0991 r_free=0.1822 adp: r_work=0.0990 r_free=0.1833 ADP+occupancy (water only), MIN, final r_work=0.0990 r_free=0.1833 r_work=0.0990 r_free=0.1833 | n_water=216 | time (s): 6.320 (total time: 28.840) Filter (q & B) r_work=0.0990 r_free=0.1833 | n_water=215 | time (s): 1.520 (total time: 30.360) Filter (dist only) r_work=0.0990 r_free=0.1833 | n_water=215 | time (s): 16.610 (total time: 46.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.986463 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.253590 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.0925 0.1855 0.0930 0.010 1.1 5.8 0.5 0.0 0 0.493 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.25 18.55 9.30 7.841 18.122 0.254 5.059 9.05 18.65 9.60 8.820 18.238 0.254 4.998 Individual atomic B min max mean iso aniso Overall: 0.00 107.33 16.68 11.62 1742 0 Protein: 0.00 107.33 15.83 11.56 1519 0 Water: 0.00 60.41 22.34 N/A 215 0 Other: 5.83 45.53 26.13 N/A 8 0 Chain A: 0.00 107.33 16.24 N/A 1632 0 Chain S: 0.00 52.65 23.14 N/A 110 0 Histogram: Values Number of atoms 0.00 - 10.73 646 10.73 - 21.47 650 21.47 - 32.20 258 32.20 - 42.93 108 42.93 - 53.67 46 53.67 - 64.40 15 64.40 - 75.13 7 75.13 - 85.86 5 85.86 - 96.60 4 96.60 - 107.33 3 =========================== Idealize ADP of riding H ========================== r_work=0.0905 r_free=0.1865 r_work=0.0909 r_free=0.1868 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0909 r_free = 0.1868 target_work(ml) = 5.003 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0902 r_free = 0.1853 target_work(ml) = 4.999 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0902 r_free= 0.1853 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 4.998807 | | target function (ml) not normalized (work): 24604.125832 | | target function (ml) not normalized (free): 2122.237696 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1261 0.1827 5.5407 6.1819| | 2: 3.78 - 3.00 1.00 2430 110 0.0464 0.1897 4.4431 11.313| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.79 2492 142 0.92 12.04 1.00 0.99 12945.45| | 2: 3.78 - 3.00 2430 110 0.99 2.07 1.00 1.01 1038.12| |alpha: min = 0.98 max = 1.01 mean = 1.00| |beta: min = 671.95 max = 21351.32 mean = 7066.78| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.84 mean = 7.12| |phase err.(test): min = 0.00 max = 72.17 mean = 7.47| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0949 0.0902 0.1853 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2175 0.2180 0.2224 n_refl.: 5174 remove outliers: r(all,work,free)=0.2175 0.2180 0.2224 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2175 0.2180 0.2224 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0948 0.0901 0.1849 n_refl.: 5174 remove outliers: r(all,work,free)=0.0948 0.0901 0.1849 n_refl.: 5174 ======================== 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 0.3742 330.114 300.878 0.613 0.991 0.330 11.894-9.307 99.02 97 4 0.1874 525.372 511.247 0.956 0.997 0.328 9.237-7.194 100.00 213 7 0.2091 429.650 419.545 0.997 1.000 0.326 7.162-5.571 100.00 427 22 0.2065 322.400 312.208 0.983 1.001 0.310 5.546-4.326 100.00 867 58 0.1022 442.610 437.360 1.008 1.002 0.250 4.315-3.360 100.00 1859 96 0.0588 420.927 420.608 1.077 1.003 0.220 3.356-3.002 100.00 1373 60 0.0453 324.216 323.488 1.063 1.003 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.4978 ================= 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 : 0.3611 0.1982 0.082 5.435 8.8 119.3 19.9 258 0.000 1_bss: 0.1549 0.1575 0.082 5.435 6.0 116.4 17.0 258 0.000 1_settarget: 