Starting phenix.refine on Sun Dec 29 09:10:03 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9171019.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 { 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_9171019.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9171019.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== 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: 1.79, per 1000 atoms: 0.53 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: 0.39 Conformation dependent library (CDL) restraints added in 146.6 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.93: 574 0.93 - 1.20: 1102 1.20 - 1.46: 785 1.46 - 1.73: 677 1.73 - 2.00: 15 Bond restraints: 3153 Sorted by residual: bond pdb=" CA BLYS A 93 " pdb=" C BLYS A 93 " ideal model delta sigma weight residual 1.524 1.760 -0.236 1.27e-02 6.20e+03 3.45e+02 bond pdb=" N PRO A 184 " pdb=" CA PRO A 184 " ideal model delta sigma weight residual 1.470 1.246 0.224 1.22e-02 6.72e+03 3.36e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.140 0.181 1.00e-02 1.00e+04 3.27e+02 bond pdb=" C VAL A 146 " pdb=" O VAL A 146 " ideal model delta sigma weight residual 1.236 1.411 -0.175 9.90e-03 1.02e+04 3.12e+02 bond pdb=" C GLU A 143 " pdb=" N ASN A 144 " ideal model delta sigma weight residual 1.331 1.557 -0.226 1.31e-02 5.83e+03 2.97e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.15: 3445 5.15 - 10.29: 1760 10.29 - 15.44: 505 15.44 - 20.58: 60 20.58 - 25.73: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA GLU A 143 " pdb=" C GLU A 143 " pdb=" O GLU A 143 " ideal model delta sigma weight residual 119.32 137.03 -17.71 1.19e+00 7.06e-01 2.21e+02 angle pdb=" O VAL A 25 " pdb=" C VAL A 25 " pdb=" N MET A 26 " ideal model delta sigma weight residual 121.91 107.67 14.24 9.80e-01 1.04e+00 2.11e+02 angle pdb=" O VAL A 51 " pdb=" C VAL A 51 " pdb=" N ILE A 52 " ideal model delta sigma weight residual 123.20 137.97 -14.77 1.06e+00 8.90e-01 1.94e+02 angle pdb=" OD1 ASN A 81 " pdb=" CG ASN A 81 " pdb=" ND2 ASN A 81 " ideal model delta sigma weight residual 122.60 109.16 13.44 1.00e+00 1.00e+00 1.81e+02 angle pdb=" C BCYS A 53 " pdb=" N PRO A 54 " pdb=" CA PRO A 54 " ideal model delta sigma weight residual 119.85 133.37 -13.52 1.01e+00 9.80e-01 1.79e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 1308 17.88 - 35.76: 128 35.76 - 53.64: 33 53.64 - 71.53: 11 71.53 - 89.41: 1 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C THR A 110 " pdb=" N THR A 110 " pdb=" CA THR A 110 " pdb=" CB THR A 110 " ideal model delta harmonic sigma weight residual -122.00 -139.44 17.44 0 2.50e+00 1.60e-01 4.86e+01 dihedral pdb=" C ILE A 105 " pdb=" N ILE A 105 " pdb=" CA ILE A 105 " pdb=" CB ILE A 105 " ideal model delta harmonic sigma weight residual -122.00 -139.24 17.24 0 2.50e+00 1.60e-01 4.76e+01 dihedral pdb=" N GLU A 116 " pdb=" C GLU A 116 " pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " ideal model delta harmonic sigma weight residual 122.80 139.77 -16.97 0 2.50e+00 1.60e-01 4.61e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.192: 98 0.192 - 0.383: 67 0.383 - 0.573: 45 0.573 - 0.764: 23 0.764 - 0.954: 10 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA THR A 34 " pdb=" N THR A 34 " pdb=" C THR A 34 " pdb=" CB THR A 34 " both_signs ideal model delta sigma weight residual False 2.53 3.48 -0.95 2.00e-01 2.50e+01 2.28e+01 chirality pdb=" CA ASP A 49 " pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CB ASP A 49 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CA VAL A 25 " pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CB VAL A 25 " both_signs ideal model delta sigma weight residual False 2.44 1.55 0.90 2.00e-01 2.50e+01 2.01e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.113 2.00e-02 