Starting phenix.refine on Sun Dec 29 09:24:43 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7326401.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_7326401.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7326401.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 =============================================================================== 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: 2.06, per 1000 atoms: 0.61 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 108.6 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.90: 467 0.90 - 1.15: 1156 1.15 - 1.40: 583 1.40 - 1.65: 876 1.65 - 1.90: 71 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ALEU A 153 " pdb=" C ALEU A 153 " ideal model delta sigma weight residual 1.521 1.296 0.226 1.17e-02 7.31e+03 3.72e+02 bond pdb=" CG HIS A 138 " pdb=" ND1 HIS A 138 " ideal model delta sigma weight residual 1.378 1.176 0.202 1.10e-02 8.26e+03 3.37e+02 bond pdb=" N LEU A 151 " pdb=" CA LEU A 151 " ideal model delta sigma weight residual 1.456 1.215 0.241 1.32e-02 5.74e+03 3.33e+02 bond pdb=" CA VAL A 186 " pdb=" C VAL A 186 " ideal model delta sigma weight residual 1.523 1.739 -0.216 1.27e-02 6.20e+03 2.90e+02 bond pdb=" C VAL A 71 " pdb=" O VAL A 71 " ideal model delta sigma weight residual 1.238 1.434 -0.197 1.17e-02 7.31e+03 2.83e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.73: 3246 4.73 - 9.45: 1828 9.45 - 14.18: 583 14.18 - 18.90: 113 18.90 - 23.63: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ILE A 52 " pdb=" C ILE A 52 " pdb=" O ILE A 52 " ideal model delta sigma weight residual 120.39 136.33 -15.94 1.05e+00 9.07e-01 2.31e+02 angle pdb=" CA PHE A 164 " pdb=" CB PHE A 164 " pdb=" CG PHE A 164 " ideal model delta sigma weight residual 113.80 128.63 -14.83 1.00e+00 1.00e+00 2.20e+02 angle pdb=" O ILE A 168 " pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 121.91 136.04 -14.13 9.80e-01 1.04e+00 2.08e+02 angle pdb=" O ARG A 27 " pdb=" C ARG A 27 " pdb=" N ARG A 28 " ideal model delta sigma weight residual 122.12 136.84 -14.72 1.06e+00 8.90e-01 1.93e+02 angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH1 ARG A 5 " ideal model delta sigma weight residual 121.50 134.80 -13.30 1.00e+00 1.00e+00 1.77e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.83: 1346 19.83 - 39.66: 96 39.66 - 59.49: 34 59.49 - 79.32: 4 79.32 - 99.15: 1 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N PRO A 109 " pdb=" C PRO A 109 " pdb=" CA PRO A 109 " pdb=" CB PRO A 109 " ideal model delta harmonic sigma weight residual 115.10 137.74 -22.64 0 2.50e+00 1.60e-01 8.20e+01 dihedral pdb=" C PRO A 109 " pdb=" N PRO A 109 " pdb=" CA PRO A 109 " pdb=" CB PRO A 109 " ideal model delta harmonic sigma weight residual -120.70 -141.88 21.18 0 2.50e+00 1.60e-01 7.18e+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 122.80 142.97 -20.17 0 2.50e+00 1.60e-01 6.51e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.223: 95 0.223 - 0.442: 86 0.442 - 0.662: 42 0.662 - 0.881: 16 0.881 - 1.101: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA PRO A 109 " pdb=" N PRO A 109 " pdb=" C PRO A 109 " pdb=" CB PRO A 109 " both_signs ideal model delta sigma weight residual False 2.72 1.62 1.10 2.00e-01 2.50e+01 3.03e+01 chirality pdb=" CA VAL A 50 " pdb=" N VAL A 50 " pdb=" C VAL A 50 " pdb=" CB VAL A 50 " both_signs ideal model delta sigma weight residual False 2.44 3.52 -1.08 2.00e-01 2.50e+01 2.89e+01 chirality pdb=" CB VAL A 20 " pdb=" CA VAL A 20 " pdb=" CG1 VAL A 20 " pdb=" CG2 VAL A 20 " both_signs ideal model delta sigma weight residual False -2.63 -1.61 -1.02 2.00e-01 2.50e+01 2.59e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.042 2.00e-02 2.50e+03 6.79e-02 1.38e+02 pdb=" CG TYR A 141 " 0.099 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.092 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.101 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.126 