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_4912670.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4912670.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4912670.pdb" 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 2 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: 2.01, per 1000 atoms: 0.59 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 160.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.94: 731 0.94 - 1.21: 965 1.21 - 1.47: 787 1.47 - 1.74: 658 1.74 - 2.01: 12 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 107 " pdb=" N GLY A 108 " ideal model delta sigma weight residual 1.340 1.189 0.151 6.60e-03 2.30e+04 5.24e+02 bond pdb=" CA GLY A 174 " pdb=" C GLY A 174 " ideal model delta sigma weight residual 1.519 1.303 0.216 1.04e-02 9.25e+03 4.30e+02 bond pdb=" C ASP A 149 " pdb=" O ASP A 149 " ideal model delta sigma weight residual 1.235 1.020 0.215 1.14e-02 7.69e+03 3.55e+02 bond pdb=" C ARG A 5 " pdb=" O ARG A 5 " ideal model delta sigma weight residual 1.234 1.026 0.209 1.11e-02 8.12e+03 3.53e+02 bond pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 1.330 1.087 0.243 1.30e-02 5.92e+03 3.49e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 3018 4.49 - 8.97: 1903 8.97 - 13.46: 684 13.46 - 17.95: 152 17.95 - 22.44: 20 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 108 " pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 121.07 113.83 7.24 3.60e-01 7.72e+00 4.04e+02 angle pdb=" O VAL A 23 " pdb=" C VAL A 23 " pdb=" N ASP A 24 " ideal model delta sigma weight residual 121.94 106.42 15.52 1.00e+00 1.00e+00 2.41e+02 angle pdb=" CA VAL A 23 " pdb=" C VAL A 23 " pdb=" O VAL A 23 " ideal model delta sigma weight residual 121.27 135.78 -14.51 1.04e+00 9.25e-01 1.95e+02 angle pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " pdb=" CG ASP A 49 " ideal model delta sigma weight residual 112.60 126.44 -13.84 1.00e+00 1.00e+00 1.91e+02 angle pdb=" O ILE A 102 " pdb=" C ILE A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 123.20 108.37 14.83 1.08e+00 8.57e-01 1.88e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 1291 16.17 - 32.33: 125 32.33 - 48.50: 42 48.50 - 64.67: 19 64.67 - 80.83: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ALYS A 99 " pdb=" N ALYS A 99 " pdb=" CA ALYS A 99 " pdb=" CB ALYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -141.59 18.99 0 2.50e+00 1.60e-01 5.77e+01 dihedral pdb=" C ASP A 68 " pdb=" N ASP A 68 " pdb=" CA ASP A 68 " pdb=" CB ASP A 68 " ideal model delta harmonic sigma weight residual -122.60 -140.95 18.35 0 2.50e+00 1.60e-01 5.39e+01 dihedral pdb=" C LEU A 77 " pdb=" N LEU A 77 " pdb=" CA LEU A 77 " pdb=" CB LEU A 77 " ideal model delta harmonic sigma weight residual -122.60 -139.94 17.34 0 2.50e+00 1.60e-01 4.81e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.207: 102 0.207 - 0.412: 72 0.412 - 0.616: 45 0.616 - 0.821: 22 0.821 - 1.026: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 68 " pdb=" N ASP A 68 " pdb=" C ASP A 68 " pdb=" CB ASP A 68 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.63e+01 chirality pdb=" CA GLU A 59 " pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CB GLU A 59 " both_signs ideal model delta sigma weight residual False 2.51 1.68 0.83 2.00e-01 2.50e+01 1.74e+01 chirality pdb=" CA VAL A 181 " pdb=" N VAL A 181 " pdb=" C VAL A 181 " pdb=" CB VAL A 181 " both_signs ideal model delta sigma weight residual False 2.44 3.26 -0.82 2.00e-01 2.50e+01 1.68e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.119 2.00e-02 2.50e+03 6.85e-02 1.41e+02 pdb=" CG PHE A 119 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.052 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.126 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.071 