2.50e+03 6.52e-02 1.28e+02 pdb=" CG PHE A 119 " -0.179 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.051 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.020 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.020 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.035 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.071 2.00e-02 2.50e+03 5.79e-02 1.01e+02 pdb=" CG PHE A 164 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.121 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.026 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.076 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.033 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 95 " -0.043 2.00e-02 2.50e+03 9.32e-02 8.69e+01 pdb=" C GLN A 95 " 0.161 2.00e-02 2.50e+03 pdb=" O GLN A 95 " -0.060 2.00e-02 2.50e+03 pdb=" N AGLU A 96 " -0.058 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 841 2.29 - 2.87: 7976 2.87 - 3.44: 10512 3.44 - 4.02: 15324 4.02 - 4.60: 21971 Nonbonded interactions: 56624 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.712 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.765 2.100 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.795 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.834 2.450 nonbonded pdb=" O GLU A 147 " pdb=" H ATHR A 154 " model vdw 1.855 2.450 ... (remaining 56619 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_9171019_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= 0.3617 r_free= 0.2032 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.472311 | | target function (ml) not normalized (work): 22048.494726 | | target function (ml) not normalized (free): 1152.493105 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3798 0.2238 4.8503 4.9145| | 2: 3.78 - 3.00 1.00 2430 110 0.3396 0.1685 4.0834 4.1331| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.77 0.83 0.13 6604.83| | 2: 3.78 - 3.00 2430 110 0.93 11.56 1.48 0.26 460.77| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 396.59 max = 12063.12 mean = 3576.42| |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 = 89.98 mean = 33.36| |-----------------------------------------------------------------------------| ----------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 : 0.079 0.236 1557 Z= 5.337 Angle : 5.264 22.096 2118 Z= 3.767 Chirality : 0.373 0.954 243 Planarity : 0.033 0.166 284 Dihedral : 13.785 89.406 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % Cbeta Deviations : 26.49 % 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: -2.56 (0.49), residues: 224 helix: -2.67 (0.40), residues: 102 sheet: -0.50 (0.82), residues: 38 loop : -0.62 (0.60), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.100 0.023 ARG A 28 TYR 0.090 0.032 TYR A 141 PHE 0.185 0.046 PHE A 119 HIS 0.090 0.040 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= 0.3617 r_free= 0.2032 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.472311 | | target function (ml) not normalized (work): 22048.494726 | | target function (ml) not normalized (free): 1152.493105 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3571 0.3647 0.2149 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3571 0.3647 0.2149 n_refl.: 5182 remove outliers: r(all,work,free)=0.2525 0.2549 0.2149 n_refl.: 5178 overall B=-2.90 to atoms: r(all,work,free)=0.2414 0.2434 0.2114 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1579 0.1575 0.1654 n_refl.: 5178 remove outliers: r(all,work,free)=0.1577 0.1572 0.1654 n_refl.: 5177 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.4115 445.198 408.792 0.677 1.051 0.400 11.894-9.307 99.02 97 4 0.1837 714.710 698.021 0.958 1.048 0.382 9.237-7.194 100.00 213 7 0.2178 584.491 579.193 0.985 1.043 0.353 7.162-5.571 100.00 427 22 0.2323 