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.050 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.040 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.053 2.00e-02 2.50e+03 6.77e-02 1.38e+02 pdb=" CG TYR A 139 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.143 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.053 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.044 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.115 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.124 2.00e-02 2.50e+03 6.76e-02 1.37e+02 pdb=" CG PHE A 119 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.045 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.073 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.091 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.139 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.018 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.034 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 802 2.28 - 2.86: 7824 2.86 - 3.44: 10634 3.44 - 4.02: 15246 4.02 - 4.60: 22030 Nonbonded interactions: 56536 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.700 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.772 2.450 x-y,-y,-z-4/3 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.800 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.809 2.100 nonbonded pdb=" O GLU A 147 " pdb=" H BTHR A 154 " model vdw 1.822 2.450 ... (remaining 56531 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_7326401_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= 0.2791 r_free= 0.1859 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.410136 | | target function (ml) not normalized (work): 71633.839569 | | target function (ml) not normalized (free): 3280.198331 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3194 0.2164 7.4928 5.0239| | 2: 3.63 - 2.88 1.00 2711 122 0.2630 0.1770 4.3364 4.3358| | 3: 2.88 - 2.52 1.00 2682 148 0.2558 0.1700 4.1854 4.1987| | 4: 2.52 - 2.29 1.00 2661 139 0.2569 0.1548 3.5243 3.614| | 5: 2.29 - 2.13 1.00 2678 122 0.2659 0.1634 3.4253 3.4646| | 6: 2.13 - 2.00 1.00 2692 117 0.2768 0.1943 3.3354 3.4703| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.67 0.77 0.23 1310.37| | 2: 3.63 - 2.88 2711 122 0.83 23.91 1.31 0.23 1310.37| | 3: 2.88 - 2.52 2682 148 0.73 33.01 1.28 0.23 1310.37| | 4: 2.52 - 2.29 2661 139 0.93 11.96 1.30 0.26 145.69| | 5: 2.29 - 2.13 2678 122 0.92 14.08 1.32 0.26 145.69| | 6: 2.13 - 2.00 2692 117 0.89 16.95 1.34 0.26 145.69| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 145.69 max = 1310.37 mean = 734.52| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.98 mean = 19.60| |phase err.(test): min = 0.00 max = 89.49 mean = 19.89| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.261 1557 Z= 5.552 Angle : 5.318 21.366 2118 Z= 3.709 Chirality : 0.386 1.101 243 Planarity : 0.031 0.103 284 Dihedral : 13.847 99.154 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.32 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 27.03 % 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: -2.10 (0.47), residues: 224 helix: -2.20 (0.38), residues: 102 sheet: -1.12 (0.86), residues: 28 loop : -0.19 (0.58), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.150 0.035 ARG A 28 TYR 0.123 0.059 TYR A 141 PHE 0.085 0.028 PHE A 119 HIS 0.068 0.023 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2791 r_free= 0.1859 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.410136 | | target function (ml) not normalized (work): 71633.839569 | | target function (ml) not normalized (free): 3280.198331 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2958 percent. r_work = 0.2920 r_free = 0.2042 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2867 0.2920 0.2042 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2867 0.2920 0.2042 n_refl.: 17050 remove outliers: r(all,work,free)=0.2161 0.2170 0.2042 n_refl.: 17045 overall B=-0.42 to atoms: r(all,work,free)=0.2133 