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.081 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.021 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " -0.132 9.50e-02 1.11e+02 8.48e-02 1.20e+02 pdb=" NE ARG A 5 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.106 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " 0.105 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " 0.069 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " -0.106 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " -0.011 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " -0.050 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.107 2.00e-02 2.50e+03 5.45e-02 8.92e+01 pdb=" CG ATYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.060 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.086 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.000 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.043 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.047 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.059 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.013 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 635 2.26 - 2.84: 7701 2.84 - 3.43: 10630 3.43 - 4.01: 15493 4.01 - 4.60: 22152 Nonbonded interactions: 56611 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.673 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.815 2.450 nonbonded pdb=" HG3BGLU A 90 " pdb=" O HOH A 373 " model vdw 1.848 2.620 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.851 2.450 nonbonded pdb=" H LYS A 122 " pdb=" OD2 ASP A 149 " model vdw 1.855 2.450 ... (remaining 56606 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_4912670_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= 0.3619 r_free= 0.1954 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.475457 | | target function (ml) not normalized (work): 22064.004644 | | target function (ml) not normalized (free): 1150.471583 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3810 0.2170 4.8542 4.9123| | 2: 3.78 - 3.00 1.00 2430 110 0.3386 0.1590 4.0858 4.1175| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.82 0.83 0.13 6616.10| | 2: 3.78 - 3.00 2430 110 0.93 11.59 1.48 0.26 459.65| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 392.12 max = 12077.45 mean = 3581.58| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.47| |phase err.(test): min = 0.00 max = 89.99 mean = 33.35| |-----------------------------------------------------------------------------| ----------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 0.243 1557 Z= 5.444 Angle : 5.386 18.870 2118 Z= 3.769 Chirality : 0.364 1.026 243 Planarity : 0.031 0.082 284 Dihedral : 14.033 80.833 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 0.62 % Allowed : 3.11 % Favored : 96.27 % Cbeta Deviations : 30.81 % 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: -2.70 (0.47), residues: 224 helix: -2.91 (0.33), residues: 102 sheet: -0.96 (0.72), residues: 38 loop : -0.27 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.088 0.013 ARG A 145 TYR 0.073 0.030 TYR A 139 PHE 0.111 0.049 PHE A 119 HIS 0.079 0.048 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3619 r_free= 0.1954 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.475457 | | target function (ml) not normalized (work): 22064.004644 | | target function (ml) not normalized (free): 1150.471583 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3569 0.3648 0.2050 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3569 0.3648 0.2050 n_refl.: 5182 remove outliers: r(all,work,free)=0.2518 0.2546 0.2050 n_refl.: 5178 overall B=-2.76 to atoms: r(all,work,free)=0.2414 0.2438 0.2008 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1571 0.1570 0.1591 n_refl.: 5178 remove outliers: r(all,work,free)=0.1567 