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_6017437.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6017437.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6017437.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" 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" } 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: 1.21, per 1000 atoms: 0.36 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: 0.33 Conformation dependent library (CDL) restraints added in 119.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.89: 392 0.89 - 1.16: 1231 1.16 - 1.43: 698 1.43 - 1.70: 807 1.70 - 1.97: 25 Bond restraints: 3153 Sorted by residual: bond pdb=" N MET A 17 " pdb=" CA MET A 17 " ideal model delta sigma weight residual 1.459 1.669 -0.210 1.19e-02 7.06e+03 3.11e+02 bond pdb=" CA ALA A 36 " pdb=" C ALA A 36 " ideal model delta sigma weight residual 1.525 1.309 0.216 1.28e-02 6.10e+03 2.85e+02 bond pdb=" C LYS A 122 " pdb=" N VAL A 123 " ideal model delta sigma weight residual 1.332 1.134 0.198 1.20e-02 6.94e+03 2.73e+02 bond pdb=" CG HIS A 115 " pdb=" ND1 HIS A 115 " ideal model delta sigma weight residual 1.378 1.201 0.177 1.10e-02 8.26e+03 2.59e+02 bond pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 1.330 1.539 -0.209 1.30e-02 5.92e+03 2.58e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 2948 4.41 - 8.82: 1933 8.82 - 13.22: 713 13.22 - 17.63: 166 17.63 - 22.03: 17 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 181 " pdb=" C VAL A 181 " pdb=" N LYS A 182 " ideal model delta sigma weight residual 121.87 104.73 17.14 9.70e-01 1.06e+00 3.12e+02 angle pdb=" CA LEU A 58 " pdb=" C LEU A 58 " pdb=" O LEU A 58 " ideal model delta sigma weight residual 120.92 137.20 -16.28 1.12e+00 7.97e-01 2.11e+02 angle pdb=" O GLY A 120 " pdb=" C GLY A 120 " pdb=" N SER A 121 " ideal model delta sigma weight residual 122.77 110.06 12.71 9.40e-01 1.13e+00 1.83e+02 angle pdb=" N PRO A 43 " pdb=" CA PRO A 43 " pdb=" CB PRO A 43 " ideal model delta sigma weight residual 103.32 114.67 -11.35 8.40e-01 1.42e+00 1.83e+02 angle pdb=" O LYS A 130 " pdb=" C LYS A 130 " pdb=" N ASP A 131 " ideal model delta sigma weight residual 122.07 109.18 12.89 1.03e+00 9.43e-01 1.57e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.29: 1310 17.29 - 34.58: 121 34.58 - 51.86: 32 51.86 - 69.15: 16 69.15 - 86.43: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C AGLU A 94 " pdb=" N AGLU A 94 " pdb=" CA AGLU A 94 " pdb=" CB AGLU A 94 " ideal model delta harmonic sigma weight residual -122.60 -142.08 19.48 0 2.50e+00 1.60e-01 6.07e+01 dihedral pdb=" C ALA A 86 " pdb=" N ALA A 86 " pdb=" CA ALA A 86 " pdb=" CB ALA A 86 " ideal model delta harmonic sigma weight residual -122.60 -141.23 18.63 0 2.50e+00 1.60e-01 5.55e+01 dihedral pdb=" N ALA A 14 " pdb=" C ALA A 14 " pdb=" CA ALA A 14 " pdb=" CB ALA A 14 " ideal model delta harmonic sigma weight residual 122.90 105.05 17.85 0 2.50e+00 1.60e-01 5.10e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.195: 102 0.195 - 0.390: 66 0.390 - 0.585: 44 0.585 - 0.779: 22 0.779 - 0.974: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA PRO A 127 " pdb=" N PRO A 127 " pdb=" C PRO A 127 " pdb=" CB PRO A 127 " both_signs ideal model delta sigma weight residual False 2.72 1.74 0.97 2.00e-01 2.50e+01 2.37e+01 chirality pdb=" CA BGLU A 94 " pdb=" N BGLU A 94 " pdb=" C BGLU A 94 " pdb=" CB BGLU A 94 " both_signs ideal model delta sigma weight residual False 2.51 3.42 -0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.74 -0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.076 2.00e-02 2.50e+03 6.01e-02 1.08e+02 pdb=" CG PHE A 119 " -0.087 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.062 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.078 