Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1664580.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { 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_1664580.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1664580.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } 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: 1.24, per 1000 atoms: 0.37 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: 0.31 Conformation dependent library (CDL) restraints added in 116.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.88: 403 0.88 - 1.14: 1201 1.14 - 1.40: 589 1.40 - 1.66: 906 1.66 - 1.92: 54 Bond restraints: 3153 Sorted by residual: bond pdb=" N VAL A 33 " pdb=" CA VAL A 33 " ideal model delta sigma weight residual 1.459 1.238 0.221 1.20e-02 6.94e+03 3.38e+02 bond pdb=" N ILE A 52 " pdb=" CA ILE A 52 " ideal model delta sigma weight residual 1.459 1.673 -0.215 1.20e-02 6.94e+03 3.20e+02 bond pdb=" C GLY A 159 " pdb=" O GLY A 159 " ideal model delta sigma weight residual 1.236 1.057 0.179 1.08e-02 8.57e+03 2.76e+02 bond pdb=" C VAL A 51 " pdb=" O VAL A 51 " ideal model delta sigma weight residual 1.236 1.053 0.183 1.12e-02 7.97e+03 2.67e+02 bond pdb=" CA VAL A 44 " pdb=" CB VAL A 44 " ideal model delta sigma weight residual 1.540 1.739 -0.199 1.23e-02 6.61e+03 2.62e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.64: 3071 4.64 - 9.27: 1907 9.27 - 13.91: 663 13.91 - 18.54: 124 18.54 - 23.18: 12 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ALA A 165 " pdb=" C ALA A 165 " pdb=" N LEU A 166 " ideal model delta sigma weight residual 122.07 107.39 14.68 1.03e+00 9.43e-01 2.03e+02 angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 107.84 13.93 1.00e+00 1.00e+00 1.94e+02 angle pdb=" CA VAL A 186 " pdb=" C VAL A 186 " pdb=" O VAL A 186 " ideal model delta sigma weight residual 120.78 137.07 -16.29 1.25e+00 6.40e-01 1.70e+02 angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 131.37 -10.14 8.10e-01 1.52e+00 1.57e+02 angle pdb=" CA GLY A 136 " pdb=" C GLY A 136 " pdb=" O GLY A 136 " ideal model delta sigma weight residual 119.27 132.58 -13.31 1.07e+00 8.73e-01 1.55e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.66: 1304 16.66 - 33.31: 119 33.31 - 49.96: 39 49.96 - 66.61: 16 66.61 - 83.26: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C GLU A 143 " pdb=" N GLU A 143 " pdb=" CA GLU A 143 " pdb=" CB GLU A 143 " ideal model delta harmonic sigma weight residual -122.60 -145.66 23.06 0 2.50e+00 1.60e-01 8.50e+01 dihedral pdb=" C ARG A 48 " pdb=" N ARG A 48 " pdb=" CA ARG A 48 " pdb=" CB ARG A 48 " ideal model delta harmonic sigma weight residual -122.60 -145.42 22.82 0 2.50e+00 1.60e-01 8.33e+01 dihedral pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CA ARG A 48 " pdb=" CB ARG A 48 " ideal model delta harmonic sigma weight residual 122.80 144.94 -22.14 0 2.50e+00 1.60e-01 7.84e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.267: 117 0.267 - 0.532: 88 0.532 - 0.798: 24 0.798 - 1.064: 11 1.064 - 1.330: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA GLU A 143 " pdb=" N GLU A 143 " pdb=" C GLU A 143 " pdb=" CB GLU A 143 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.33 2.00e-01 2.50e+01 4.42e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.33 -1.26 2.00e-01 2.50e+01 3.96e+01 chirality pdb=" CA ARG A 48 " pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CB ARG A 48 " both_signs ideal model delta sigma weight residual False 2.51 1.33 1.18 2.00e-01 2.50e+01 3.45e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " -0.095 9.50e-02 1.11e+02 7.29e-02 9.78e+01 pdb=" NE ARG A 145 " -0.070 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " 0.073 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " -0.090 2.00e-02 2.50e+03 pdb="HH11 ARG A 145 " 0.083 2.00e-02 2.50e+03 pdb="HH12 ARG A 145 " -0.091 2.00e-02 2.50e+03 pdb="HH21 ARG A 145 " 0.065 2.00e-02 2.50e+03 