438.589 424.864 0.942 1.033 0.288 5.546-4.326 100.00 867 58 0.1393 602.121 594.755 0.993 1.018 0.216 4.315-3.360 100.00 1859 96 0.1342 572.624 565.801 1.052 0.992 0.190 3.356-3.002 100.00 1373 60 0.1576 441.059 433.212 1.055 0.967 0.086 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.7232 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1572 r_free=0.1654 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 144 ASN A 173 ASN A 180 GLN Total number of N/Q/H flips: 4 r_work=0.1574 r_free=0.1657 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.890632 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.871634 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 0.1154 0.1799 0.0645 0.010 1.0 3.2 0.5 0.0 0 9.445 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.54 17.99 6.45 3.013 15.962 1.872 0.018 10.20 17.83 7.63 4.770 16.127 1.872 0.015 Individual atomic B min max mean iso aniso Overall: 1.87 111.40 17.30 5.18 1785 0 Protein: 1.87 110.89 14.58 5.17 1519 0 Water: 3.97 111.40 33.11 N/A 258 0 Other: 16.46 36.55 23.54 N/A 8 0 Chain A: 1.87 111.40 17.30 N/A 1785 0 Histogram: Values Number of atoms 1.87 - 12.83 914 12.83 - 23.78 481 23.78 - 34.73 193 34.73 - 45.69 106 45.69 - 56.64 60 56.64 - 67.59 14 67.59 - 78.54 8 78.54 - 89.50 5 89.50 - 100.45 1 100.45 - 111.40 3 =========================== Idealize ADP of riding H ========================== r_work=0.1020 r_free=0.1783 r_work=0.1014 r_free=0.1788 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1014 r_free = 0.1788 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 = 0.1006 r_free = 0.1783 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1006 r_free= 0.1783 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.013996 | | target function (ls_wunit_k1) not normalized (work): 68.928173 | | target function (ls_wunit_k1) not normalized (free): 10.415717 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1045 0.1006 0.1783 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2087 0.2085 0.2230 n_refl.: 5177 remove outliers: r(all,work,free)=0.2087 0.2085 0.2230 n_refl.: 5177 overall B=-1.00 to atoms: r(all,work,free)=0.2044 0.2041 0.2219 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1049 0.1009 0.1787 n_refl.: 5177 remove outliers: r(all,work,free)=0.1047 0.1007 0.1787 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 0.3397 324.878 307.962 0.665 1.003 0.370 11.894-9.307 99.02 97 4 0.1502 526.041 519.247 0.996 1.004 0.361 9.237-7.194 100.00 213 7 0.1674 430.197 431.449 1.033 1.004 0.315 7.162-5.571 100.00 427 22 0.1646 322.811 319.047 0.986 1.003 0.292 5.546-4.326 100.00 867 58 0.0888 443.173 440.239 1.003 1.002 0.187 4.315-3.360 100.00 1859 96 0.0758 421.462 421.312 1.043 1.000 0.183 3.356-3.002 100.00 1373 60 0.1004 324.628 323.134 1.014 0.998 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.5727 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1007 r_free=0.1787 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A A 144 ASN A 173 ASN A 180 GLN Total number of N/Q/H flips: 4 r_work=0.1012 r_free=0.1792 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1012 r_free=0.1792 | n_water=258 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.1032 r_free=0.1775 | n_water=251 | time (s): 21.360 (total time: 22.000) Filter (q & B) r_work=0.1033 r_free=0.1777 | n_water=248 | time (s): 1.480 (total time: 23.480) Compute maps r_work=0.1033 r_free=0.1777 | n_water=248 | time (s): 0.650 (total time: 24.130) Filter (map) r_work=0.1318 r_free=0.1883 | n_water=152 | time (s): 1.870 (total time: 26.000) Find peaks r_work=0.1318 r_free=0.1883 | n_water=152 | time (s): 0.490 (total time: 26.490) Add new water r_work=0.1668 r_free=0.2215 | n_water=244 | time (s): 1.620 (total time: 28.110) Refine new water occ: r_work=0.1151 r_free=0.1696 adp: r_work=0.1124 r_free=0.1695 occ: r_work=0.1122 r_free=0.1666 adp: r_work=0.1109 r_free=0.1669 occ: r_work=0.1108 r_free=0.1651 adp: r_work=0.1104 r_free=0.1652 ADP+occupancy (water only), MIN, final r_work=0.1104 r_free=0.1652 r_work=0.1104 r_free=0.1652 | n_water=244 | time (s): 4.520 (total time: 32.630) Filter (q & B) r_work=0.1104 r_free=0.1655 | n_water=243 | time (s): 1.560 (total time: 34.190) Filter (dist only) r_work=0.1102 r_free=0.1653 | n_water=242 | time (s): 18.320 (total time: 52.