0.2141 0.2023 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1624 0.1619 0.1712 n_refl.: 17045 remove outliers: r(all,work,free)=0.1623 0.1618 0.1712 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 0.4032 395.118 365.233 0.654 1.010 0.397 11.894-9.307 99.02 97 4 0.1934 634.176 614.302 0.934 1.011 0.380 9.237-7.194 100.00 213 7 0.2128 518.692 510.209 0.967 1.011 0.371 7.162-5.571 100.00 427 22 0.2422 389.279 376.165 0.926 1.010 0.279 5.546-4.326 100.00 867 58 0.1402 534.417 528.535 0.960 1.008 0.220 4.315-3.360 100.00 1859 96 0.1295 508.236 504.724 1.018 1.005 0.202 3.356-2.611 100.00 3867 181 0.1654 333.882 329.373 1.013 1.000 0.048 2.608-2.000 99.99 8818 434 0.1651 217.634 213.744 1.031 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4892 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1618 r_free=0.1712 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B Total number of N/Q/H flips: 1 r_work=0.1619 r_free=0.1715 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.604229 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.947980 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 0.1350 0.1643 0.0292 0.009 1.0 1.3 0.5 0.0 0 11.302 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.50 16.43 2.92 3.013 18.442 0.948 0.023 12.76 16.64 3.88 3.675 18.721 0.948 0.020 Individual atomic B min max mean iso aniso Overall: 6.15 113.88 20.00 4.13 1785 0 Protein: 6.15 113.19 17.23 4.13 1519 0 Water: 8.82 113.88 36.07 N/A 258 0 Other: 21.84 37.19 26.56 N/A 8 0 Chain A: 6.15 113.88 20.00 N/A 1785 0 Histogram: Values Number of atoms 6.15 - 16.93 1084 16.93 - 27.70 339 27.70 - 38.47 189 38.47 - 49.24 96 49.24 - 60.02 49 60.02 - 70.79 13 70.79 - 81.56 7 81.56 - 92.34 4 92.34 - 103.11 1 103.11 - 113.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1276 r_free=0.1664 r_work=0.1279 r_free=0.1668 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1279 r_free = 0.1668 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 = 0.1273 r_free = 0.1655 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 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= 0.1273 r_free= 0.1655 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019927 | | target function (ls_wunit_k1) not normalized (work): 323.559342 | | target function (ls_wunit_k1) not normalized (free): 27.178561 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1291 0.1273 0.1655 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1914 0.1913 0.1990 n_refl.: 17044 remove outliers: r(all,work,free)=0.1914 0.1913 0.1990 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1885 0.1883 0.1974 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1291 0.1273 0.1646 n_refl.: 17044 remove outliers: r(all,work,free)=0.1289 0.1272 0.1646 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 0.3537 303.504 279.639 0.626 1.009 0.370 11.894-9.307 99.02 97 4 0.1658 488.138 478.188 0.918 1.010 0.367 9.237-7.194 100.00 213 7 0.1811 399.247 396.600 0.962 1.010 0.351 7.162-5.571 100.00 427 22 0.1795 299.636 295.030 0.933 1.009 0.300 5.546-4.326 100.00 867 58 0.1036 411.351 409.221 0.957 1.007 0.205 4.315-3.360 100.00 1859 96 0.0925 391.199 390.769 1.018 1.005 0.191 3.356-2.611 100.00 3867 181 0.1301 256.996 255.719 1.015 1.000 0.101 2.608-2.000 99.99 8818 434 0.1350 167.517 165.994 1.024 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4016 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1272 r_free=0.1646 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1272 r_free=0.1646 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1272 r_free=0.1646 | n_water=258 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.1276 r_free=0.1640 | n_water=253 | time (s): 20.820 (total time: 21.470) Filter (q & B) r_work=0.1277 r_free=0.1640 | n_water=251 | time (s): 1.490 (total time: 22.960) Compute maps r_work=0.1277 r_free=0.1640 | n_water=251 | time (s): 0.700 (total time: 23.660) Filter (map) r_work=0.1312 