pdb="HH22 ARG A 145 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.101 2.00e-02 2.50e+03 5.43e-02 8.84e+01 pdb=" CG PHE A 164 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.074 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.078 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.045 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.014 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.038 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.039 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.014 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG BGLN A 80 " 0.059 2.00e-02 2.50e+03 7.62e-02 8.71e+01 pdb=" CD BGLN A 80 " -0.100 2.00e-02 2.50e+03 pdb=" OE1BGLN A 80 " -0.007 2.00e-02 2.50e+03 pdb=" NE2BGLN A 80 " 0.106 2.00e-02 2.50e+03 pdb="HE21BGLN A 80 " -0.094 2.00e-02 2.50e+03 pdb="HE22BGLN A 80 " 0.035 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 784 2.28 - 2.86: 7812 2.86 - 3.44: 10667 3.44 - 4.02: 15259 4.02 - 4.60: 22099 Nonbonded interactions: 56621 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.697 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.813 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.821 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.836 2.100 nonbonded pdb=" H VAL A 44 " pdb=" O ILE A 52 " model vdw 1.840 2.450 ... (remaining 56616 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 2 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_1664580_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2790 r_free= 0.1818 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.408948 | | target function (ml) not normalized (work): 71614.545206 | | target function (ml) not normalized (free): 3262.001184 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3214 0.2133 7.6115 5.0237| | 2: 3.63 - 2.88 1.00 2711 122 0.2626 0.1710 4.3193 4.3156| | 3: 2.88 - 2.52 1.00 2682 148 0.2567 0.1696 4.1751 4.1873| | 4: 2.52 - 2.29 1.00 2661 139 0.2555 0.1590 3.4894 3.5952| | 5: 2.29 - 2.13 1.00 2678 122 0.2621 0.1510 3.3877 3.4313| | 6: 2.13 - 2.00 1.00 2692 117 0.2765 0.1819 3.3035 3.4073| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.64 2819 159 0.88 17.39 0.77 0.23 1279.06| | 2: 3.63 - 2.88 2711 122 0.83 23.55 1.31 0.23 1279.06| | 3: 2.88 - 2.52 2682 148 0.73 32.55 1.29 0.23 1279.06| | 4: 2.52 - 2.29 2661 139 0.93 11.39 1.30 0.26 133.00| | 5: 2.29 - 2.13 2678 122 0.92 13.16 1.31 0.26 133.00| | 6: 2.13 - 2.00 2692 117 0.90 16.01 1.34 0.26 133.00| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 133.00 max = 1279.06 mean = 712.42| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 90.00 mean = 19.01| |phase err.(test): min = 0.00 max = 89.59 mean = 19.27| |-----------------------------------------------------------------------------| ----------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 0.259 1557 Z= 5.326 Angle : 5.330 17.017 2118 Z= 3.694 Chirality : 0.404 1.330 243 Planarity : 0.032 0.104 284 Dihedral : 13.685 83.258 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 31.89 % 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: -2.85 (0.47), residues: 224 helix: -3.06 (0.33), residues: 103 sheet: -0.23 (0.89), residues: 28 loop : -0.69 (0.59), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.093 0.025 ARG A 145 TYR 0.066 0.031 TYR A 141 PHE 0.082 0.042 PHE A 162 HIS 0.044 0.016 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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2790 r_free= 0.1818 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.408948 | | target function (ml) not normalized (work): 71614.545206 | | target function (ml) not normalized (free): 3262.001184 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2838 percent. r_work = 0.2919 r_free = 0.2019 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2866 0.2919 0.2019 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2866 0.2919 0.2019 