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.444317 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.714225 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 0.0992 0.1776 0.0784 0.010 1.0 4.2 0.5 0.6 0 12.722 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.92 17.76 7.84 4.587 16.716 2.714 0.013 9.27 17.90 8.63 5.410 17.062 2.714 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 106.27 16.55 6.39 1769 0 Protein: 0.00 106.27 14.74 6.38 1519 0 Water: 0.00 62.92 27.72 N/A 242 0 Other: 11.41 33.15 23.00 N/A 8 0 Chain A: 0.00 106.27 15.58 N/A 1678 0 Chain S: 4.07 61.98 34.51 N/A 91 0 Histogram: Values Number of atoms 0.00 - 10.63 694 10.63 - 21.25 647 21.25 - 31.88 223 31.88 - 42.51 116 42.51 - 53.13 44 53.13 - 63.76 32 63.76 - 74.39 6 74.39 - 85.01 2 85.01 - 95.64 2 95.64 - 106.27 3 =========================== Idealize ADP of riding H ========================== r_work=0.0927 r_free=0.1790 r_work=0.0924 r_free=0.1790 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0924 r_free = 0.1790 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0917 r_free = 0.1768 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.29 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= 0.0917 r_free= 0.1768 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ls_wunit_k1) (work): 0.011606 | | target function (ls_wunit_k1) not normalized (work): 57.146665 | | target function (ls_wunit_k1) not normalized (free): 9.751440 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0960 0.0917 0.1768 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2087 0.2089 0.2198 n_refl.: 5176 remove outliers: r(all,work,free)=0.2087 0.2089 0.2198 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2087 0.2089 0.2198 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0958 0.0914 0.1773 n_refl.: 5176 remove outliers: r(all,work,free)=0.0958 0.0914 0.1773 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 0.3355 324.878 310.653 0.656 1.007 0.359 11.894-9.307 99.02 97 4 0.1415 526.041 521.500 0.989 1.008 0.358 9.237-7.194 100.00 213 7 0.1433 430.197 432.180 1.031 1.007 0.300 7.162-5.571 100.00 427 22 0.1396 322.811 320.462 0.993 1.006 0.280 5.546-4.326 100.00 867 58 0.0755 443.173 440.321 1.011 1.004 0.204 4.315-3.360 100.00 1859 96 0.0700 421.462 421.151 1.056 1.000 0.198 3.356-3.002 100.00 1373 60 0.0955 324.628 323.706 1.034 0.996 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.2865 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0914 r_free=0.1773 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.0916 r_free=0.1775 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0916 r_free=0.1775 | n_water=242 | time (s): 0.590 (total time: 0.590) Filter (dist) r_work=0.0947 r_free=0.1782 | n_water=236 | time (s): 18.150 (total time: 18.740) Filter (q & B) r_work=0.1006 r_free=0.1789 | n_water=234 | time (s): 1.600 (total time: 20.340) Compute maps r_work=0.1006 r_free=0.1789 | n_water=234 | time (s): 0.470 (total time: 20.810) Filter (map) r_work=0.1281 r_free=0.1859 | n_water=155 | time (s): 1.730 (total time: 22.540) Find peaks r_work=0.1281 r_free=0.1859 | n_water=155 | time (s): 0.410 (total time: 22.950) Add new water r_work=0.1639 r_free=0.2146 | n_water=237 | time (s): 1.440 (total time: 24.390) Refine new water occ: r_work=0.1037 r_free=0.1745 adp: r_work=0.1031 r_free=0.1760 occ: r_work=0.1023 r_free=0.1736 adp: r_work=0.1022 r_free=0.1745 occ: r_work=0.1014 r_free=0.1717 adp: r_work=0.1013 r_free=0.1727 ADP+occupancy (water only), MIN, final r_work=0.1013 r_free=0.1727 r_work=0.1013 r_free=0.1727 | n_water=237 | time (s): 9.830 (total time: 34.220) Filter (q & B) r_work=0.1013 r_free=0.1727 | n_water=237 | time (s): 0.730 (total time: 34.950) Filter (dist only) r_work=0.1025 r_free=0.1732 | n_water=235 | time (s): 18.530 (total time: 53.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.096701 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.230522 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 0.0930 0.1784 0.0853 0.011 1.1 3.8 0.5 1.2 0 0.548 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.30 17.84 8.53 5.333 17.484 0.231 5.155 8.85 18.22 9.37 7.175 17.505 0.231 5.057 Individual atomic B min max mean iso aniso Overall: 0.00 105.26 16.20 8.88 1762 0 Protein: 0.00 105.26 14.87 8.88 1519 0 Water: 0.00 61.36 24.50 N/A 235 0 Other: 9.27 37.69 23.82 N/A 8 0 Chain A: 0.00 105.26 15.65 N/A 1664 0 Chain S: 0.00 61.36 25.44 N/A 98 0 Histogram: Values Number of atoms 0.00 - 10.53 694 10.53 - 21.05 641 21.05 - 31.58 236 31.58 - 42.10 120 42.10 - 52.63 32 52.63 - 63.15 21 63.15 - 73.68 9 73.68 - 84.21 4 84.21 - 94.73 3 94.73 - 105.26 2 =========================== Idealize ADP of riding H ========================== r_work=0.0885 r_free=0.1822 r_work=0.0890 r_free=0.1834 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0890 r_free = 0.1834 target_work(ml) = 5.061 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0884 r_free = 0.1813 target_work(ml) = 5.056 | | 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.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0884 r_free= 0.1813 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.056274 | | target function (ml) not normalized (work): 24897.093738 | | target function (ml) not normalized (free): 1842.608061 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0931 0.0884 0.1813 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2092 0.2100 0.2105 n_refl.: 5176 remove outliers: r(all,work,free)=0.2092 0.2100 0.2105 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2092 0.2100 0.2105 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0924 0.0878 0.1808 n_refl.: 5176 remove outliers: r(all,work,free)=0.0922 0.0876 0.1808 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 0.3714 327.001 291.875 0.575 0.994 0.332 11.894-9.307 99.02 97 4 0.1896 526.041 509.894 0.948 0.997 0.327 9.237-7.194 100.00 213 7 0.1852 430.197 425.134 1.012 0.999 0.290 7.162-5.571 100.00 427 22 0.1797 322.811 314.666 0.981 0.999 0.290 5.546-4.326 100.00 867 58 0.0892 443.173 437.965 1.006 1.001 0.220 4.315-3.360 100.00 1859 96 0.0582 421.462 421.385 1.055 1.002 0.210 3.356-3.002 100.00 1373 60 0.0594 324.628 324.505 1.034 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9172 b_overall=-6.4190 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0876 r_free=0.1808 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0876 r_free=0.1808 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0876 r_free=0.1808 | n_water=235 | time (s): 0.530 (total time: 0.530) Filter (dist) r_work=0.0888 r_free=0.1802 | n_water=232 | time (s): 18.050 (total time: 18.580) Filter (q & B) r_work=0.1037 r_free=0.1851 | n_water=227 | time (s): 1.800 (total time: 20.380) Compute maps r_work=0.1037 r_free=0.1851 | n_water=227 | time (s): 0.670 (total time: 21.050) Filter (map) r_work=0.1285 r_free=0.1900 | n_water=158 | time (s): 1.580 (total time: 22.630) Find peaks r_work=0.1285 r_free=0.1900 | n_water=158 | time (s): 0.440 (total time: 23.070) Add new water r_work=0.1585 r_free=0.2131 | n_water=233 | time (s): 1.490 (total time: 24.560) Refine new water occ: r_work=0.0996 r_free=0.1783 adp: r_work=0.0982 r_free=0.1789 occ: r_work=0.0977 r_free=0.1772 adp: r_work=0.0977 r_free=0.1772 occ: r_work=0.0977 r_free=0.1772 adp: r_work=0.0977 r_free=0.1772 ADP+occupancy (water only), MIN, final r_work=0.0977 r_free=0.1772 r_work=0.0977 r_free=0.1772 | n_water=233 | time (s): 7.230 (total time: 31.790) Filter (q & B) r_work=0.0977 r_free=0.1772 | n_water=233 | time (s): 0.720 (total time: 32.510) Filter (dist only) r_work=0.0991 r_free=0.1780 | n_water=229 | time (s): 17.730 (total time: 50.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.021319 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.208704 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 0.0899 0.1849 0.0950 0.011 1.0 4.8 0.5 0.6 0 0.511 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.99 18.49 9.50 6.906 17.546 0.209 5.036 8.79 18.66 9.88 7.950 17.690 0.209 4.977 Individual atomic B min max mean iso aniso Overall: 0.00 103.09 16.29 10.30 1756 0 Protein: 0.00 103.09 15.32 10.30 1519 0 Water: 0.00 56.78 22.38 N/A 229 0 Other: 9.72 38.71 26.14 N/A 8 0 Chain A: 0.00 103.09 15.93 N/A 1647 0 Chain S: 0.00 51.87 21.67 N/A 109 0 Histogram: Values Number of atoms 0.00 - 10.31 649 10.31 - 20.62 664 20.62 - 30.93 253 30.93 - 41.24 112 41.24 - 51.54 39 51.54 - 61.85 15 61.85 - 72.16 11 72.16 - 82.47 6 82.47 - 92.78 4 92.78 - 103.09 3 =========================== Idealize ADP of riding H ========================== r_work=0.0879 r_free=0.1866 r_work=0.0883 r_free=0.1867 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0883 r_free = 0.1867 target_work(ml) = 4.982 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0877 r_free = 0.1851 target_work(ml) = 4.977 | | 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.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0877 r_free= 0.1851 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.976771 | | target function (ml) not normalized (work): 24500.645112 | | target function (ml) not normalized (free): 2092.538649 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0926 0.0877 0.1851 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2070 0.2070 0.2204 n_refl.: 5175 remove outliers: r(all,work,free)=0.2070 0.2070 0.2204 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2070 0.2070 0.2204 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0925 0.0876 0.1854 n_refl.: 5175 remove outliers: r(all,work,free)=0.0925 0.0876 0.1854 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 0.3907 327.001 294.275 0.573 0.986 0.319 11.894-9.307 99.02 97 4 0.1946 526.041 505.913 0.953 0.991 0.319 9.237-7.194 100.00 213 7 0.2079 430.197 422.290 1.010 0.994 0.293 7.162-5.571 100.00 427 22 0.2027 322.811 312.569 0.991 0.996 0.273 5.546-4.326 100.00 867 58 0.0953 443.173 437.500 1.022 0.998 0.229 4.315-3.360 100.00 1859 96 0.0554 421.462 421.515 1.077 1.002 0.220 3.356-3.002 100.00 1373 60 0.0457 324.628 324.473 1.057 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.4642 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0876 r_free=0.1854 After: r_work=0.0879 r_free=0.1854 ================================== NQH flips ================================== r_work=0.0879 r_free=0.1854 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0879 r_free=0.1854 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0879 r_free=0.1854 | n_water=229 | time (s): 0.480 (total time: 0.480) Filter (dist) r_work=0.0884 r_free=0.1857 | n_water=227 | time (s): 18.530 (total time: 19.010) Filter (q & B) r_work=0.1021 r_free=0.1892 | n_water=223 | time (s): 1.280 (total time: 20.290) Compute maps r_work=0.1021 