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.107 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.041 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.072 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.006 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.032 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.022 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.049 2.00e-02 2.50e+03 5.91e-02 1.05e+02 pdb=" CG PHE A 164 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.138 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.035 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.089 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.019 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.014 2.00e-02 2.50e+03 6.46e-02 9.40e+01 pdb=" CG HIS A 115 " 0.072 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " 0.094 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " -0.115 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " -0.068 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " 0.011 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " 0.065 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 900 2.30 - 2.88: 8022 2.88 - 3.45: 10553 3.45 - 4.03: 15292 4.03 - 4.60: 21823 Nonbonded interactions: 56590 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.726 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.817 2.450 x-y,-y,-z-4/3 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.832 2.450 nonbonded pdb=" O LEU A 7 " pdb=" H VAL A 71 " model vdw 1.839 2.450 nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.850 2.450 ... (remaining 56585 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_6017437_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= 0.3624 r_free= 0.2021 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.472007 | | target function (ml) not normalized (work): 22046.993307 | | target function (ml) not normalized (free): 1156.914359 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3807 0.2208 4.8569 4.9143| | 2: 3.78 - 3.00 1.00 2430 110 0.3400 0.1706 4.076 4.1735| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.85 0.83 0.13 6614.09| | 2: 3.78 - 3.00 2430 110 0.93 11.47 1.48 0.26 454.13| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 383.02 max = 12065.49 mean = 3577.84| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.43| |phase err.(test): min = 0.00 max = 89.89 mean = 33.16| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.273 1557 Z= 5.355 Angle : 5.322 17.136 2118 Z= 3.696 Chirality : 0.367 0.974 243 Planarity : 0.032 0.088 284 Dihedral : 13.812 86.433 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 1.08 % Allowed : 3.24 % Favored : 95.68 % Rotamer: Outliers : 0.62 % Allowed : 4.35 % Favored : 95.03 % Cbeta Deviations : 32.97 % 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: -2.79 (0.45), residues: 224 helix: -2.86 (0.34), residues: 106 sheet: -2.09 (0.75), residues: 28 loop : -0.04 (0.57), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.083 0.017 ARG A 48 TYR 0.064 0.030 TYR A 141 PHE 0.103 0.044 PHE A 119 HIS 0.073 0.031 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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3624 r_free= 0.2021 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.472007 | | target function (ml) not normalized (work): 22046.993307 | | target function (ml) not normalized (free): 1156.914359 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3580 0.3657 0.2123 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3580 0.3657 0.2123 n_refl.: 5182 remove outliers: r(all,work,free)=0.2530 0.2555 0.2123 n_refl.: 5178 overall B=-2.45 to atoms: r(all,work,free)=0.2435 0.2457 0.2093 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1576 0.1574 0.1626 n_refl.: 5178 