r_free=0.1630 | n_water=212 | time (s): 1.650 (total time: 25.310) Find peaks r_work=0.1312 r_free=0.1630 | n_water=212 | time (s): 0.640 (total time: 25.950) Add new water r_work=0.1530 r_free=0.1859 | n_water=369 | time (s): 1.750 (total time: 27.700) Refine new water occ: r_work=0.1326 r_free=0.1561 adp: r_work=0.1269 r_free=0.1559 occ: r_work=0.1273 r_free=0.1528 adp: r_work=0.1242 r_free=0.1534 occ: r_work=0.1244 r_free=0.1532 adp: r_work=0.1230 r_free=0.1526 ADP+occupancy (water only), MIN, final r_work=0.1230 r_free=0.1526 r_work=0.1230 r_free=0.1526 | n_water=369 | time (s): 19.640 (total time: 47.340) Filter (q & B) r_work=0.1232 r_free=0.1530 | n_water=362 | time (s): 1.980 (total time: 49.320) Filter (dist only) r_work=0.1233 r_free=0.1535 | n_water=361 | time (s): 27.500 (total time: 76.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.207325 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.939644 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 0.1202 0.1601 0.0399 0.009 0.9 2.2 0.5 0.0 0 12.604 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 16.01 3.99 4.203 21.093 0.940 0.018 11.91 16.15 4.24 4.151 21.321 0.940 0.017 Individual atomic B min max mean iso aniso Overall: 6.74 107.80 21.29 4.15 1888 0 Protein: 6.74 107.80 17.69 4.14 1519 0 Water: 8.39 65.77 36.16 N/A 361 0 Other: 24.49 42.39 33.08 N/A 8 0 Chain A: 6.74 107.80 19.42 N/A 1739 0 Chain S: 16.92 63.98 43.17 N/A 149 0 Histogram: Values Number of atoms 6.74 - 16.85 1027 16.85 - 26.95 378 26.95 - 37.06 230 37.06 - 47.16 149 47.16 - 57.27 71 57.27 - 67.38 23 67.38 - 77.48 3 77.48 - 87.59 4 87.59 - 97.69 1 97.69 - 107.80 2 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1615 r_work=0.1192 r_free=0.1616 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1616 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1625 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 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= 0.1188 r_free= 0.1625 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016894 | | target function (ls_wunit_k1) not normalized (work): 274.271789 | | target function (ls_wunit_k1) not normalized (free): 24.731469 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1209 0.1188 0.1625 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1757 0.1747 0.1983 n_refl.: 17042 remove outliers: r(all,work,free)=0.1757 0.1747 0.1983 n_refl.: 17042 overall B=-0.40 to atoms: r(all,work,free)=0.1730 0.1720 0.1965 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1182 0.1617 n_refl.: 17042 remove outliers: r(all,work,free)=0.1202 0.1181 0.1617 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 0.3260 300.340 283.963 0.595 1.002 0.340 11.894-9.307 99.02 97 4 0.1534 488.138 484.476 0.919 1.003 0.334 9.237-7.194 100.00 213 7 0.1673 399.247 400.201 0.976 1.003 0.290 7.162-5.571 100.00 427 22 0.1509 299.636 295.633 0.938 1.003 0.271 5.546-4.326 100.00 867 58 0.0870 411.351 407.816 0.963 1.003 0.221 4.315-3.360 100.00 1859 96 0.0817 391.199 390.045 1.017 1.002 0.191 3.356-2.611 100.00 3867 181 0.1195 256.996 256.358 1.014 1.001 0.121 2.608-2.000 99.99 8818 434 0.1321 167.517 166.984 1.019 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4456 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1181 r_free=0.1617 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1183 r_free=0.1620 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1183 r_free=0.1620 | n_water=361 | time (s): 0.890 (total time: 0.890) Filter (dist) r_work=0.1182 r_free=0.1621 | n_water=360 | time (s): 29.680 (total time: 30.570) Filter (q & B) r_work=0.1182 r_free=0.1621 | n_water=360 | time (s): 1.220 (total time: 31.790) Compute maps r_work=0.1182 r_free=0.1621 | n_water=360 | time (s): 0.810 (total time: 32.600) Filter (map) r_work=0.1250 r_free=0.1658 | n_water=268 | time (s): 2.100 (total time: 34.700) Find peaks r_work=0.1250 r_free=0.1658 | n_water=268 | time (s): 0.680 (total time: 35.380) Add new water r_work=0.1419 r_free=0.1821 | n_water=418 | time (s): 2.140 (total time: 37.520) Refine new water occ: r_work=0.1229 r_free=0.1586 adp: r_work=0.1221 r_free=0.1591 occ: r_work=0.1204 r_free=0.1563 adp: r_work=0.1193 r_free=0.1566 occ: r_work=0.1186 r_free=0.1552 adp: r_work=0.1176 r_free=0.1553 ADP+occupancy (water only), MIN, final r_work=0.1176 r_free=0.1553 r_work=0.1176 r_free=0.1553 | n_water=418 | time (s): 31.650 (total time: 69.170) Filter (q & B) r_work=0.1179 r_free=0.1560 | n_water=407 | time (s): 1.840 (total time: 71.010) Filter (dist only) r_work=0.1179 r_free=0.1560 | n_water=407 | time (s): 33.110 (total time: 104.120) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.922351 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.150711 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 0.1162 0.1567 0.0405 0.009 1.0 3.2 0.5 0.0 0 0.961 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.62 15.67 4.05 4.264 21.489 0.151 4.994 11.43 15.67 4.24 4.757 21.423 0.151 4.971 Individual atomic B min max mean iso aniso Overall: 6.37 105.26 20.94 4.59 1934 0 Protein: 6.37 105.26 17.00 4.58 1519 0 Water: 8.73 62.12 35.40 N/A 407 0 Other: 26.18 44.59 34.17 N/A 8 0 Chain A: 6.37 105.26 18.82 N/A 1739 0 Chain S: 14.49 62.12 39.86 N/A 195 0 Histogram: Values Number of atoms 6.37 - 16.26 1066 16.26 - 26.14 350 26.14 - 36.03 231 36.03 - 45.92 174 45.92 - 55.81 71 55.81 - 65.70 30 65.70 - 75.59 5 75.59 - 85.48 2 85.48 - 95.37 3 95.37 - 105.26 2 =========================== Idealize ADP of riding H ========================== r_work=0.1143 r_free=0.1567 r_work=0.1143 r_free=0.1569 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1143 r_free = 0.1569 target_work(ml) = 4.972 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1137 r_free = 0.1564 target_work(ml) = 4.967 | | occupancies: max = 1.00 min = 0.21 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= 0.1137 r_free= 0.1564 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.967401 | | target function (ml) not normalized (work): 80640.782902 | | target function (ml) not normalized (free): 4191.775597 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1158 0.1137 0.1564 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1679 0.1673 0.1868 n_refl.: 17041 remove outliers: r(all,work,free)=0.1679 0.1673 0.1868 n_refl.: 17041 overall B=-0.47 to atoms: r(all,work,free)=0.1647 0.1639 0.1852 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1157 0.1136 0.1567 n_refl.: 17041 remove outliers: r(all,work,free)=0.1157 0.1136 0.1567 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 0.3469 300.340 281.647 0.580 1.005 0.350 11.894-9.307 99.02 97 4 0.1666 488.138 484.191 0.917 1.006 0.327 9.237-7.194 100.00 213 7 0.1769 399.247 401.024 0.987 1.007 0.270 7.162-5.571 100.00 427 22 0.1585 299.636 294.274 0.937 1.006 0.230 5.546-4.326 100.00 867 58 0.0919 411.351 407.858 0.963 1.005 0.216 4.315-3.360 100.00 1859 96 0.0880 391.199 388.630 1.012 1.004 0.212 3.356-2.611 100.00 3867 181 0.1276 256.996 254.883 1.011 1.001 0.152 2.608-2.000 99.99 8818 434 0.1086 167.517 166.109 1.013 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1854 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1136 r_free=0.1567 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1136 r_free=0.1567 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1136 r_free=0.1567 | n_water=407 | time (s): 0.840 (total time: 0.840) Filter (dist) r_work=0.1136 r_free=0.1569 | n_water=406 | time (s): 33.750 (total time: 34.590) Filter (q & B) r_work=0.1136 r_free=0.1569 | n_water=406 | time (s): 0.970 (total time: 35.560) Compute maps r_work=0.1136 r_free=0.1569 | n_water=406 | time (s): 0.670 (total time: 36.230) Filter (map) r_work=0.1196 r_free=0.1600 | n_water=318 | time (s): 1.520 (total time: 37.750) Find peaks r_work=0.1196 r_free=0.1600 | n_water=318 | time (s): 0.440 (total time: 38.190) Add new water