n_refl.: 17050 remove outliers: r(all,work,free)=0.2156 0.2166 0.2019 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2129 0.2138 0.2002 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1609 0.1605 0.1697 n_refl.: 17045 remove outliers: r(all,work,free)=0.1608 0.1604 0.1697 n_refl.: 17044 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.4099 394.735 359.328 0.650 1.013 0.393 11.894-9.307 99.02 97 4 0.1906 633.562 614.179 0.925 1.014 0.380 9.237-7.194 100.00 213 7 0.2199 518.189 510.027 0.946 1.013 0.360 7.162-5.571 100.00 427 22 0.2315 388.902 376.792 0.918 1.012 0.298 5.546-4.326 100.00 867 58 0.1389 533.900 528.734 0.966 1.010 0.251 4.315-3.360 100.00 1859 96 0.1302 507.744 503.729 1.018 1.006 0.181 3.356-2.611 100.00 3867 181 0.1643 333.559 329.227 1.012 1.000 0.091 2.608-2.000 99.99 8818 434 0.1626 217.423 213.390 1.030 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4528 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1604 r_free=0.1697 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.1605 r_free=0.1698 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.394377 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.855569 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1351 0.1635 0.0285 0.009 1.0 1.3 0.5 0.0 0 11.197 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.35 2.85 3.013 18.452 0.856 0.023 12.77 16.56 3.79 3.557 18.690 0.856 0.020 Individual atomic B min max mean iso aniso Overall: 6.17 113.89 19.93 4.04 1785 0 Protein: 6.17 113.13 17.16 4.05 1519 0 Water: 8.73 113.89 36.03 N/A 258 0 Other: 21.72 37.37 26.29 N/A 8 0 Chain A: 6.17 113.89 19.93 N/A 1785 0 Histogram: Values Number of atoms 6.17 - 16.94 1094 16.94 - 27.71 333 27.71 - 38.49 186 38.49 - 49.26 96 49.26 - 60.03 49 60.03 - 70.80 12 70.80 - 81.58 7 81.58 - 92.35 4 92.35 - 103.12 1 103.12 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1277 r_free=0.1656 r_work=0.1279 r_free=0.1662 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1279 r_free = 0.1662 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1274 r_free = 0.1660 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1274 r_free= 0.1660 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.020000 | | target function (ls_wunit_k1) not normalized (work): 324.735600 | | target function (ls_wunit_k1) not normalized (free): 27.091383 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1274 0.1660 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1911 0.1910 0.1984 n_refl.: 17044 remove outliers: r(all,work,free)=0.1911 0.1910 0.1984 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1883 0.1881 0.1969 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1275 0.1655 n_refl.: 17044 remove outliers: r(all,work,free)=0.1291 0.1273 0.1655 n_refl.: 17042 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3529 303.557 280.484 0.619 1.010 0.368 11.894-9.307 99.02 97 4 0.1685 488.224 478.124 0.914 1.011 0.366 9.237-7.194 100.00 213 7 0.1833 399.318 396.203 0.956 1.010 0.351 7.162-5.571 100.00 427 22 0.1844 299.689 294.877 0.928 1.009 0.301 5.546-4.326 100.00 867 58 0.1046 411.424 409.171 0.961 1.008 0.241 4.315-3.360 100.00 1859 96 0.0922 391.269 390.927 1.017 1.005 0.191 3.356-2.611 100.00 3867 181 0.1301 257.041 255.787 1.014 1.000 0.111 2.608-2.000 99.99 8818 434 0.1346 167.547 166.082 1.022 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3745 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1655 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1273 r_free=0.1655 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1655 | n_water=258 | time (s): 0.820 (total time: 0.820) Filter (dist) r_work=0.1277 r_free=0.1644 | n_water=254 | time (s): 19.590 (total time: 20.410) Filter (q & B) r_work=0.1277 r_free=0.1642 | n_water=252 | time (s): 1.420 (total time: 21.830) Compute maps r_work=0.1277 r_free=0.1642 | n_water=252 | time (s): 0.550 (total time: 