remove outliers: r(all,work,free)=0.1572 0.1569 0.1626 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 0.3847 449.886 410.740 0.637 1.072 0.404 11.894-9.307 99.02 97 4 0.1857 714.681 698.504 0.900 1.068 0.392 9.237-7.194 100.00 213 7 0.2175 584.467 575.270 0.934 1.061 0.363 7.162-5.571 100.00 427 22 0.2357 438.571 423.961 0.897 1.047 0.292 5.546-4.326 100.00 867 58 0.1394 602.096 594.114 0.944 1.026 0.215 4.315-3.360 100.00 1859 96 0.1318 572.600 566.289 1.027 0.989 0.199 3.356-3.002 100.00 1373 60 0.1611 441.041 433.175 1.041 0.953 0.064 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9173 b_overall=-4.2588 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1569 r_free=0.1626 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 r_work=0.1577 r_free=0.1639 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.152893 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.944398 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 0.1156 0.1808 0.0652 0.009 0.9 2.6 0.5 0.0 0 9.076 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.56 18.08 6.52 3.013 16.404 1.944 0.018 10.16 18.11 7.95 5.092 16.641 1.944 0.014 Individual atomic B min max mean iso aniso Overall: 2.11 111.84 17.88 5.45 1785 0 Protein: 2.11 111.20 15.16 5.44 1519 0 Water: 4.41 111.84 33.67 N/A 258 0 Other: 16.70 37.13 24.56 N/A 8 0 Chain A: 2.11 111.84 17.88 N/A 1785 0 Histogram: Values Number of atoms 2.11 - 13.09 883 13.09 - 24.06 502 24.06 - 35.03 197 35.03 - 46.01 111 46.01 - 56.98 59 56.98 - 67.95 15 67.95 - 78.93 8 78.93 - 89.90 6 89.90 - 100.87 1 100.87 - 111.84 3 =========================== Idealize ADP of riding H ========================== r_work=0.1016 r_free=0.1811 r_work=0.1010 r_free=0.1816 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1010 r_free = 0.1816 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 = 0.1003 r_free = 0.1816 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 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= 0.1003 r_free= 0.1816 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.013810 | | target function (ls_wunit_k1) not normalized (work): 68.001481 | | target function (ls_wunit_k1) not normalized (free): 10.817065 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1044 0.1003 0.1816 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2101 0.2100 0.2235 n_refl.: 5176 remove outliers: r(all,work,free)=0.2101 0.2100 0.2235 n_refl.: 5176 overall B=-1.06 to atoms: r(all,work,free)=0.2055 0.2053 0.2222 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1048 0.1007 0.1821 n_refl.: 5176 remove outliers: r(all,work,free)=0.1048 0.1007 0.1821 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 0.3322 317.964 301.933 0.671 1.024 0.385 11.894-9.307 99.02 97 4 0.1496 505.111 496.733 0.973 1.024 0.358 9.237-7.194 100.00 213 7 0.1658 413.080 413.564 1.010 1.021 0.320 7.162-5.571 100.00 427 22 0.1640 309.967 306.182 0.973 1.017 0.292 5.546-4.326 100.00 867 58 0.0900 425.540 422.669 0.994 1.009 0.202 4.315-3.360 100.00 1859 96 0.0759 404.693 404.662 1.054 0.995 0.194 3.356-3.002 100.00 1373 60 0.0996 311.712 310.281 1.036 0.982 0.051 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.7997 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1007 r_free=0.1821 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1007 r_free=0.1821 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1007 r_free=0.1821 | n_water=258 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.1034 r_free=0.1817 | n_water=249 | time (s): 21.160 (total time: 21.820) Filter (q & B) r_work=0.1036 r_free=0.1821 | n_water=246 | time (s): 1.220 (total time: 23.040) Compute maps r_work=0.1036 r_free=0.1821 | n_water=246 | time (s): 0.470 (total time: 23.510) Filter (map) r_work=0.1342 r_free=0.1877 | n_water=147 | time (s): 1.590 (total time: 25.100) Find peaks r_work=0.1342 r_free=0.1877 | n_water=147 | time (s): 0.430 (total time: 25.530) Add new water r_work=0.1696 r_free=0.2150 | n_water=237 | time (s): 1.150 (total time: 26.680) Refine new water occ: r_work=0.1164 r_free=0.1701 adp: r_work=0.1134 r_free=0.1712 occ: r_work=0.1136 r_free=0.1677 adp: r_work=0.1120 r_free=0.1687 occ: r_work=0.1120 r_free=0.1672 adp: r_work=0.1117 r_free=0.1675 ADP+occupancy (water only), MIN, final r_work=0.1117 r_free=0.1675 r_work=0.1117 r_free=0.1675 | n_water=237 | time (s): 7.940 (total time: 34.620) Filter (q & B) r_work=0.1117 r_free=0.1675 | n_water=237 | time (s): 0.810 (total time: 35.430) Filter (dist only) r_work=0.1118 r_free=0.1670 | n_water=236 | time (s): 20.840 (total time: 56.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.721883 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.604582 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 0.1001 0.1767 0.0765 0.009 1.0 5.1 0.5 0.6 0 11.361 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.01 17.67 7.65 4.791 17.274 2.605 0.014 9.39 17.86 8.47 5.346 17.583 2.605 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 108.07 16.91 6.28 1763 0 Protein: 1.06 108.07 15.20 6.27 1519 0 Water: 0.00 74.87 27.61 N/A 236 0 Other: 13.19 36.36 24.85 N/A 8 0 Chain A: 0.00 108.07 16.02 N/A 1673 0 Chain S: 2.56 63.70 33.39 N/A 90 0 Histogram: Values Number of atoms 0.00 - 10.81 668 10.81 - 21.61 681 21.61 - 32.42 214 32.42 - 43.23 118 43.23 - 54.03 39 54.03 - 64.84 29 64.84 - 75.65 7 75.65 - 86.45 3 86.45 - 97.26 2 97.26 - 108.07 2 =========================== Idealize ADP of riding H ========================== r_work=0.0939 r_free=0.1786 r_work=0.0937 r_free=0.1789 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0937 r_free = 0.1789 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0932 r_free = 0.1783 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.28 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= 0.0932 r_free= 0.1783 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ls_wunit_k1) (work): 0.011882 | | target function (ls_wunit_k1) not normalized (work): 58.508976 | | target function (ls_wunit_k1) not normalized (free): 9.668652 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0974 0.0932 0.1783 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2104 0.2108 0.2191 n_refl.: 5176 remove outliers: r(all,work,free)=0.2104 0.2108 0.2191 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2104 0.2108 0.2191 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0976 0.0934 0.1794 n_refl.: 5176 remove outliers: r(all,work,free)=0.0974 0.0932 0.1794 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 0.3174 315.286 303.572 0.680 1.012 0.374 11.894-9.307 99.02 97 4 0.1484 505.111 501.199 0.975 1.013 0.355 9.237-7.194 100.00 213 7 0.1466 413.080 415.120 1.014 1.012 0.300 7.162-5.571 100.00 427 22 0.1384 309.967 307.469 0.990 1.010 0.290 5.546-4.326 100.00 867 58 0.0794 425.540 422.592 1.004 1.006 0.230 4.315-3.360 100.00 1859 96 0.0717 404.693 404.247 1.058 0.999 0.200 3.356-3.002 100.00 1373 60 0.0967 311.712 311.271 1.036 0.992 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-4.2216 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0932 r_free=0.1794 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.0937 r_free=0.1788 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0937 r_free=0.1788 | n_water=236 | time (s): 0.590 (total time: 0.590) Filter (dist) r_work=0.0952 r_free=0.1764 | n_water=231 | time (s): 18.920 (total time: 19.510) Filter (q & B) r_work=0.1011 r_free=0.1797 | n_water=229 | time (s): 1.720 (total time: 21.230) Compute maps r_work=0.1011 r_free=0.1797 | n_water=229 | time (s): 0.600 (total time: 21.830) Filter (map) r_work=0.1284 