0.1565 0.1591 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 0.3851 449.625 406.412 0.656 1.078 0.398 11.894-9.307 99.02 97 4 0.1875 714.265 694.653 0.933 1.073 0.377 9.237-7.194 100.00 213 7 0.2216 584.127 574.100 0.963 1.065 0.353 7.162-5.571 100.00 427 22 0.2361 438.317 421.604 0.927 1.050 0.288 5.546-4.326 100.00 867 58 0.1377 601.746 594.806 0.976 1.027 0.224 4.315-3.360 100.00 1859 96 0.1319 572.267 566.783 1.058 0.987 0.206 3.356-3.002 100.00 1373 60 0.1593 440.784 432.946 1.069 0.948 0.096 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-3.5272 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1565 r_free=0.1591 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=0.1567 r_free=0.1588 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.504613 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.803350 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 0.1164 0.1759 0.0595 0.010 1.0 2.6 0.5 0.0 0 9.752 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.64 17.59 5.95 3.013 16.099 1.803 0.018 10.25 17.57 7.32 4.693 16.236 1.803 0.015 Individual atomic B min max mean iso aniso Overall: 2.42 111.54 17.39 5.11 1785 0 Protein: 2.42 111.51 14.67 5.11 1519 0 Water: 4.11 111.54 33.18 N/A 258 0 Other: 17.65 33.42 23.67 N/A 8 0 Chain A: 2.42 111.54 17.39 N/A 1785 0 Histogram: Values Number of atoms 2.42 - 13.33 940 13.33 - 24.24 466 24.24 - 35.15 187 35.15 - 46.07 104 46.07 - 56.98 56 56.98 - 67.89 15 67.89 - 78.80 8 78.80 - 89.71 5 89.71 - 100.63 1 100.63 - 111.54 3 =========================== Idealize ADP of riding H ========================== r_work=0.1025 r_free=0.1757 r_work=0.1018 r_free=0.1762 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1018 r_free = 0.1762 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1014 r_free = 0.1763 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.28 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= 0.1014 r_free= 0.1763 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014067 | | target function (ls_wunit_k1) not normalized (work): 69.267215 | | target function (ls_wunit_k1) not normalized (free): 10.289540 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1052 0.1014 0.1763 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2085 0.2083 0.2234 n_refl.: 5176 remove outliers: r(all,work,free)=0.2085 0.2083 0.2234 n_refl.: 5176 overall B=-0.91 to atoms: r(all,work,free)=0.2047 0.2044 0.2221 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1058 0.1019 0.1770 n_refl.: 5176 remove outliers: r(all,work,free)=0.1058 0.1019 0.1770 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 0.3318 330.110 311.544 0.665 1.026 0.382 11.894-9.307 99.02 97 4 0.1530 524.407 515.658 0.967 1.025 0.362 9.237-7.194 100.00 213 7 0.1657 428.861 429.321 1.010 1.022 0.339 7.162-5.571 100.00 427 22 0.1629 321.808 318.642 0.966 1.017 0.292 5.546-4.326 100.00 867 58 0.0915 441.797 438.651 0.990 1.009 0.213 4.315-3.360 100.00 1859 96 0.0772 420.153 420.208 1.045 0.995 0.205 3.356-3.002 100.00 1373 60 0.1013 323.620 321.664 1.021 0.982 0.089 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.2673 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1019 r_free=0.1770 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1019 r_free=0.1770 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1019 r_free=0.1770 | n_water=258 | time (s): 0.450 (total time: 0.450) Filter (dist) r_work=0.1044 r_free=0.1773 | n_water=248 | time (s): 20.080 (total time: 20.530) Filter (q & B) r_work=0.1044 r_free=0.1777 | n_water=245 | time (s): 1.540 (total time: 22.070) Compute maps r_work=0.1044 r_free=0.1777 | n_water=245 | time (s): 0.450 (total time: 22.520) Filter (map) r_work=0.1358 r_free=0.1783 | n_water=142 | time (s): 1.340 (total time: 23.860) Find peaks