22.380) Filter (map) r_work=0.1307 r_free=0.1652 | n_water=216 | time (s): 1.640 (total time: 24.020) Find peaks r_work=0.1307 r_free=0.1652 | n_water=216 | time (s): 0.470 (total time: 24.490) Add new water r_work=0.1526 r_free=0.1910 | n_water=370 | time (s): 1.390 (total time: 25.880) Refine new water occ: r_work=0.1330 r_free=0.1588 adp: r_work=0.1273 r_free=0.1593 occ: r_work=0.1279 r_free=0.1550 adp: r_work=0.1245 r_free=0.1563 occ: r_work=0.1247 r_free=0.1535 adp: r_work=0.1234 r_free=0.1548 ADP+occupancy (water only), MIN, final r_work=0.1234 r_free=0.1548 r_work=0.1234 r_free=0.1548 | n_water=370 | time (s): 11.780 (total time: 37.660) Filter (q & B) r_work=0.1236 r_free=0.1550 | n_water=361 | time (s): 2.000 (total time: 39.660) Filter (dist only) r_work=0.1237 r_free=0.1553 | n_water=360 | time (s): 29.750 (total time: 69.410) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.439677 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.989081 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1216 0.1602 0.0386 0.008 0.9 2.9 0.5 0.0 0 12.220 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.16 16.02 3.86 4.151 21.017 0.989 0.018 12.02 16.20 4.18 4.211 21.255 0.989 0.018 Individual atomic B min max mean iso aniso Overall: 6.59 107.75 21.25 4.27 1887 0 Protein: 6.59 107.75 17.65 4.27 1519 0 Water: 8.89 67.01 36.28 N/A 360 0 Other: 22.85 37.51 29.03 N/A 8 0 Chain A: 6.59 107.75 19.42 N/A 1743 0 Chain S: 17.89 67.01 43.49 N/A 144 0 Histogram: Values Number of atoms 6.59 - 16.70 1033 16.70 - 26.82 367 26.82 - 36.94 224 36.94 - 47.05 154 47.05 - 57.17 71 57.17 - 67.28 28 67.28 - 77.40 3 77.40 - 87.52 4 87.52 - 97.63 1 97.63 - 107.75 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1620 r_work=0.1203 r_free=0.1622 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1622 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1611 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1194 r_free= 0.1611 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017108 | | target function (ls_wunit_k1) not normalized (work): 277.756166 | | target function (ls_wunit_k1) not normalized (free): 24.474619 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1194 0.1611 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1748 0.1739 0.1942 n_refl.: 17042 remove outliers: r(all,work,free)=0.1748 0.1739 0.1942 n_refl.: 17042 overall B=-0.37 to atoms: r(all,work,free)=0.1724 0.1715 0.1927 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1188 0.1596 n_refl.: 17042 remove outliers: r(all,work,free)=0.1206 0.1187 0.1596 n_refl.: 17041 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3282 300.394 283.852 0.590 1.005 0.340 11.894-9.307 99.02 97 4 0.1539 488.224 486.757 0.913 1.006 0.334 9.237-7.194 100.00 213 7 0.1635 399.318 401.845 0.972 1.006 0.286 7.162-5.571 100.00 427 22 0.1540 299.689 296.535 0.934 1.006 0.263 5.546-4.326 100.00 867 58 0.0868 411.424 408.804 0.960 1.005 0.215 4.315-3.360 100.00 1859 96 0.0828 391.269 390.588 1.014 1.003 0.201 3.356-2.611 100.00 3867 181 0.1200 257.041 256.136 1.011 1.001 0.131 2.608-2.000 99.99 8818 434 0.1327 167.547 166.528 1.015 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3083 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1596 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1596 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1596 | n_water=360 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.1187 r_free=0.1596 | n_water=359 | time (s): 28.650 (total time: 29.340) Filter (q & B) r_work=0.1187 r_free=0.1596 | n_water=359 | time (s): 0.900 (total time: 30.240) Compute maps r_work=0.1187 r_free=0.1596 | n_water=359 | time (s): 0.620 (total time: 30.860) Filter (map) r_work=0.1252 r_free=0.1634 | n_water=266 | time (s): 1.650 (total time: 32.510) Find peaks r_work=0.1252 r_free=0.1634 | n_water=266 | time (s): 0.590 (total time: 33.100) Add new water r_work=0.1418 