r_free=0.1841 | n_water=149 | time (s): 2.010 (total time: 23.840) Find peaks r_work=0.1284 r_free=0.1841 | n_water=149 | time (s): 0.470 (total time: 24.310) Add new water r_work=0.1653 r_free=0.2157 | n_water=230 | time (s): 1.770 (total time: 26.080) Refine new water occ: r_work=0.1084 r_free=0.1737 adp: r_work=0.1079 r_free=0.1741 occ: r_work=0.1067 r_free=0.1726 adp: r_work=0.1068 r_free=0.1731 occ: r_work=0.1058 r_free=0.1716 adp: r_work=0.1058 r_free=0.1725 ADP+occupancy (water only), MIN, final r_work=0.1058 r_free=0.1725 r_work=0.1058 r_free=0.1725 | n_water=230 | time (s): 12.020 (total time: 38.100) Filter (q & B) r_work=0.1058 r_free=0.1725 | n_water=230 | time (s): 1.140 (total time: 39.240) Filter (dist only) r_work=0.1072 r_free=0.1725 | n_water=227 | time (s): 17.330 (total time: 56.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.049980 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.238679 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 0.0973 0.1787 0.0814 0.011 1.0 4.5 0.5 0.0 0 0.525 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.73 17.87 8.14 5.291 17.976 0.239 5.157 9.27 17.99 8.72 7.407 17.978 0.239 5.056 Individual atomic B min max mean iso aniso Overall: 0.00 107.82 16.57 9.08 1754 0 Protein: 0.00 107.82 15.33 9.07 1519 0 Water: 0.00 58.07 24.49 N/A 227 0 Other: 15.21 43.40 26.92 N/A 8 0 Chain A: 0.00 107.82 15.99 N/A 1656 0 Chain S: 0.00 54.32 26.41 N/A 98 0 Histogram: Values Number of atoms 0.00 - 10.78 650 10.78 - 21.56 683 21.56 - 32.35 228 32.35 - 43.13 124 43.13 - 53.91 31 53.91 - 64.69 21 64.69 - 75.47 7 75.47 - 86.26 5 86.26 - 97.04 4 97.04 - 107.82 1 =========================== Idealize ADP of riding H ========================== r_work=0.0927 r_free=0.1799 r_work=0.0934 r_free=0.1813 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0934 r_free = 0.1813 target_work(ml) = 5.060 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0919 r_free = 0.1788 target_work(ml) = 5.052 | | 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= 0.0919 r_free= 0.1788 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.051534 | | target function (ml) not normalized (work): 24868.702366 | | target function (ml) not normalized (free): 1810.357938 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0964 0.0919 0.1788 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2150 0.2159 0.2129 n_refl.: 5175 remove outliers: r(all,work,free)=0.2150 0.2159 0.2129 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2150 0.2159 0.2129 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0957 0.0913 0.1777 n_refl.: 5175 remove outliers: r(all,work,free)=0.0955 0.0911 0.1777 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 0.3608 317.383 286.663 0.602 0.999 0.342 11.894-9.307 99.02 97 4 0.1804 505.111 495.123 0.950 1.002 0.337 9.237-7.194 100.00 213 7 0.1891 413.080 409.784 0.992 1.003 0.300 7.162-5.571 100.00 427 22 0.1930 309.967 300.094 0.977 1.003 0.280 5.546-4.326 100.00 867 58 0.0931 425.540 420.731 0.999 1.002 0.240 4.315-3.360 100.00 1859 96 0.0624 404.693 404.170 1.062 1.001 0.210 3.356-3.002 100.00 1373 60 0.0608 311.712 311.165 1.040 0.999 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.5465 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0911 r_free=0.1777 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=0.0912 r_free=0.1783 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0912 r_free=0.1783 | n_water=227 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.0912 r_free=0.1788 | n_water=226 | time (s): 18.930 (total time: 19.530) Filter (q & B) r_work=0.0948 r_free=0.1818 | n_water=225 | time (s): 1.420 (total time: 20.950) Compute maps r_work=0.0948 r_free=0.1818 | n_water=225 | time (s): 0.510 (total time: 21.460) Filter (map) r_work=0.1198 