r_work=0.1348 r_free=0.1729 | n_water=462 | time (s): 1.920 (total time: 40.110) Refine new water occ: r_work=0.1179 r_free=0.1552 adp: r_work=0.1172 r_free=0.1558 occ: r_work=0.1153 r_free=0.1527 adp: r_work=0.1145 r_free=0.1535 occ: r_work=0.1136 r_free=0.1514 adp: r_work=0.1128 r_free=0.1522 ADP+occupancy (water only), MIN, final r_work=0.1128 r_free=0.1522 r_work=0.1128 r_free=0.1522 | n_water=462 | time (s): 31.660 (total time: 71.770) Filter (q & B) r_work=0.1131 r_free=0.1532 | n_water=453 | time (s): 2.230 (total time: 74.000) Filter (dist only) r_work=0.1134 r_free=0.1528 | n_water=451 | time (s): 38.570 (total time: 112.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.951923 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.191785 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 0.1119 0.1563 0.0444 0.010 1.0 4.2 0.5 0.0 0 0.976 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.19 15.63 4.44 4.437 21.073 0.192 4.965 11.07 15.69 4.62 4.651 21.122 0.192 4.956 Individual atomic B min max mean iso aniso Overall: 5.61 102.79 21.10 4.92 1978 0 Protein: 5.61 102.79 16.48 4.91 1519 0 Water: 8.71 66.65 36.45 N/A 451 0 Other: 25.96 44.34 33.33 N/A 8 0 Chain A: 5.61 102.79 18.24 N/A 1737 0 Chain S: 14.85 66.65 41.72 N/A 241 0 Histogram: Values Number of atoms 5.61 - 15.32 1036 15.32 - 25.04 371 25.04 - 34.76 213 34.76 - 44.48 193 44.48 - 54.20 108 54.20 - 63.92 41 63.92 - 73.63 7 73.63 - 83.35 4 83.35 - 93.07 2 93.07 - 102.79 3 =========================== Idealize ADP of riding H ========================== r_work=0.1107 r_free=0.1569 r_work=0.1107 r_free=0.1569 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1107 r_free = 0.1569 target_work(ml) = 4.956 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1100 r_free = 0.1561 target_work(ml) = 4.950 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1100 r_free= 0.1561 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.949556 | | target function (ml) not normalized (work): 80351.095766 | | target function (ml) not normalized (free): 4184.510221 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1122 0.1100 0.1561 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1599 0.1587 0.1867 n_refl.: 17041 remove outliers: r(all,work,free)=0.1599 0.1587 0.1867 n_refl.: 17041 overall B=-0.28 to atoms: r(all,work,free)=0.1582 0.1569 0.1857 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1120 0.1097 0.1559 n_refl.: 17041 remove outliers: r(all,work,free)=0.1120 0.1097 0.1559 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 0.3634 300.340 281.156 0.564 1.001 0.340 11.894-9.307 99.02 97 4 0.1694 488.138 483.687 0.918 1.003 0.340 9.237-7.194 100.00 213 7 0.1691 399.247 400.673 0.988 1.004 0.245 7.162-5.571 100.00 427 22 0.1543 299.636 294.838 0.941 1.004 0.225 5.546-4.326 100.00 867 58 0.0904 411.351 407.989 0.964 1.003 0.211 4.315-3.360 100.00 1859 96 0.0843 391.199 388.909 1.007 1.003 0.201 3.356-2.611 100.00 3867 181 0.1226 256.996 254.818 1.003 1.001 0.171 2.608-2.000 99.99 8818 434 0.1046 167.517 166.273 1.000 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9676 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1097 r_free=0.1559 After: r_work=0.1100 r_free=0.1557 ================================== NQH flips ================================== r_work=0.1100 r_free=0.1557 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1100 r_free=0.1557 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1100 r_free=0.1557 | n_water=451 | time (s): 0.700 (total time: 0.700) Filter (dist) r_work=0.1100 r_free=0.1557 | n_water=451 | time (s): 35.430 (total time: 36.130) Filter (q & B) r_work=0.1100 r_free=0.1558 | n_water=449 | time (s): 1.600 (total time: 37.730) Compute maps r_work=0.1100 r_free=0.1558 | n_water=449 | time (s): 0.580 (total time: 38.310) Filter (map) r_work=0.1181 r_free=0.1587 | n_water=336 | time (s): 1.560 (total time: 39.870) Find peaks r_work=0.1181 r_free=0.1587 | n_water=336 | time (s): 0.600 (total time: 40.470) Add new water r_work=0.1313 r_free=0.1756 | n_water=471 | time (s): 2.230 (total time: 42.700) Refine new water occ: r_work=0.1151 r_free=0.1556 adp: r_work=0.1146 r_free=0.1565 occ: r_work=0.1131 r_free=0.1518 adp: r_work=0.1124 r_free=0.1529 occ: r_work=0.1116 r_free=0.1495 adp: r_work=0.1110 r_free=0.1503 ADP+occupancy (water only), MIN, final r_work=0.1110 r_free=0.1503 r_work=0.1110 r_free=0.1503 | n_water=471 | time (s): 35.690 (total time: 78.390) Filter (q & B) r_work=0.1112 r_free=0.1511 | n_water=462 | time (s): 2.170 (total time: 80.560) Filter (dist only) r_work=0.1112 r_free=0.1511 | n_water=462 | time (s): 36.980 (total time: 117.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.902201 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.144379 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 0.1129 0.1525 0.0396 0.010 1.1 4.5 0.5 0.0 0 0.951 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.29 15.25 3.96 4.578 20.809 0.144 4.958 11.19 15.14 3.95 4.609 20.851 0.144 4.950 Individual atomic B min max mean iso aniso Overall: 5.20 100.33 20.93 4.87 1989 0 Protein: 5.20 100.33 16.22 4.87 1519 0 Water: 8.15 63.18 36.24 N/A 462 0 Other: 25.28 40.99 32.14 N/A 8 0 Chain A: 5.20 100.33 17.89 N/A 1735 0 Chain S: 13.87 63.18 41.74 N/A 254 0 Histogram: Values Number of atoms 5.20 - 14.71 1006 14.71 - 24.23 390 24.23 - 33.74 209 33.74 - 43.25 194 43.25 - 52.76 137 52.76 - 62.28 35 62.28 - 71.79 8 71.79 - 81.30 3 81.30 - 90.81 3 90.81 - 100.33 4 =========================== Idealize ADP of riding H ========================== r_work=0.1119 r_free=0.1514 r_work=0.1119 r_free=0.1514 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1119 r_free = 0.1514 target_work(ml) = 4.950 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1113 r_free = 0.1505 target_work(ml) = 4.945 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1113 r_free= 0.1505 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.945095 | | target function (ml) not normalized (work): 80278.676630 | | target function (ml) not normalized (free): 4167.774084 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2811 159 0.1130 0.1400 5.4658 5.6498| | 2: 3.63 - 2.88 1.00 2711 122 0.1088 0.1457 5.215 5.3351| | 3: 2.88 - 2.52 1.00 2681 148 0.1350 0.1656 5.1206 5.2055| | 4: 2.52 - 2.29 1.00 2661 139 0.0954 0.1504 4.6486 4.9576| | 5: 2.29 - 2.13 1.00 2678 122 0.0970 0.1511 4.5982 4.912| | 6: 2.13 - 2.00 1.00 2692 117 0.1130 0.1735 4.5929 4.7843| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2811 159 0.95 8.90 1.00 0.96 6194.03| | 2: 3.63 - 2.88 2711 122 0.93 12.63 1.01 0.96 6194.03| | 3: 2.88 - 2.52 2681 148 0.88 18.71 0.99 0.96 6194.03| | 4: 2.52 - 2.29 2661 139 0.92 12.52 1.01 0.98 2228.69| | 5: 2.29 - 2.13 2678 122 0.91 14.57 1.00 0.98 2228.69| | 6: 2.13 - 2.00 2692 117 0.89 17.30 0.99 0.98 2228.69| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2228.69 max = 6194.03 mean = 4232.37| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.81 mean = 14.07| |phase err.(test): min = 0.00 max = 88.13 mean = 13.60| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1132 0.1113 0.1505 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1589 0.1579 0.1814 n_refl.: 17041 remove outliers: r(all,work,free)=0.1589 0.1579 0.1814 n_refl.: 17041 overall B=-0.23 to atoms: r(all,work,free)=0.1575 0.1565 0.1806 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1132 0.1114 0.1500 n_refl.: 17041 remove outliers: r(all,work,free)=0.1132 0.1113 0.1500 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 0.3533 297.664 281.930 0.559 1.003 0.340 11.894-9.307 99.02 97 4 0.1790 488.138 482.117 0.916 1.005 0.310 9.237-7.194 100.00 213 7 0.1713 399.247 400.547 0.987 1.005 0.240 7.162-5.571 100.00 427 22 0.1611 299.636 294.547 0.935 1.005 0.215 5.546-4.326 100.00 867 58 0.0945 411.351 407.625 0.962 1.004 0.207 4.315-3.360 100.00 1859 96 0.0875 391.199 388.815 