r_free=0.1892 | n_water=223 | time (s): 0.450 (total time: 20.740) Filter (map) r_work=0.1272 r_free=0.1932 | n_water=161 | time (s): 1.490 (total time: 22.230) Find peaks r_work=0.1272 r_free=0.1932 | n_water=161 | time (s): 0.500 (total time: 22.730) Add new water r_work=0.1524 r_free=0.2134 | n_water=226 | time (s): 1.360 (total time: 24.090) Refine new water occ: r_work=0.0998 r_free=0.1863 adp: r_work=0.0986 r_free=0.1866 occ: r_work=0.0983 r_free=0.1863 adp: r_work=0.0981 r_free=0.1861 occ: r_work=0.0979 r_free=0.1861 adp: r_work=0.0977 r_free=0.1859 ADP+occupancy (water only), MIN, final r_work=0.0977 r_free=0.1859 r_work=0.0977 r_free=0.1859 | n_water=226 | time (s): 11.620 (total time: 35.710) Filter (q & B) r_work=0.0977 r_free=0.1860 | n_water=224 | time (s): 2.270 (total time: 37.980) Filter (dist only) r_work=0.0980 r_free=0.1870 | n_water=222 | time (s): 17.350 (total time: 55.330) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.948066 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.222545 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 0.0915 0.1862 0.0947 0.011 1.1 10.6 0.5 0.6 0 0.474 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.15 18.62 9.47 7.853 17.957 0.223 5.033 8.92 18.55 9.62 8.832 18.118 0.223 4.977 Individual atomic B min max mean iso aniso Overall: 0.00 103.49 16.74 11.68 1749 0 Protein: 0.00 103.49 15.82 11.67 1519 0 Water: 0.00 56.39 22.72 N/A 222 0 Other: 8.99 38.77 25.99 N/A 8 0 Chain A: 0.00 103.49 16.34 N/A 1643 0 Chain S: 0.00 46.87 23.00 N/A 106 0 Histogram: Values Number of atoms 0.00 - 10.35 627 10.35 - 20.70 637 20.70 - 31.05 280 31.05 - 41.39 119 41.39 - 51.74 46 51.74 - 62.09 14 62.09 - 72.44 11 72.44 - 82.79 6 82.79 - 93.14 7 93.14 - 103.49 2 =========================== Idealize ADP of riding H ========================== r_work=0.0892 r_free=0.1855 r_work=0.0896 r_free=0.1855 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0896 r_free = 0.1855 target_work(ml) = 4.981 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0891 r_free = 0.1845 target_work(ml) = 4.977 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0891 r_free= 0.1845 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.977035 | | target function (ml) not normalized (work): 24501.943481 | | target function (ml) not normalized (free): 2179.603075 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2493 142 0.1257 0.1837 5.5352 6.2669| | 2: 3.78 - 3.00 1.00 2430 110 0.0446 0.1858 4.4044 11.725| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2493 142 0.92 12.00 1.00 0.98 12880.12| | 2: 3.78 - 3.00 2430 110 0.99 2.03 1.00 1.00 997.68| |alpha: min = 0.97 max = 1.00 mean = 0.99| |beta: min = 649.28 max = 21403.54 mean = 7014.93| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.84 mean = 7.08| |phase err.(test): min = 0.00 max = 85.89 mean = 7.08| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0940 0.0891 0.1845 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2113 0.2113 0.2225 n_refl.: 5175 remove outliers: r(all,work,free)=0.2113 0.2113 0.2225 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2113 0.2113 0.2225 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0937 0.0889 0.1853 n_refl.: 5175 remove outliers: r(all,work,free)=0.0937 0.0889 0.1853 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 0.3915 327.001 296.359 0.582 0.985 0.320 11.894-9.307 99.02 97 4 0.1878 526.041 506.813 0.963 0.991 0.320 9.237-7.194 100.00 213 7 0.2089 430.197 420.609 1.011 0.994 0.305 7.162-5.571 100.00 427 22 0.2069 322.811 312.629 0.991 0.996 0.300 5.546-4.326 100.00 867 58 0.1005 443.173 436.833 1.024 0.999 0.238 4.315-3.360 100.00 1859 96 0.0572 421.462 421.497 1.087 1.002 0.226 3.356-3.002 100.00 1373 60 0.0431 324.628 324.823 1.071 