r_free=0.1906 | n_water=162 | time (s): 1.290 (total time: 22.750) Find peaks r_work=0.1198 r_free=0.1906 | n_water=162 | time (s): 0.440 (total time: 23.190) Add new water r_work=0.1493 r_free=0.2227 | n_water=239 | time (s): 1.380 (total time: 24.570) Refine new water occ: r_work=0.0989 r_free=0.1805 adp: r_work=0.0984 r_free=0.1820 occ: r_work=0.0976 r_free=0.1792 adp: r_work=0.0975 r_free=0.1806 occ: r_work=0.0966 r_free=0.1779 adp: r_work=0.0966 r_free=0.1790 ADP+occupancy (water only), MIN, final r_work=0.0966 r_free=0.1790 r_work=0.0966 r_free=0.1790 | n_water=239 | time (s): 15.910 (total time: 40.480) Filter (q & B) r_work=0.0966 r_free=0.1794 | n_water=236 | time (s): 1.770 (total time: 42.250) Filter (dist only) r_work=0.0979 r_free=0.1809 | n_water=234 | time (s): 20.490 (total time: 62.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.955609 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.203388 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 0.0909 0.1898 0.0989 0.010 1.0 3.5 0.5 0.0 0 0.478 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.09 18.98 9.89 7.053 18.170 0.203 4.995 8.88 19.02 10.14 8.122 18.290 0.203 4.934 Individual atomic B min max mean iso aniso Overall: 0.00 108.32 16.99 10.62 1761 0 Protein: 0.00 108.32 15.76 10.61 1519 0 Water: 0.00 55.00 24.57 N/A 234 0 Other: 15.49 45.51 27.82 N/A 8 0 Chain A: 0.00 108.32 16.30 N/A 1647 0 Chain S: 0.00 55.00 26.87 N/A 114 0 Histogram: Values Number of atoms 0.00 - 10.83 638 10.83 - 21.66 673 21.66 - 32.50 254 32.50 - 43.33 116 43.33 - 54.16 46 54.16 - 64.99 16 64.99 - 75.82 7 75.82 - 86.66 7 86.66 - 97.49 3 97.49 - 108.32 1 =========================== Idealize ADP of riding H ========================== r_work=0.0888 r_free=0.1902 r_work=0.0893 r_free=0.1905 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0893 r_free = 0.1905 target_work(ml) = 4.939 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0880 r_free = 0.1883 target_work(ml) = 4.929 | | 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= 0.0880 r_free= 0.1883 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.929253 | | target function (ml) not normalized (work): 24261.785071 | | target function (ml) not normalized (free): 2167.561298 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0931 0.0880 0.1883 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2089 0.2089 0.2247 n_refl.: 5174 remove outliers: r(all,work,free)=0.2089 0.2089 0.2247 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2089 0.2089 0.2247 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0929 0.0879 0.1878 n_refl.: 5174 remove outliers: r(all,work,free)=0.0929 0.0879 0.1878 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 0.3765 317.383 292.071 0.601 0.987 0.330 11.894-9.307 99.02 97 4 0.1783 505.111 493.550 0.957 0.993 0.330 9.237-7.194 100.00 213 7 0.2116 413.080 407.258 1.002 0.996 0.290 7.162-5.571 100.00 427 22 0.2082 309.967 299.240 0.986 0.998 0.260 5.546-4.326 100.00 867 58 0.0963 425.540 420.015 1.010 1.000 0.225 4.315-3.360 100.00 1859 96 0.0570 404.693 404.355 1.081 1.002 0.220 3.356-3.002 100.00 1373 60 0.0436 311.712 311.744 1.057 1.004 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.4462 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0879 r_free=0.1878 After: r_work=0.0881 r_free=0.1876 ================================== NQH flips ================================== r_work=0.0881 r_free=0.1876 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=0.0883 r_free=0.1875 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0883 r_free=0.1875 | n_water=234 | time (s): 0.630 (total time: 0.630) Filter (dist) r_work=0.0890 r_free=0.1880 | n_water=232 | time (s): 19.480 (total time: 20.110) Filter (q & B) r_work=0.1028 r_free=0.1916 | n_water=228 | time (s): 1.490 (total time: 21.600) Compute maps r_work=0.1028 r_free=0.1916 | n_water=228 | time (s): 0.460 (total time: 22.060) Filter (map) r_work=0.1249 r_free=0.1962 | n_water=170 | time (s): 1.340 (total time: 23.400) Find peaks r_work=0.1249 r_free=0.1962 | n_water=170 | time (s): 0.410 (total time: 23.810) Add new water r_work=0.1468 r_free=0.2158 | n_water=232 | time (s): 1.340 (total time: 25.150) Refine new water occ: r_work=0.0977 r_free=0.1879 adp: r_work=0.0963 r_free=0.1884 occ: r_work=0.0958 r_free=0.1880 adp: r_work=0.0958 r_free=0.1880 occ: r_work=0.0953 r_free=0.1874 adp: r_work=0.0952 r_free=0.1874 ADP+occupancy (water only), MIN, final r_work=0.0952 r_free=0.1874 r_work=0.0952 r_free=0.1874 | n_water=232 | time (s): 11.170 (total time: 36.320) Filter (q & B) r_work=0.0952 r_free=0.1875 | n_water=229 | time (s): 1.510 (total time: 37.830) Filter (dist only) r_work=0.0952 r_free=0.1875 | n_water=229 | time (s): 16.500 (total time: 54.330) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.907634 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.203198 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 0.0912 0.1908 0.0996 0.011 1.1 8.0 0.5 0.0 0 0.454 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.12 19.08 9.96 8.079 18.528 0.203 4.967 8.95 19.48 10.53 8.875 18.614 0.203 4.909 Individual atomic B min max mean iso aniso Overall: 0.00 109.64 17.20 11.75 1756 0 Protein: 0.00 109.64 16.10 11.72 1519 0 Water: 0.00 60.59 24.16 N/A 229 0 Other: 10.98 45.52 27.59 N/A 8 0 Chain A: 0.00 109.64 16.57 N/A 1642 0 Chain S: 0.00 60.59 26.19 N/A 114 0 Histogram: Values Number of atoms 0.00 - 10.96 645 10.96 - 21.93 648 21.93 - 32.89 266 32.89 - 43.86 123 43.86 - 54.82 41 54.82 - 65.78 15 65.78 - 76.75 6 76.75 - 87.71 7 87.71 - 98.68 4 98.68 - 109.64 1 =========================== Idealize ADP of riding H ========================== r_work=0.0895 r_free=0.1948 r_work=0.0897 r_free=0.1955 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0897 r_free = 0.1955 target_work(ml) = 4.914 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0890 r_free = 0.1946 target_work(ml) = 4.908 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0890 r_free= 0.1946 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.908034 | | target function (ml) not normalized (work): 24157.344653 | | target function (ml) not normalized (free): 2345.770108 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1277 0.1898 5.5095 6.2016| | 2: 3.78 - 3.00 1.00 2430 110 0.0417 0.2028 4.2912 13.319| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 11.87 1.00 0.94 11940.39| | 2: 3.78 - 3.00 2430 110 0.99 1.77 1.00 0.97 815.85| |alpha: min = 0.93 max = 0.97 mean = 0.95| |beta: min = 509.95 max = 19760.10 mean = 6448.18| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.86 mean = 6.89| |phase err.(test): min = 0.00 max = 72.87 mean = 6.85| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0944 0.0890 0.1946 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2148 0.2147 0.2331 n_refl.: 5174 remove outliers: r(all,work,free)=0.2148 0.2147 0.2331 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2148 0.2147 0.2331 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0943 0.0889 0.1956 n_refl.: 5174 remove outliers: r(all,work,free)=0.0943 0.0889 0.1956 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 0.3738 317.383 285.698 0.592 0.986 0.330 11.894-9.307 99.02 97 4 0.1808 505.111 500.909 0.971 0.992 0.330 9.237-7.194 100.00 213 7 0.2136 413.080 407.836 1.011 0.996 0.290 7.162-5.571 100.00 427 22 0.2080 309.967 300.121 0.992 0.997 0.290 5.546-4.326 100.00 867 58 0.1036 425.540 419.199 1.011 1.000 0.235 4.315-3.360 100.00 1859 96 0.0580 404.693 404.685 1.097 1.002 0.230 3.356-3.002 100.00 1373 60 0.0396 311.712 311.469 