r_free=0.1785 | n_water=412 | time (s): 1.890 (total time: 34.990) Refine new water occ: r_work=0.1223 r_free=0.1555 adp: r_work=0.1215 r_free=0.1564 occ: r_work=0.1203 r_free=0.1534 adp: r_work=0.1192 r_free=0.1539 occ: r_work=0.1187 r_free=0.1523 adp: r_work=0.1179 r_free=0.1526 ADP+occupancy (water only), MIN, final r_work=0.1179 r_free=0.1526 r_work=0.1179 r_free=0.1526 | n_water=412 | time (s): 38.560 (total time: 73.550) Filter (q & B) r_work=0.1183 r_free=0.1537 | n_water=400 | time (s): 1.630 (total time: 75.180) Filter (dist only) r_work=0.1183 r_free=0.1537 | n_water=400 | time (s): 32.890 (total time: 108.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.765094 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.150399 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1161 0.1538 0.0377 0.009 1.0 3.8 0.5 0.0 0 0.883 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.61 15.38 3.77 4.332 21.409 0.150 4.987 11.39 15.46 4.06 4.884 21.403 0.150 4.964 Individual atomic B min max mean iso aniso Overall: 6.25 104.73 20.88 4.78 1927 0 Protein: 6.25 104.73 17.07 4.77 1519 0 Water: 9.05 65.42 35.17 N/A 400 0 Other: 23.61 44.08 30.91 N/A 8 0 Chain A: 6.25 104.73 18.84 N/A 1738 0 Chain S: 16.65 65.42 39.67 N/A 189 0 Histogram: Values Number of atoms 6.25 - 16.10 1055 16.10 - 25.94 351 25.94 - 35.79 228 35.79 - 45.64 170 45.64 - 55.49 84 55.49 - 65.34 25 65.34 - 75.18 5 75.18 - 85.03 4 85.03 - 94.88 3 94.88 - 104.73 2 =========================== Idealize ADP of riding H ========================== r_work=0.1139 r_free=0.1546 r_work=0.1140 r_free=0.1546 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1140 r_free = 0.1546 target_work(ml) = 4.964 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1132 r_free = 0.1540 target_work(ml) = 4.959 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1132 r_free= 0.1540 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 4.959124 | | target function (ml) not normalized (work): 80506.413325 | | target function (ml) not normalized (free): 4184.651267 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1152 0.1132 0.1540 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1675 0.1666 0.1876 n_refl.: 17041 remove outliers: r(all,work,free)=0.1675 0.1666 0.1876 n_refl.: 17041 overall B=-0.51 to atoms: r(all,work,free)=0.1640 0.1631 0.1857 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1150 0.1130 0.1542 n_refl.: 17041 remove outliers: r(all,work,free)=0.1149 0.1129 0.1542 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3430 296.827 281.455 0.570 1.005 0.340 11.894-9.307 99.02 97 4 0.1746 488.224 483.136 0.916 1.006 0.330 9.237-7.194 100.00 213 7 0.1731 399.318 401.250 0.985 1.007 0.265 7.162-5.571 100.00 427 22 0.1598 299.689 294.785 0.938 1.006 0.230 5.546-4.326 100.00 867 58 0.0921 411.424 407.895 0.963 1.005 0.211 4.315-3.360 100.00 1859 96 0.0871 391.269 389.023 1.012 1.004 0.212 3.356-2.611 100.00 3867 181 0.1254 257.041 254.971 1.010 1.001 0.152 2.608-2.000 99.99 8818 434 0.1088 167.547 166.174 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1560 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1129 r_free=0.1542 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1129 r_free=0.1542 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1129 r_free=0.1542 | n_water=400 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.1130 r_free=0.1547 | n_water=399 | time (s): 30.930 (total time: 31.650) Filter (q & B) r_work=0.1130 r_free=0.1547 | n_water=399 | time (s): 0.870 (total time: 32.520) Compute maps r_work=0.1130 r_free=0.1547 | n_water=399 | time (s): 0.620 (total time: 33.140) Filter (map) r_work=0.1193 r_free=0.1581 | n_water=314 | time (s): 1.610 (total time: 34.750) Find peaks r_work=0.1193 r_free=0.1581 | n_water=314 | time (s): 0.510 (total time: 35.260) Add new water r_work=0.1341 r_free=0.1714 | n_water=449 | time (s): 2.070 (total time: 37.330) Refine new water occ: r_work=0.1170 r_free=0.1550 adp: r_work=0.1164 r_free=0.1556 occ: r_work=0.1146 r_free=0.1518 adp: r_work=0.1138 r_free=0.1525 occ: r_work=0.1130 r_free=0.1500 adp: r_work=0.1123 r_free=0.1505 ADP+occupancy (water only), MIN, final r_work=0.1123 r_free=0.1505 r_work=0.1123 r_free=0.1505 | n_water=449 | time (s): 35.860 (total time: 73.190) Filter (q & B) r_work=0.1127 r_free=0.1511 | n_water=440 | time (s): 1.810 (total time: 75.000) Filter (dist only) r_work=0.1127 r_free=0.1512 | n_water=439 | time (s): 36.710 (total time: 111.