r_work=0.1358 r_free=0.1783 | n_water=142 | time (s): 0.430 (total time: 24.290) Add new water r_work=0.1717 r_free=0.2009 | n_water=221 | time (s): 1.360 (total time: 25.650) Refine new water occ: r_work=0.1167 r_free=0.1655 adp: r_work=0.1149 r_free=0.1660 occ: r_work=0.1146 r_free=0.1638 adp: r_work=0.1139 r_free=0.1646 occ: r_work=0.1138 r_free=0.1630 adp: r_work=0.1136 r_free=0.1636 ADP+occupancy (water only), MIN, final r_work=0.1136 r_free=0.1636 r_work=0.1136 r_free=0.1636 | n_water=221 | time (s): 3.980 (total time: 29.630) Filter (q & B) r_work=0.1136 r_free=0.1641 | n_water=220 | time (s): 1.560 (total time: 31.190) Filter (dist only) r_work=0.1148 r_free=0.1643 | n_water=215 | time (s): 18.000 (total time: 49.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.778693 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 3.028508 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 0.1035 0.1745 0.0710 0.009 1.0 3.5 0.5 0.6 0 11.389 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.35 17.45 7.10 4.554 16.699 3.029 0.015 9.68 17.85 8.17 5.386 16.925 3.029 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 109.36 16.13 6.37 1742 0 Protein: 0.00 109.36 14.65 6.36 1519 0 Water: 0.00 62.91 26.23 N/A 215 0 Other: 12.23 33.19 24.33 N/A 8 0 Chain A: 0.00 109.36 15.42 N/A 1666 0 Chain S: 9.16 60.36 31.68 N/A 76 0 Histogram: Values Number of atoms 0.00 - 10.94 733 10.94 - 21.87 630 21.87 - 32.81 200 32.81 - 43.74 110 43.74 - 54.68 33 54.68 - 65.62 26 65.62 - 76.55 4 76.55 - 87.49 2 87.49 - 98.42 2 98.42 - 109.36 2 =========================== Idealize ADP of riding H ========================== r_work=0.0968 r_free=0.1785 r_work=0.0966 r_free=0.1788 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0966 r_free = 0.1788 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0964 r_free = 0.1768 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0964 r_free= 0.1768 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.012748 | | target function (ls_wunit_k1) not normalized (work): 62.770170 | | target function (ls_wunit_k1) not normalized (free): 9.551082 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1006 0.0964 0.1768 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2149 0.2158 0.2128 n_refl.: 5176 remove outliers: r(all,work,free)=0.2149 0.2158 0.2128 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2149 0.2158 0.2128 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1006 0.0964 0.1786 n_refl.: 5176 remove outliers: r(all,work,free)=0.1006 0.0964 0.1786 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 0.3378 330.110 311.967 0.693 1.015 0.391 11.894-9.307 99.02 97 4 0.1476 524.407 517.863 0.974 1.016 0.370 9.237-7.194 100.00 213 7 0.1500 428.861 430.030 1.010 1.015 0.320 7.162-5.571 100.00 427 22 0.1451 321.808 319.421 0.978 1.012 0.310 5.546-4.326 100.00 867 58 0.0822 441.797 439.240 0.996 1.007 0.240 4.315-3.360 100.00 1859 96 0.0744 420.153 419.966 1.048 0.999 0.200 3.356-3.002 100.00 1373 60 0.0990 323.620 322.396 1.024 0.990 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.6739 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0964 r_free=0.1786 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0964 r_free=0.1786 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0964 r_free=0.1786 | n_water=215 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.0969 r_free=0.1781 | n_water=213 | time (s): 16.620 (total time: 17.240) Filter (q & B) r_work=0.1051 r_free=0.1761 | n_water=210 | time (s): 1.370 (total time: 18.610) Compute maps r_work=0.1051 r_free=0.1761 | n_water=210 | time (s): 0.480 (total time: 19.090) Filter (map) r_work=0.1284 r_free=0.1857 | n_water=149 | time (s): 1.430 (total time: 20.520) Find peaks r_work=0.1284 r_free=0.1857 | n_water=149 | time (s): 0.480 (total time: 21.000) Add new water r_work=0.1648 r_free=0.2174 | n_water=228 | time (s): 1.430 (total time: 22.430) Refine new water occ: r_work=0.1064 r_free=0.1745 adp: r_work=0.1056 r_free=0.1765 occ: r_work=0.1046 r_free=0.1742 adp: r_work=0.1045 r_free=0.1751 occ: r_work=0.1037 r_free=0.1733 adp: r_work=0.1036 r_free=0.1742 ADP+occupancy (water only), MIN, final r_work=0.1036 r_free=0.1742 r_work=0.1036 r_free=0.1742 | n_water=228 | time (s): 8.370 (total time: 30.800) Filter (q & B) r_work=0.1036 r_free=0.1742 | n_water=228 | time (s): 1.100 (total time: 31.900) Filter (dist only) r_work=0.1038 r_free=0.1753 | n_water=226 | time (s): 17.340 (total time: 49.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.126867 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.230498 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 0.0940 0.1804 0.0863 0.011 1.1 4.5 0.5 0.6 0 0.563 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.40 18.04 8.63 5.324 17.451 0.230 5.160 9.03 17.91 8.88 7.149 17.449 0.230 5.071 Individual atomic B min max mean iso aniso Overall: 0.00 108.32 16.09 8.79 1753 0 Protein: 0.00 108.32 14.77 8.78 1519 0 Water: 0.00 57.91 24.67 N/A 226 0 Other: 15.03 40.02 25.99 N/A 8 0 Chain A: 0.00 108.32 15.52 N/A 1657 0 Chain S: 0.00 52.24 26.05 N/A 96 0 Histogram: Values Number of atoms 0.00 - 10.83 720 10.83 - 21.66 630 21.66 - 32.50 214 32.50 - 43.33 124 43.33 - 54.16 31 54.16 - 64.99 16 64.99 - 75.82 11 75.82 - 86.65 4 86.65 - 97.49 1 97.49 - 108.32 2 =========================== Idealize ADP of riding H ========================== r_work=0.0903 r_free=0.1791 r_work=0.0909 r_free=0.1801 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0909 r_free = 0.1801 target_work(ml) = 5.075 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0895 r_free = 0.1774 target_work(ml) = 5.067 | | occupancies: max = 1.00 min = 0.18 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= 0.0895 r_free= 0.1774 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.066593 | | target function (ml) not normalized (work): 24947.905472 | | target function (ml) not normalized (free): 1794.003338 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0940 0.0895 0.1774 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2162 0.2177 0.2077 n_refl.: 5176 remove outliers: r(all,work,free)=0.2162 0.2177 0.2077 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2162 0.2177 0.2077 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0938 0.0895 0.1768 n_refl.: 5176 remove outliers: r(all,work,free)=0.0934 0.0890 0.1768 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 0.3631 329.507 299.420 0.616 1.002 0.350 11.894-9.307 99.02 97 4 0.1755 524.407 513.077 0.948 1.005 0.339 9.237-7.194 100.00 213 7 0.1883 428.861 423.096 0.993 1.006 0.300 7.162-5.571 100.00 427 22 0.1812 321.808 314.931 0.968 1.005 0.290 5.546-4.326 100.00 867 58 0.0917 441.797 437.035 0.983 1.003 0.237 4.315-3.360 100.00 1859 96 0.0599 420.153 419.702 1.042 1.001 0.210 3.356-3.002 100.00 1373 60 0.0614 323.620 322.663 1.019 0.997 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9175 b_overall=-5.5445 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0890 r_free=0.1768 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B A 80 GLN B Total number of N/Q/H flips: 2 r_work=0.0892 r_free=0.1761 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0892 r_free=0.1761 | n_water=226 | time (s): 0.590 (total time: 0.590) Filter (dist) r_work=0.0909 r_free=0.1765 | n_water=222 | time (s): 17.430 (total time: 18.020) Filter (q & B) r_work=0.0945 r_free=0.1762 | n_water=220 | time (s): 1.740 (total time: 19.760) Compute maps r_work=0.0945 r_free=0.1762 | n_water=220 | time (s): 0.580 (total time: 20.340) Filter (map) r_work=0.1199 r_free=0.1929 | n_water=151 | time (s): 1.680 (total time: 22.020) Find peaks r_work=0.1199 r_free=0.1929 | n_water=151 | time (s): 0.580 (total time: 22.600) Add new water r_work=0.1522 r_free=0.2295 | n_water=225 | time (s): 1.500 (total time: 24.100) Refine new water occ: r_work=0.1009 r_free=0.1818 adp: r_work=0.1004 r_free=0.1827 occ: r_work=0.0996 r_free=0.1806 adp: r_work=0.0996 r_free=0.1814 occ: r_work=0.0988 r_free=0.1792 adp: r_work=0.0987 r_free=0.1801 ADP+occupancy (water only), MIN, final r_work=0.0987 r_free=0.1801 r_work=0.0987 r_free=0.1801 | n_water=225 | time (s): 8.430 (total time: 32.530) Filter (q & B) r_work=0.0987 r_free=0.1801 | n_water=224 | time (s): 1.860 (total time: 34.390) Filter (dist only) r_work=0.0987 r_free=0.1795 | n_water=223 | time (s): 18.000 (total time: 52.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.993306 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.287735 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 0.0908 0.1861 0.0954 0.011 1.1 4.2 0.5 0.6 0 0.497 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.08 18.61 9.54 6.850 17.482 0.288 5.038 8.90 18.86 9.96 8.121 17.581 0.288 4.983 Individual atomic B min max mean iso aniso Overall: 0.00 106.83 16.26 10.64 1750 0 Protein: 0.00 106.83 15.13 10.63 1519 0 Water: 0.00 56.34 23.50 N/A 223 0 Other: 14.14 45.76 28.33 N/A 8 0 Chain A: 0.00 106.83 15.77 N/A 1646 0 Chain S: 0.00 56.34 23.90 N/A 104 0 Histogram: Values Number of atoms 0.00 - 10.68 698 10.68 - 21.37 627 21.37 - 32.05 246 32.05 - 42.73 101 42.73 - 53.41 44 53.41 - 64.10 14 64.10 - 74.78 11 74.78 - 85.46 5 85.46 - 96.14 1 96.14 - 106.83 3 =========================== Idealize ADP of riding H ========================== r_work=0.0890 r_free=0.1886 r_work=0.0894 r_free=0.1889 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0894 r_free = 0.1889 target_work(ml) = 4.988 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0883 r_free = 0.1861 target_work(ml) = 4.980 | | 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= 0.0883 r_free= 0.1861 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 4.979643 | | target function (ml) not normalized (work): 24509.802241 | | target function (ml) not normalized (free): 2062.623028 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0932 0.0883 0.1861 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2082 0.2085 0.2187 n_refl.: 5174 remove outliers: r(all,work,free)=0.2082 0.2085 0.2187 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2082 0.2085 0.2187 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0930 0.0882 0.1857 n_refl.: 5174 remove outliers: r(all,work,free)=0.0930 0.0882 0.1857 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 0.3857 329.507 299.899 0.598 0.987 0.330 11.894-9.307 99.02 97 4 0.1843 524.407 510.526 0.963 0.992 0.323 9.237-7.194 100.00 213 7 0.2103 428.861 420.776 1.001 0.995 0.280 7.162-5.571 100.00 427 22 0.1972 321.808 312.151 0.986 0.997 0.280 5.546-4.326 100.00 867 58 0.0981 441.797 436.291 1.006 0.999 0.229 4.315-3.360 100.00 1859 96 0.0569 420.153 419.904 1.070 1.003 0.210 3.356-3.002 100.00 1373 60 0.0458 323.620 323.838 1.044 1.006 0.078 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.0150 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0882 r_free=0.1857 After: r_work=0.0884 r_free=0.1856 ================================== NQH flips ================================== r_work=0.0884 r_free=0.1856 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0884 r_free=0.1856 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0884 r_free=0.1856 | n_water=223 | time (s): 0.520 (total time: 0.520) Filter (dist) r_work=0.0902 r_free=0.1862 | n_water=219 | time (s): 16.380 (total time: 16.900) Filter (q & B) r_work=0.1068 r_free=0.1923 | n_water=214 | time (s): 1.380 (total time: 18.280) Compute maps r_work=0.1068 r_free=0.1923 | n_water=214 | time (s): 0.470 (total time: 18.750) Filter (map) r_work=0.1286 r_free=0.1976 | n_water=148 | time (s): 1.360 (total time: 20.110) Find peaks r_work=0.1286 r_free=0.1976 | n_water=148 | time (s): 0.390 (total time: 20.500) Add new water r_work=0.1569 r_free=0.2225 | n_water=218 | time (s): 1.380 (total time: 21.880) Refine new water occ: r_work=0.1035 r_free=0.1928 adp: r_work=0.1023 r_free=0.1941 occ: r_work=0.1016 r_free=0.1928 adp: r_work=0.1015 r_free=0.1933 occ: r_work=0.1009 r_free=0.1917 adp: r_work=0.1008 r_free=0.1923 ADP+occupancy (water only), MIN, final r_work=0.1008 r_free=0.1923 r_work=0.1008 r_free=0.1923 | n_water=218 | time (s): 11.130 (total time: 33.010) Filter (q & B) r_work=0.1008 r_free=0.1921 | n_water=215 | time (s): 1.300 (total time: 34.310) Filter (dist only) r_work=0.1019 r_free=0.1923 | n_water=214 | time (s): 15.620 (total time: 49.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.001010 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.234772 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 0.0955 0.1847 0.0892 0.011 1.1 9.0 0.5 0.0 0 0.501 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.55 18.47 8.92 8.078 17.849 0.235 5.079 9.34 18.49 9.15 8.839 17.929 0.235 5.025 Individual atomic B min max mean iso aniso Overall: 0.00 107.97 16.53 11.63 1741 0 Protein: 0.00 107.97 15.43 11.61 1519 0 Water: 0.00 57.45 23.90 N/A 214 0 Other: 11.26 46.37 27.80 N/A 8 0 Chain A: 0.00 107.97 15.99 N/A 1635 0 Chain S: 0.00 57.07 24.92 N/A 106 0 Histogram: Values Number of atoms 0.00 - 10.80 682 10.80 - 21.59 606 21.59 - 32.39 261 32.39 - 43.19 104 43.19 - 53.98 52 53.98 - 64.78 14 64.78 - 75.58 10 75.58 - 86.37 7 86.37 - 97.17 3 97.17 - 107.97 2 =========================== Idealize ADP of riding H ========================== r_work=0.0934 r_free=0.1849 r_work=0.0938 r_free=0.1853 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0938 r_free = 0.1853 target_work(ml) = 5.032 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0931 r_free = 0.1844 target_work(ml) = 5.027 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0931 r_free= 0.1844 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 5.026663 | | target function (ml) not normalized (work): 24741.233613 | | target function (ml) not normalized (free): 1946.959879 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1303 0.1881 5.571 6.146| | 2: 3.78 - 3.00 1.00 2430 110 0.0478 0.1780 4.4684 9.7657| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.91 12.52 1.00 0.97 13924.26| | 2: 3.78 - 3.00 2430 110 0.99 2.21 1.01 1.00 1108.39| |alpha: min = 0.96 max = 1.00 mean = 0.99| |beta: min = 727.38 max = 23145.66 mean = 7597.04| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 88.83 mean = 7.43| |phase err.(test): min = 0.00 max = 82.41 mean = 8.15| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0977 0.0931 0.1844 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2160 0.2167 0.2178 n_refl.: 5174 remove outliers: r(all,work,free)=0.2160 0.2167 0.2178 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2160 0.2167 0.2178 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0975 0.0929 0.1855 n_refl.: 5174 remove outliers: r(all,work,free)=0.0975 0.0929 0.1855 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 0.3938 329.507 296.541 0.624 0.986 0.360 11.894-9.307 99.02 97 4 0.1761 524.407 507.863 0.985 0.993 0.360 9.237-7.194 100.00 213 7 0.2262 428.861 417.711 0.995 0.996 0.298 7.162-5.571 100.00 427 22 0.2076 321.808 312.898 0.983 0.998 0.290 5.546-4.326 100.00 867 58 0.1081 441.797 435.416 1.015 1.000 0.233 4.315-3.360 100.00 1859 96 0.0601 420.153 420.352 1.094 1.003 0.227 3.356-3.002 100.00 1373 60 0.0460 323.620 324.058 