1.071 1.005 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.0861 ================= 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 : 0.3624 0.2021 0.081 5.322 8.8 119.3 19.9 258 0.000 1_bss: 0.1569 0.1626 0.081 5.322 6.4 116.8 17.4 258 0.000 1_settarget: 0.1569 0.1626 0.081 5.322 6.4 116.8 17.4 258 0.000 1_nqh: 0.1577 0.1639 0.081 5.322 6.4 116.8 17.4 258 0.007 1_weight: 0.1577 0.1639 0.081 5.322 6.4 116.8 17.4 258 0.007 1_xyzrec: 0.1156 0.1808 0.009 0.943 6.4 116.8 17.4 258 0.218 1_adp: 0.1016 0.1811 0.009 0.943 2.1 111.8 17.9 258 0.218 1_regHadp: 0.1010 0.1816 0.009 0.943 2.1 111.8 17.9 258 0.218 1_occ: 0.1003 0.1816 0.009 0.943 2.1 111.8 17.9 258 0.218 2_bss: 0.1007 0.1821 0.009 0.943 1.1 110.8 16.8 258 0.218 2_settarget: 0.1007 0.1821 0.009 0.943 1.1 110.8 16.8 258 0.218 2_updatecdl: 0.1007 0.1821 0.009 0.975 1.1 110.8 16.8 258 0.218 2_nqh: 0.1007 0.1821 0.009 0.975 1.1 110.8 16.8 258 0.218 2_sol: 0.1118 0.1670 0.009 0.975 1.1 110.1 16.3 236 n/a 2_weight: 0.1118 0.1670 0.009 0.975 1.1 110.1 16.3 236 n/a 2_xyzrec: 0.1001 0.1767 0.009 0.969 1.1 110.1 16.3 236 n/a 2_adp: 0.0939 0.1786 0.009 0.969 0.0 108.1 16.9 236 n/a 2_regHadp: 0.0937 0.1789 0.009 0.969 0.0 108.1 16.9 236 n/a 2_occ: 0.0932 0.1783 0.009 0.969 0.0 108.1 16.9 236 n/a 3_bss: 0.0932 0.1794 0.009 0.969 0.0 108.1 16.9 236 n/a 3_settarget: 0.0932 0.1794 0.009 0.969 0.0 108.1 16.9 236 n/a 3_updatecdl: 0.0932 0.1794 0.009 0.979 0.0 108.1 16.9 236 n/a 3_nqh: 0.0937 0.1788 0.009 0.979 0.0 108.1 16.9 236 n/a 3_sol: 0.1072 0.1725 0.009 0.979 1.0 108.1 16.6 227 n/a 3_weight: 0.1072 0.1725 0.009 0.979 1.0 108.1 16.6 227 n/a 3_xyzrec: 0.0973 0.1787 0.011 1.016 1.0 108.1 16.6 227 n/a 3_adp: 0.0927 0.1799 0.011 1.016 0.0 107.8 16.6 227 n/a 3_regHadp: 0.0934 0.1813 0.011 1.016 0.0 107.8 16.6 227 n/a 3_occ: 0.0919 0.1788 0.011 1.016 0.0 107.8 16.6 227 n/a 4_bss: 0.0911 0.1777 0.011 1.016 0.0 107.8 16.6 227 n/a 4_settarget: 0.0911 0.1777 0.011 1.016 0.0 107.8 16.6 227 n/a 4_updatecdl: 0.0911 0.1777 0.011 1.021 0.0 107.8 16.6 227 n/a 4_nqh: 0.0912 0.1783 0.011 1.021 0.0 107.8 16.6 227 n/a 4_sol: 0.0979 0.1809 0.011 1.021 0.0 107.8 16.8 234 n/a 4_weight: 0.0979 0.1809 0.011 1.021 0.0 107.8 16.8 234 n/a 4_xyzrec: 0.0909 0.1898 0.010 1.015 0.0 107.8 16.8 234 n/a 4_adp: 0.0888 0.1902 0.010 1.015 0.0 108.3 17.0 234 n/a 4_regHadp: 0.0893 0.1905 0.010 1.015 0.0 108.3 17.0 234 n/a 4_occ: 0.0880 0.1883 0.010 1.015 0.0 108.3 17.0 234 n/a 5_bss: 0.0879 0.1878 0.010 1.015 0.0 108.3 17.0 234 n/a 5_settarget: 0.0879 0.1878 0.010 1.015 0.0 108.3 17.0 234 n/a 5_updatecdl: 0.0879 0.1878 0.010 1.021 0.0 108.3 17.0 234 n/a 5_setrh: 0.0881 0.1876 0.010 1.021 0.0 108.3 17.0 234 n/a 5_nqh: 0.0883 0.1875 0.010 1.021 0.0 108.3 17.0 234 n/a 5_sol: 0.0952 0.1875 0.010 1.021 0.0 108.3 17.0 229 n/a 5_weight: 0.0952 0.1875 0.010 1.021 0.0 108.3 17.0 229 n/a 5_xyzrec: 0.0912 0.1908 0.011 1.094 0.0 108.3 17.0 229 n/a 5_adp: 0.0895 0.1948 0.011 1.094 0.0 109.6 17.2 229 n/a 5_regHadp: 0.0897 0.1955 0.011 1.094 0.0 109.6 17.2 229 n/a 5_occ: 0.0890 0.1946 0.011 1.094 0.0 109.6 17.2 229 n/a end: 0.0889 0.1956 0.011 1.094 0.0 109.6 17.2 229 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6017437_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6017437_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.6100 Refinement macro-cycles (run) : 501.1200 Write final files (write_after_run_outputs) : 9.0600 Total : 513.7900 Total CPU time: 8.91 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:16 PST -0800 (1735492756.19 s) Start R-work = 0.1569, R-free = 0.1626 Final R-work = 0.0889, R-free = 0.1956 =============================================================================== Job complete usr+sys time: 541.86 seconds wall clock time: 9 minutes 24.32 seconds (564.32 seconds total)