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.991704 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.153692 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1112 0.1540 0.0429 0.010 1.0 3.8 0.5 0.0 0 0.996 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.12 15.40 4.29 4.560 21.027 0.154 4.950 11.03 15.40 4.37 4.690 21.068 0.154 4.944 Individual atomic B min max mean iso aniso Overall: 5.57 101.73 20.93 4.85 1966 0 Protein: 5.57 101.73 16.54 4.84 1519 0 Water: 8.91 69.42 35.96 N/A 439 0 Other: 22.56 40.18 29.32 N/A 8 0 Chain A: 5.57 101.73 18.26 N/A 1738 0 Chain S: 16.98 69.42 41.32 N/A 228 0 Histogram: Values Number of atoms 5.57 - 15.19 1001 15.19 - 24.80 400 24.80 - 34.42 221 34.42 - 44.03 189 44.03 - 53.65 100 53.65 - 63.26 35 63.26 - 72.88 10 72.88 - 82.50 5 82.50 - 92.11 1 92.11 - 101.73 4 =========================== Idealize ADP of riding H ========================== r_work=0.1103 r_free=0.1540 r_work=0.1103 r_free=0.1541 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1103 r_free = 0.1541 target_work(ml) = 4.944 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1095 r_free = 0.1547 target_work(ml) = 4.940 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1095 r_free= 0.1547 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.940094 | | target function (ml) not normalized (work): 80192.539448 | | target function (ml) not normalized (free): 4180.506550 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1117 0.1095 0.1547 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1581 0.1569 0.1854 n_refl.: 17040 remove outliers: r(all,work,free)=0.1581 0.1569 0.1854 n_refl.: 17040 overall B=-0.29 to atoms: r(all,work,free)=0.1563 0.1551 0.1844 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1115 0.1093 0.1545 n_refl.: 17040 remove outliers: r(all,work,free)=0.1115 0.1093 0.1545 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3725 296.827 276.740 0.540 1.002 0.314 11.894-9.307 99.02 97 4 0.1779 488.224 481.069 0.916 1.003 0.303 9.237-7.194 100.00 213 7 0.1714 399.318 399.979 0.989 1.004 0.240 7.162-5.571 100.00 427 22 0.1514 299.689 294.649 0.939 1.004 0.215 5.546-4.326 100.00 867 58 0.0904 411.424 408.125 0.965 1.004 0.201 4.315-3.360 100.00 1859 96 0.0839 391.269 388.621 1.007 1.003 0.201 3.356-2.611 100.00 3867 181 0.1229 257.041 254.806 1.005 1.001 0.141 2.608-2.000 99.99 8818 434 0.1033 167.547 166.398 1.001 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9903 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1093 r_free=0.1545 After: r_work=0.1095 r_free=0.1544 ================================== NQH flips ================================== r_work=0.1095 r_free=0.1544 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1095 r_free=0.1544 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1095 r_free=0.1544 | n_water=439 | time (s): 0.770 (total time: 0.770) Filter (dist) r_work=0.1101 r_free=0.1537 | n_water=437 | time (s): 38.030 (total time: 38.800) Filter (q & B) r_work=0.1101 r_free=0.1537 | n_water=437 | time (s): 0.960 (total time: 39.760) Compute maps r_work=0.1101 r_free=0.1537 | n_water=437 | time (s): 0.800 (total time: 40.560) Filter (map) r_work=0.1175 r_free=0.1552 | n_water=336 | time (s): 1.930 (total time: 42.490) Find peaks r_work=0.1175 r_free=0.1552 | n_water=336 | time (s): 0.510 (total time: 43.000) Add