1.004 1.003 0.191 3.356-2.611 100.00 3867 181 0.1237 256.996 254.587 1.000 1.001 0.151 2.608-2.000 99.99 8818 434 0.1046 167.517 166.128 0.993 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.8046 ================= 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 : 0.2791 0.1859 0.084 5.318 8.8 119.3 19.9 258 0.000 1_bss: 0.1618 0.1712 0.084 5.318 8.4 118.9 19.5 258 0.000 1_settarget: 0.1618 0.1712 0.084 5.318 8.4 118.9 19.5 258 0.000 1_nqh: 0.1619 0.1715 0.084 5.318 8.4 118.9 19.5 258 0.003 1_weight: 0.1619 0.1715 0.084 5.318 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1350 0.1643 0.009 0.976 8.4 118.9 19.5 258 0.150 1_adp: 0.1276 0.1664 0.009 0.976 6.2 113.9 20.0 258 0.150 1_regHadp: 0.1279 0.1668 0.009 0.976 6.2 113.9 20.0 258 0.150 1_occ: 0.1273 0.1655 0.009 0.976 6.2 113.9 20.0 258 0.150 2_bss: 0.1272 0.1646 0.009 0.976 5.8 113.5 19.6 258 0.150 2_settarget: 0.1272 0.1646 0.009 0.976 5.8 113.5 19.6 258 0.150 2_updatecdl: 0.1272 0.1646 0.009 0.997 5.8 113.5 19.6 258 0.150 2_nqh: 0.1272 0.1646 0.009 0.997 5.8 113.5 19.6 258 0.150 2_sol: 0.1233 0.1535 0.009 0.997 5.8 112.8 20.9 361 n/a 2_weight: 0.1233 0.1535 0.009 0.997 5.8 112.8 20.9 361 n/a 2_xyzrec: 0.1202 0.1601 0.009 0.942 5.8 112.8 20.9 361 n/a 2_adp: 0.1191 0.1615 0.009 0.942 6.7 107.8 21.3 361 n/a 2_regHadp: 0.1192 0.1616 0.009 0.942 6.7 107.8 21.3 361 n/a 2_occ: 0.1188 0.1625 0.009 0.942 6.7 107.8 21.3 361 n/a 3_bss: 0.1181 0.1617 0.009 0.942 6.3 107.4 20.9 361 n/a 3_settarget: 0.1181 0.1617 0.009 0.942 6.3 107.4 20.9 361 n/a 3_updatecdl: 0.1181 0.1617 0.009 0.938 6.3 107.4 20.9 361 n/a 3_nqh: 0.1183 0.1620 0.009 0.938 6.3 107.4 20.9 361 n/a 3_sol: 0.1179 0.1560 0.009 0.938 6.3 107.4 21.1 407 n/a 3_weight: 0.1179 0.1560 0.009 0.938 6.3 107.4 21.1 407 n/a 3_xyzrec: 0.1162 0.1567 0.009 0.967 6.3 107.4 21.1 407 n/a 3_adp: 0.1143 0.1567 0.009 0.967 6.4 105.3 20.9 407 n/a 3_regHadp: 0.1143 0.1569 0.009 0.967 6.4 105.3 20.9 407 n/a 3_occ: 0.1137 0.1564 0.009 0.967 6.4 105.3 20.9 407 n/a 4_bss: 0.1136 0.1567 0.009 0.967 5.9 104.8 20.5 407 n/a 4_settarget: 0.1136 0.1567 0.009 0.967 5.9 104.8 20.5 407 n/a 4_updatecdl: 0.1136 0.1567 0.009 0.968 5.9 104.8 20.5 407 n/a 4_nqh: 0.1136 0.1567 0.009 0.968 5.9 104.8 20.5 407 n/a 4_sol: 0.1134 0.1528 0.009 0.968 5.9 104.8 21.0 451 n/a 4_weight: 0.1134 0.1528 0.009 0.968 5.9 104.8 21.0 451 n/a 4_xyzrec: 0.1119 0.1563 0.010 0.983 5.9 104.8 21.0 451 n/a 4_adp: 0.1107 0.1569 0.010 0.983 5.6 102.8 21.1 451 n/a 4_regHadp: 0.1107 0.1569 0.010 0.983 5.6 102.8 21.1 451 n/a 4_occ: 0.1100 0.1561 0.010 0.983 5.6 102.8 21.1 451 n/a 5_bss: 0.1097 0.1559 0.010 0.983 5.3 102.5 20.8 451 n/a 5_settarget: 0.1097 0.1559 0.010 0.983 5.3 102.5 20.8 451 n/a 5_updatecdl: 0.1097 0.1559 0.010 0.985 5.3 102.5 20.8 451 n/a 5_setrh: 0.1100 0.1557 0.010 0.985 5.3 102.5 20.8 451 n/a 5_nqh: 0.1100 0.1557 0.010 0.985 5.3 102.5 20.8 451 n/a 5_sol: 0.1112 0.1511 0.010 0.985 5.3 102.5 20.9 462 n/a 5_weight: 0.1112 0.1511 0.010 0.985 5.3 102.5 20.9 462 n/a 5_xyzrec: 0.1129 0.1525 0.010 1.065 5.3 102.5 20.9 462 n/a 5_adp: 0.1119 0.1514 0.010 1.065 5.2 100.3 20.9 462 n/a 5_regHadp: 0.1119 0.1514 0.010 1.065 5.2 100.3 20.9 462 n/a 5_occ: 0.1113 0.1505 0.010 1.065 5.2 100.3 20.9 462 n/a end: 0.1113 0.1500 0.010 1.065 5.0 100.1 20.7 462 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7326401_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7326401_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0400 Refinement macro-cycles (run) : 947.3200 Write final files (write_after_run_outputs) : 18.1600 Total : 968.5200 Total CPU time: 16.53 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:33 PST -0800 (1735494093.39 s) Start R-work = 0.1618, R-free = 0.1712 Final R-work = 0.1113, R-free = 0.1500 =============================================================================== Job complete usr+sys time: 1011.01 seconds wall clock time: 17 minutes 14.25 seconds (1034.25 seconds total)