0.1549 0.1575 0.082 5.435 6.0 116.4 17.0 258 0.000 1_nqh: 0.1549 0.1576 0.082 5.435 6.0 116.4 17.0 258 0.003 1_weight: 0.1549 0.1576 0.082 5.435 6.0 116.4 17.0 258 0.003 1_xyzrec: 0.1167 0.1809 0.010 1.007 6.0 116.4 17.0 258 0.197 1_adp: 0.1026 0.1819 0.010 1.007 2.2 111.7 17.4 258 0.197 1_regHadp: 0.1020 0.1826 0.010 1.007 2.2 111.7 17.4 258 0.197 1_occ: 0.1012 0.1812 0.010 1.007 2.2 111.7 17.4 258 0.197 2_bss: 0.1011 0.1809 0.010 1.007 1.2 110.8 16.5 258 0.197 2_settarget: 0.1011 0.1809 0.010 1.007 1.2 110.8 16.5 258 0.197 2_updatecdl: 0.1011 0.1809 0.011 1.035 1.2 110.8 16.5 258 0.197 2_nqh: 0.1012 0.1809 0.011 1.035 1.2 110.8 16.5 258 0.197 2_sol: 0.1119 0.1713 0.011 1.035 1.0 110.8 15.8 227 n/a 2_weight: 0.1119 0.1713 0.011 1.035 1.0 110.8 15.8 227 n/a 2_xyzrec: 0.1011 0.1831 0.009 0.957 1.0 110.8 15.8 227 n/a 2_adp: 0.0942 0.1869 0.009 0.957 0.0 108.4 16.5 227 n/a 2_regHadp: 0.0939 0.1871 0.009 0.957 0.0 108.4 16.5 227 n/a 2_occ: 0.0933 0.1829 0.009 0.957 0.0 108.4 16.5 227 n/a 3_bss: 0.0934 0.1837 0.009 0.957 0.0 108.4 16.5 227 n/a 3_settarget: 0.0934 0.1837 0.009 0.957 0.0 108.4 16.5 227 n/a 3_updatecdl: 0.0934 0.1837 0.009 0.964 0.0 108.4 16.5 227 n/a 3_nqh: 0.0935 0.1839 0.009 0.964 0.0 108.4 16.5 227 n/a 3_sol: 0.1034 0.1749 0.009 0.964 0.0 108.4 16.2 238 n/a 3_weight: 0.1034 0.1749 0.009 0.964 0.0 108.4 16.2 238 n/a 3_xyzrec: 0.0926 0.1851 0.010 1.044 0.0 108.4 16.2 238 n/a 3_adp: 0.0883 0.1870 0.010 1.044 0.0 106.4 16.2 238 n/a 3_regHadp: 0.0888 0.1876 0.010 1.044 0.0 106.4 16.2 238 n/a 3_occ: 0.0877 0.1872 0.010 1.044 0.0 106.4 16.2 238 n/a 4_bss: 0.0863 0.1854 0.010 1.044 0.0 106.4 16.2 238 n/a 4_settarget: 0.0863 0.1854 0.010 1.044 0.0 106.4 16.2 238 n/a 4_updatecdl: 0.0863 0.1854 0.011 1.047 0.0 106.4 16.2 238 n/a 4_nqh: 0.0864 0.1851 0.011 1.047 0.0 106.4 16.2 238 n/a 4_sol: 0.1041 0.1781 0.011 1.047 0.0 106.4 16.3 227 n/a 4_weight: 0.1041 0.1781 0.011 1.047 0.0 106.4 16.3 227 n/a 4_xyzrec: 0.0927 0.1832 0.010 1.025 0.0 106.4 16.3 227 n/a 4_adp: 0.0897 0.1858 0.010 1.025 0.0 105.7 16.5 227 n/a 4_regHadp: 0.0901 0.1866 0.010 1.025 0.0 105.7 16.5 227 n/a 4_occ: 0.0890 0.1855 0.010 1.025 0.0 105.7 16.5 227 n/a 5_bss: 0.0889 0.1859 0.010 1.025 0.0 105.7 16.5 227 n/a 5_settarget: 0.0889 0.1859 0.010 1.025 0.0 105.7 16.5 227 n/a 5_updatecdl: 0.0889 0.1859 0.010 1.029 0.0 105.7 16.5 227 n/a 5_setrh: 0.0892 0.1860 0.010 1.029 0.0 105.7 16.5 227 n/a 5_nqh: 0.0894 0.1863 0.010 1.029 0.0 105.7 16.5 227 n/a 5_sol: 0.0990 0.1833 0.010 1.029 0.0 105.7 16.5 215 n/a 5_weight: 0.0990 0.1833 0.010 1.029 0.0 105.7 16.5 215 n/a 5_xyzrec: 0.0925 0.1855 0.010 1.083 0.0 105.7 16.5 215 n/a 5_adp: 0.0905 0.1865 0.010 1.083 0.0 107.3 16.7 215 n/a 5_regHadp: 0.0909 0.1868 0.010 1.083 0.0 107.3 16.7 215 n/a 5_occ: 0.0902 0.1853 0.010 1.083 0.0 107.3 16.7 215 n/a end: 0.0901 0.1849 0.010 1.083 0.0 107.3 16.7 215 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3337960_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3337960_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.8200 Refinement macro-cycles (run) : 487.2000 Write final files (write_after_run_outputs) : 10.2000 Total : 500.2200 Total CPU time: 8.68 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:02 PST -0800 (1735492742.05 s) Start R-work = 0.1549, R-free = 0.1575 Final R-work = 0.0901, R-free = 0.1849 =============================================================================== Job complete usr+sys time: 528.36 seconds wall clock time: 9 minutes 10.65 seconds (550.65 seconds total)