new water r_work=0.1300 r_free=0.1668 | n_water=477 | time (s): 1.800 (total time: 44.800) Refine new water occ: r_work=0.1144 r_free=0.1499 adp: r_work=0.1134 r_free=0.1511 occ: r_work=0.1123 r_free=0.1486 adp: r_work=0.1112 r_free=0.1493 occ: r_work=0.1107 r_free=0.1477 adp: r_work=0.1100 r_free=0.1484 ADP+occupancy (water only), MIN, final r_work=0.1100 r_free=0.1484 r_work=0.1100 r_free=0.1484 | n_water=477 | time (s): 50.290 (total time: 95.090) Filter (q & B) r_work=0.1103 r_free=0.1493 | n_water=465 | time (s): 1.890 (total time: 96.980) Filter (dist only) r_work=0.1103 r_free=0.1496 | n_water=464 | time (s): 38.780 (total time: 135.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.896370 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.171789 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1121 0.1513 0.0393 0.010 1.0 6.1 0.5 0.0 0 0.948 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.21 15.13 3.93 4.550 20.889 0.172 4.944 11.12 14.95 3.83 4.645 20.958 0.172 4.934 Individual atomic B min max mean iso aniso Overall: 5.53 101.98 21.08 5.08 1991 0 Protein: 5.53 101.98 16.29 5.07 1519 0 Water: 8.38 67.57 36.64 N/A 464 0 Other: 21.80 39.96 28.55 N/A 8 0 Chain A: 5.53 101.98 17.98 N/A 1737 0 Chain S: 19.58 67.57 42.31 N/A 254 0 Histogram: Values Number of atoms 5.53 - 15.18 1042 15.18 - 24.82 367 24.82 - 34.47 224 34.47 - 44.11 180 44.11 - 53.76 121 53.76 - 63.40 36 63.40 - 73.04 11 73.04 - 82.69 4 82.69 - 92.33 2 92.33 - 101.98 4 =========================== Idealize ADP of riding H ========================== r_work=0.1112 r_free=0.1495 r_work=0.1112 r_free=0.1495 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1112 r_free = 0.1495 target_work(ml) = 4.934 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1109 r_free = 0.1508 target_work(ml) = 4.932 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1109 r_free= 0.1508 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.932155 | | target function (ml) not normalized (work): 80063.672404 | | target function (ml) not normalized (free): 4160.258274 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1115 0.1397 5.4448 5.6489| | 2: 3.63 - 2.88 1.00 2711 122 0.1101 0.1526 5.2177 5.3476| | 3: 2.88 - 2.52 1.00 2681 148 0.1367 0.1688 5.1241 5.2019| | 4: 2.52 - 2.29 1.00 2661 139 0.0936 0.1488 4.6287 4.9477| | 5: 2.29 - 2.13 1.00 2678 122 0.0956 0.1460 4.5768 4.8767| | 6: 2.13 - 2.00 1.00 2692 117 0.1117 0.1668 4.5718 4.7616| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2810 159 0.95 8.90 1.00 0.96 6269.71| | 2: 3.63 - 2.88 2711 122 0.92 12.73 1.01 0.96 6269.71| | 3: 2.88 - 2.52 2681 148 0.88 18.82 0.99 0.96 6269.71| | 4: 2.52 - 2.29 2661 139 0.93 12.04 1.01 0.98 2112.90| | 5: 2.29 - 2.13 2678 122 0.91 14.13 1.00 0.98 2112.90| | 6: 2.13 - 2.00 2692 117 0.89 16.77 0.99 0.98 2112.90| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2112.90 max = 6269.71 mean = 4213.20| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.75 mean = 13.86| |phase err.(test): min = 0.00 max = 89.78 mean = 13.57| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1128 0.1109 0.1508 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1564 0.1552 0.1804 n_refl.: 17040 remove outliers: r(all,work,free)=0.1564 0.1552 0.1804 n_refl.: 17040 overall B=-0.23 to atoms: r(all,work,free)=0.1551 0.1539 0.1796 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1128 0.1109 0.1507 n_refl.: 17040 remove outliers: r(all,work,free)=0.1128 0.1109 0.1507 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3551 296.827 278.639 0.547 1.001 0.330 11.894-9.307 99.02 97 4 0.1721 488.224 482.538 0.920 1.003 0.330 9.237-7.194 100.00 213 7 0.1720 399.318 401.071 0.990 1.003 0.230 7.162-5.571 100.00 427 22 0.1558 299.689 294.314 0.937 1.003 0.210 5.546-4.326 100.00 867 58 0.0935 411.424 407.940 0.965 1.003 0.211 4.315-3.360 100.00 1859 96 0.0874 391.269 388.859 1.005 1.002 0.201 3.356-2.611 