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.9684 ================= 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 : 0.3617 0.2032 0.079 5.264 8.8 119.3 19.9 258 0.000 1_bss: 0.1572 0.1654 0.079 5.264 5.9 116.4 17.0 258 0.000 1_settarget: 0.1572 0.1654 0.079 5.264 5.9 116.4 17.0 258 0.000 1_nqh: 0.1574 0.1657 0.079 5.264 5.9 116.4 17.0 258 0.013 1_weight: 0.1574 0.1657 0.079 5.264 5.9 116.4 17.0 258 0.013 1_xyzrec: 0.1154 0.1799 0.010 0.972 5.9 116.4 17.0 258 0.226 1_adp: 0.1020 0.1783 0.010 0.972 1.9 111.4 17.3 258 0.226 1_regHadp: 0.1014 0.1788 0.010 0.972 1.9 111.4 17.3 258 0.226 1_occ: 0.1006 0.1783 0.010 0.972 1.9 111.4 17.3 258 0.226 2_bss: 0.1007 0.1787 0.010 0.972 0.9 110.4 16.3 258 0.226 2_settarget: 0.1007 0.1787 0.010 0.972 0.9 110.4 16.3 258 0.226 2_updatecdl: 0.1007 0.1787 0.010 0.999 0.9 110.4 16.3 258 0.226 2_nqh: 0.1012 0.1792 0.010 0.999 0.9 110.4 16.3 258 0.220 2_sol: 0.1102 0.1653 0.010 0.999 0.9 109.9 15.9 242 n/a 2_weight: 0.1102 0.1653 0.010 0.999 0.9 109.9 15.9 242 n/a 2_xyzrec: 0.0992 0.1776 0.010 1.015 0.9 109.9 15.9 242 n/a 2_adp: 0.0927 0.1790 0.010 1.015 0.0 106.3 16.6 242 n/a 2_regHadp: 0.0924 0.1790 0.010 1.015 0.0 106.3 16.6 242 n/a 2_occ: 0.0917 0.1768 0.010 1.015 0.0 106.3 16.6 242 n/a 3_bss: 0.0914 0.1773 0.010 1.015 0.0 106.3 16.6 242 n/a 3_settarget: 0.0914 0.1773 0.010 1.015 0.0 106.3 16.6 242 n/a 3_updatecdl: 0.0914 0.1773 0.010 1.021 0.0 106.3 16.6 242 n/a 3_nqh: 0.0916 0.1775 0.010 1.021 0.0 106.3 16.6 242 n/a 3_sol: 0.1025 0.1732 0.010 1.021 0.0 106.3 16.2 235 n/a 3_weight: 0.1025 0.1732 0.010 1.021 0.0 106.3 16.2 235 n/a 3_xyzrec: 0.0930 0.1784 0.011 1.068 0.0 106.3 16.2 235 n/a 3_adp: 0.0885 0.1822 0.011 1.068 0.0 105.3 16.2 235 n/a 3_regHadp: 0.0890 0.1834 0.011 1.068 0.0 105.3 16.2 235 n/a 3_occ: 0.0884 0.1813 0.011 1.068 0.0 105.3 16.2 235 n/a 4_bss: 0.0876 0.1808 0.011 1.068 0.0 105.3 16.2 235 n/a 4_settarget: 0.0876 0.1808 0.011 1.068 0.0 105.3 16.2 235 n/a 4_updatecdl: 0.0876 0.1808 0.011 1.086 0.0 105.3 16.2 235 n/a 4_nqh: 0.0876 0.1808 0.011 1.086 0.0 105.3 16.2 235 n/a 4_sol: 0.0991 0.1780 0.011 1.086 0.0 105.3 16.0 229 n/a 4_weight: 0.0991 0.1780 0.011 1.086 0.0 105.3 16.0 229 n/a 4_xyzrec: 0.0899 0.1849 0.011 1.037 0.0 105.3 16.0 229 n/a 4_adp: 0.0879 0.1866 0.011 1.037 0.0 103.1 16.3 229 n/a 4_regHadp: 0.0883 0.1867 0.011 1.037 0.0 103.1 16.3 229 n/a 4_occ: 0.0877 0.1851 0.011 1.037 0.0 103.1 16.3 229 n/a 5_bss: 0.0876 0.1854 0.011 1.037 0.0 103.1 16.3 229 n/a 5_settarget: 0.0876 0.1854 0.011 1.037 0.0 103.1 16.3 229 n/a 5_updatecdl: 0.0876 0.1854 0.011 1.038 0.0 103.1 16.3 229 n/a 5_setrh: 0.0879 0.1854 0.011 1.038 0.0 103.1 16.3 229 n/a 5_nqh: 0.0879 0.1854 0.011 1.038 0.0 103.1 16.3 229 n/a 5_sol: 0.0980 0.1870 0.011 1.038 0.0 103.1 16.4 222 n/a 5_weight: 0.0980 0.1870 0.011 1.038 0.0 103.1 16.4 222 n/a 5_xyzrec: 0.0915 0.1862 0.011 1.089 0.0 103.1 16.4 222 n/a 5_adp: 0.0892 0.1855 0.011 1.089 0.0 103.5 16.7 222 n/a 5_regHadp: 0.0896 0.1855 0.011 1.089 0.0 103.5 16.7 222 n/a 5_occ: 0.0891 0.1845 0.011 1.089 0.0 103.5 16.7 222 n/a end: 0.0889 0.1853 0.011 1.089 0.0 103.5 16.7 222 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_9171019_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_9171019_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3600 Refinement macro-cycles (run) : 474.4400 Write final files (write_after_run_outputs) : 11.5500 Total : 489.3500 Total CPU time: 8.55 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:54 PST -0800 (1735492734.26 s) Start R-work = 0.1572, R-free = 0.1654 Final R-work = 0.0889, R-free = 0.1853 =============================================================================== Job complete usr+sys time: 521.44 seconds wall clock time: 9 minutes 3.45 seconds (543.45 seconds total)