1.075 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.1436 ================= 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 : 0.3619 0.1954 0.081 5.386 8.8 119.3 19.9 258 0.000 1_bss: 0.1565 0.1591 0.081 5.386 6.1 116.5 17.1 258 0.000 1_settarget: 0.1565 0.1591 0.081 5.386 6.1 116.5 17.1 258 0.000 1_nqh: 0.1567 0.1588 0.081 5.386 6.1 116.5 17.1 258 0.003 1_weight: 0.1567 0.1588 0.081 5.386 6.1 116.5 17.1 258 0.003 1_xyzrec: 0.1164 0.1759 0.010 0.992 6.1 116.5 17.1 258 0.190 1_adp: 0.1025 0.1757 0.010 0.992 2.4 111.5 17.4 258 0.190 1_regHadp: 0.1018 0.1762 0.010 0.992 2.4 111.5 17.4 258 0.190 1_occ: 0.1014 0.1763 0.010 0.992 2.4 111.5 17.4 258 0.190 2_bss: 0.1019 0.1770 0.010 0.992 1.5 110.6 16.5 258 0.190 2_settarget: 0.1019 0.1770 0.010 0.992 1.5 110.6 16.5 258 0.190 2_updatecdl: 0.1019 0.1770 0.010 1.018 1.5 110.6 16.5 258 0.190 2_nqh: 0.1019 0.1770 0.010 1.018 1.5 110.6 16.5 258 0.193 2_sol: 0.1148 0.1643 0.010 1.018 1.5 110.6 15.7 215 n/a 2_weight: 0.1148 0.1643 0.010 1.018 1.5 110.6 15.7 215 n/a 2_xyzrec: 0.1035 0.1745 0.009 0.993 1.5 110.6 15.7 215 n/a 2_adp: 0.0968 0.1785 0.009 0.993 0.0 109.4 16.1 215 n/a 2_regHadp: 0.0966 0.1788 0.009 0.993 0.0 109.4 16.1 215 n/a 2_occ: 0.0964 0.1768 0.009 0.993 0.0 109.4 16.1 215 n/a 3_bss: 0.0964 0.1786 0.009 0.993 0.0 109.4 16.1 215 n/a 3_settarget: 0.0964 0.1786 0.009 0.993 0.0 109.4 16.1 215 n/a 3_updatecdl: 0.0964 0.1786 0.009 1.001 0.0 109.4 16.1 215 n/a 3_nqh: 0.0964 0.1786 0.009 1.001 0.0 109.4 16.1 215 n/a 3_sol: 0.1038 0.1753 0.009 1.001 0.0 109.4 16.1 226 n/a 3_weight: 0.1038 0.1753 0.009 1.001 0.0 109.4 16.1 226 n/a 3_xyzrec: 0.0940 0.1804 0.011 1.087 0.0 109.4 16.1 226 n/a 3_adp: 0.0903 0.1791 0.011 1.087 0.0 108.3 16.1 226 n/a 3_regHadp: 0.0909 0.1801 0.011 1.087 0.0 108.3 16.1 226 n/a 3_occ: 0.0895 0.1774 0.011 1.087 0.0 108.3 16.1 226 n/a 4_bss: 0.0890 0.1768 0.011 1.087 0.0 108.3 16.1 226 n/a 4_settarget: 0.0890 0.1768 0.011 1.087 0.0 108.3 16.1 226 n/a 4_updatecdl: 0.0890 0.1768 0.011 1.099 0.0 108.3 16.1 226 n/a 4_nqh: 0.0892 0.1761 0.011 1.099 0.0 108.3 16.1 226 n/a 4_sol: 0.0987 0.1795 0.011 1.099 0.0 108.3 16.1 223 n/a 4_weight: 0.0987 0.1795 0.011 1.099 0.0 108.3 16.1 223 n/a 4_xyzrec: 0.0908 0.1861 0.011 1.079 0.0 108.3 16.1 223 n/a 4_adp: 0.0890 0.1886 0.011 1.079 0.0 106.8 16.3 223 n/a 4_regHadp: 0.0894 0.1889 0.011 1.079 0.0 106.8 16.3 223 n/a 4_occ: 0.0883 0.1861 0.011 1.079 0.0 106.8 16.3 223 n/a 5_bss: 0.0882 0.1857 0.011 1.079 0.0 106.8 16.3 223 n/a 5_settarget: 0.0882 0.1857 0.011 1.079 0.0 106.8 16.3 223 n/a 5_updatecdl: 0.0882 0.1857 0.011 1.082 0.0 106.8 16.3 223 n/a 5_setrh: 0.0884 0.1856 0.011 1.082 0.0 106.8 16.3 223 n/a 5_nqh: 0.0884 0.1856 0.011 1.082 0.0 106.8 16.3 223 n/a 5_sol: 0.1019 0.1923 0.011 1.082 0.0 106.8 16.4 214 n/a 5_weight: 0.1019 0.1923 0.011 1.082 0.0 106.8 16.4 214 n/a 5_xyzrec: 0.0955 0.1847 0.011 1.144 0.0 106.8 16.4 214 n/a 5_adp: 0.0934 0.1849 0.011 1.144 0.0 108.0 16.5 214 n/a 5_regHadp: 0.0938 0.1853 0.011 1.144 0.0 108.0 16.5 214 n/a 5_occ: 0.0931 0.1844 0.011 1.144 0.0 108.0 16.5 214 n/a end: 0.0929 0.1855 0.011 1.144 0.0 108.0 16.5 214 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_4912670_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_4912670_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.6700 Refinement macro-cycles (run) : 474.2300 Write final files (write_after_run_outputs) : 12.0200 Total : 489.9200 Total CPU time: 8.58 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:56 PST -0800 (1735492736.84 s) Start R-work = 0.1565, R-free = 0.1591 Final R-work = 0.0929, R-free = 0.1855 =============================================================================== Job complete usr+sys time: 523.33 seconds wall clock time: 9 minutes 5.93 seconds (545.93 seconds total)