100.00 3867 181 0.1245 257.041 254.814 0.999 1.001 0.121 2.608-2.000 99.99 8818 434 0.1039 167.547 166.210 0.990 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7938 ================= 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 : 0.2790 0.1818 0.081 5.330 8.8 119.3 19.9 258 0.000 1_bss: 0.1604 0.1697 0.081 5.330 8.4 118.9 19.5 258 0.000 1_settarget: 0.1604 0.1697 0.081 5.330 8.4 118.9 19.5 258 0.000 1_nqh: 0.1605 0.1698 0.081 5.330 8.4 118.9 19.5 258 0.003 1_weight: 0.1605 0.1698 0.081 5.330 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1351 0.1635 0.009 0.979 8.4 118.9 19.5 258 0.153 1_adp: 0.1277 0.1656 0.009 0.979 6.2 113.9 19.9 258 0.153 1_regHadp: 0.1279 0.1662 0.009 0.979 6.2 113.9 19.9 258 0.153 1_occ: 0.1274 0.1660 0.009 0.979 6.2 113.9 19.9 258 0.153 2_bss: 0.1273 0.1655 0.009 0.979 5.8 113.5 19.5 258 0.153 2_settarget: 0.1273 0.1655 0.009 0.979 5.8 113.5 19.5 258 0.153 2_updatecdl: 0.1273 0.1655 0.009 0.990 5.8 113.5 19.5 258 0.153 2_nqh: 0.1273 0.1655 0.009 0.990 5.8 113.5 19.5 258 0.153 2_sol: 0.1237 0.1553 0.009 0.990 5.8 112.7 20.8 360 n/a 2_weight: 0.1237 0.1553 0.009 0.990 5.8 112.7 20.8 360 n/a 2_xyzrec: 0.1216 0.1602 0.008 0.930 5.8 112.7 20.8 360 n/a 2_adp: 0.1202 0.1620 0.008 0.930 6.6 107.7 21.3 360 n/a 2_regHadp: 0.1203 0.1622 0.008 0.930 6.6 107.7 21.3 360 n/a 2_occ: 0.1194 0.1611 0.008 0.930 6.6 107.7 21.3 360 n/a 3_bss: 0.1187 0.1596 0.008 0.930 6.2 107.4 20.9 360 n/a 3_settarget: 0.1187 0.1596 0.008 0.930 6.2 107.4 20.9 360 n/a 3_updatecdl: 0.1187 0.1596 0.008 0.935 6.2 107.4 20.9 360 n/a 3_nqh: 0.1187 0.1596 0.008 0.935 6.2 107.4 20.9 360 n/a 3_sol: 0.1183 0.1537 0.008 0.935 6.2 107.4 20.9 400 n/a 3_weight: 0.1183 0.1537 0.008 0.935 6.2 107.4 20.9 400 n/a 3_xyzrec: 0.1161 0.1538 0.009 0.953 6.2 107.4 20.9 400 n/a 3_adp: 0.1139 0.1546 0.009 0.953 6.2 104.7 20.9 400 n/a 3_regHadp: 0.1140 0.1546 0.009 0.953 6.2 104.7 20.9 400 n/a 3_occ: 0.1132 0.1540 0.009 0.953 6.2 104.7 20.9 400 n/a 4_bss: 0.1129 0.1542 0.009 0.953 5.7 104.2 20.4 400 n/a 4_settarget: 0.1129 0.1542 0.009 0.953 5.7 104.2 20.4 400 n/a 4_updatecdl: 0.1129 0.1542 0.009 0.951 5.7 104.2 20.4 400 n/a 4_nqh: 0.1129 0.1542 0.009 0.951 5.7 104.2 20.4 400 n/a 4_sol: 0.1127 0.1512 0.009 0.951 5.7 104.2 20.9 439 n/a 4_weight: 0.1127 0.1512 0.009 0.951 5.7 104.2 20.9 439 n/a 4_xyzrec: 0.1112 0.1540 0.010 0.982 5.7 104.2 20.9 439 n/a 4_adp: 0.1103 0.1540 0.010 0.982 5.6 101.7 20.9 439 n/a 4_regHadp: 0.1103 0.1541 0.010 0.982 5.6 101.7 20.9 439 n/a 4_occ: 0.1095 0.1547 0.010 0.982 5.6 101.7 20.9 439 n/a 5_bss: 0.1093 0.1545 0.010 0.982 5.3 101.4 20.6 439 n/a 5_settarget: 0.1093 0.1545 0.010 0.982 5.3 101.4 20.6 439 n/a 5_updatecdl: 0.1093 0.1545 0.010 0.981 5.3 101.4 20.6 439 n/a 5_setrh: 0.1095 0.1544 0.010 0.981 5.3 101.4 20.6 439 n/a 5_nqh: 0.1095 0.1544 0.010 0.981 5.3 101.4 20.6 439 n/a 5_sol: 0.1103 0.1496 0.010 0.981 5.3 101.4 21.0 464 n/a 5_weight: 0.1103 0.1496 0.010 0.981 5.3 101.4 21.0 464 n/a 5_xyzrec: 0.1121 0.1513 0.010 1.037 5.3 101.4 21.0 464 n/a 5_adp: 0.1112 0.1495 0.010 1.037 5.5 102.0 21.1 464 n/a 5_regHadp: 0.1112 0.1495 0.010 1.037 5.5 102.0 21.1 464 n/a 5_occ: 0.1109 0.1508 0.010 1.037 5.5 102.0 21.1 464 n/a end: 0.1109 0.1507 0.010 1.037 5.3 101.7 20.9 464 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_1664580_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_1664580_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.7900 Refinement macro-cycles (run) : 961.4700 Write final files (write_after_run_outputs) : 16.4100 Total : 981.6700 Total CPU time: 16.77 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:47 PST -0800 (1735494107.06 s) Start R-work = 0.1604, R-free = 0.1697 Final R-work = 0.1109, R-free = 0.1507 =============================================================================== Job complete usr+sys time: 1024.31 seconds wall clock time: 17 minutes 27.14 seconds (1047.14 seconds total)