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_8498250.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8498250.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8498250.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 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 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.92, per 1000 atoms: 0.57 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 138.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 524 0.91 - 1.17: 1127 1.17 - 1.42: 638 1.42 - 1.68: 824 1.68 - 1.93: 40 Bond restraints: 3153 Sorted by residual: bond pdb=" C LEU A 92 " pdb=" O LEU A 92 " ideal model delta sigma weight residual 1.237 0.948 0.289 1.16e-02 7.43e+03 6.19e+02 bond pdb=" CE1 HIS A 138 " pdb=" NE2 HIS A 138 " ideal model delta sigma weight residual 1.321 1.512 -0.191 1.00e-02 1.00e+04 3.65e+02 bond pdb=" C THR A 34 " pdb=" N VAL A 35 " ideal model delta sigma weight residual 1.331 1.522 -0.191 1.05e-02 9.07e+03 3.32e+02 bond pdb=" N SER A 142 " pdb=" CA SER A 142 " ideal model delta sigma weight residual 1.455 1.231 0.224 1.25e-02 6.40e+03 3.21e+02 bond pdb=" CA ALA A 165 " pdb=" C ALA A 165 " ideal model delta sigma weight residual 1.524 1.300 0.224 1.29e-02 6.01e+03 3.01e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.97: 3296 4.97 - 9.94: 1848 9.94 - 14.91: 558 14.91 - 19.88: 72 19.88 - 24.85: 3 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CD2 HIS A 138 " pdb=" NE2 HIS A 138 " pdb=" CE1 HIS A 138 " ideal model delta sigma weight residual 109.00 95.86 13.14 1.00e+00 1.00e+00 1.73e+02 angle pdb=" O ALA A 171 " pdb=" C ALA A 171 " pdb=" N LEU A 172 " ideal model delta sigma weight residual 122.27 138.23 -15.96 1.23e+00 6.61e-01 1.68e+02 angle pdb=" OD1BASN A 76 " pdb=" CG BASN A 76 " pdb=" ND2BASN A 76 " ideal model delta sigma weight residual 122.60 135.57 -12.97 1.00e+00 1.00e+00 1.68e+02 angle pdb=" CA LEU A 92 " pdb=" C LEU A 92 " pdb=" N ALYS A 93 " ideal model delta sigma weight residual 117.39 101.55 15.84 1.24e+00 6.50e-01 1.63e+02 angle pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " ideal model delta sigma weight residual 115.61 102.52 13.09 1.03e+00 9.43e-01 1.62e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 15.72: 1270 15.72 - 31.43: 154 31.43 - 47.13: 31 47.13 - 62.84: 22 62.84 - 78.55: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N GLU A 116 " pdb=" C GLU A 116 " pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " ideal model delta harmonic sigma weight residual 122.80 144.78 -21.98 0 2.50e+00 1.60e-01 7.73e+01 dihedral pdb=" C GLU A 116 " pdb=" N GLU A 116 " pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " ideal model delta harmonic sigma weight residual -122.60 -142.28 19.68 0 2.50e+00 1.60e-01 6.19e+01 dihedral pdb=" C HIS A 138 " pdb=" N HIS A 138 " pdb=" CA HIS A 138 " pdb=" CB HIS A 138 " ideal model delta harmonic sigma weight residual -122.60 -141.26 18.66 0 2.50e+00 1.60e-01 5.57e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.253: 115 0.253 - 0.506: 72 0.506 - 0.759: 40 0.759 - 1.011: 12 1.011 - 1.264: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 72 " pdb=" CB LEU A 72 " pdb=" CD1 LEU A 72 " pdb=" CD2 LEU A 72 " both_signs ideal model delta sigma weight residual False -2.59 -3.85 1.26 2.00e-01 2.50e+01 4.00e+01 chirality pdb=" CA HIS A 138 " pdb=" N HIS A 138 " pdb=" C HIS A 138 " pdb=" CB HIS A 138 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.77e+01 chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 1.49 1.03 2.00e-01 2.50e+01 2.67e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.006 2.00e-02 2.50e+03 6.56e-02 1.29e+02 pdb=" CG TYR A 141 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.080 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.138 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.056 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.137 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.094 2.00e-02 2.50e+03 7.07e-02 1.12e+02 pdb=" CG HIS A 126 " -0.124 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " -0.043 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.019 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.018 2.00e-02 2.50e+03 5.86e-02 1.03e+02 pdb=" CG PHE A 164 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.114 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.019 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.061 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.032 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.113 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.064 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 620 2.25 - 2.84: 7617 2.84 - 3.42: 10668 3.42 - 4.01: 15427 4.01 - 4.60: 22287 Nonbonded interactions: 56619 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.662 2.100 nonbonded pdb=" O GLY A 37 " pdb=" H LEU A 58 " model vdw 1.810 2.450 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.853 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.865 2.450 nonbonded pdb=" HA AASN A 76 " pdb="HD22AASN A 76 " model vdw 1.875 2.270 ... (remaining 56614 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_8498250_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= 0.2785 r_free= 0.1814 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.419065 | | target function (ml) not normalized (work): 71778.875276 | | target function (ml) not normalized (free): 3258.400495 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3201 0.2142 7.6292 5.0376| | 2: 3.63 - 2.88 1.00 2711 122 0.2637 0.1748 4.3236 4.3193| | 3: 2.88 - 2.52 1.00 2682 148 0.2533 0.1557 4.1687 4.1656| | 4: 2.52 - 2.29 1.00 2661 139 0.2557 0.1505 3.5031 3.5209| | 5: 2.29 - 2.13 1.00 2678 122 0.2632 0.1601 3.4073 3.5055| | 6: 2.13 - 2.00 1.00 2692 117 0.2762 0.1929 3.315 3.3922| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.27 0.77 0.23 1265.54| | 2: 3.63 - 2.88 2711 122 0.83 23.39 1.32 0.23 1265.54| | 3: 2.88 - 2.52 2682 148 0.74 32.36 1.29 0.23 1265.54| | 4: 2.52 - 2.29 2661 139 0.93 11.17 1.30 0.26 133.38| | 5: 2.29 - 2.13 2678 122 0.92 13.28 1.31 0.26 133.38| | 6: 2.13 - 2.00 2692 117 0.90 16.18 1.34 0.26 133.38| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 133.38 max = 1265.54 mean = 705.77| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.94 mean = 18.94| |phase err.(test): min = 0.00 max = 89.63 mean = 19.50| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.289 1557 Z= 5.583 Angle : 5.285 17.694 2118 Z= 3.771 Chirality : 0.415 1.264 243 Planarity : 0.033 0.111 284 Dihedral : 13.679 78.546 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 30.81 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.44), residues: 224 helix: -2.54 (0.34), residues: 108 sheet: -0.48 (0.92), residues: 28 loop : -0.44 (0.52), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.063 0.020 ARG A 5 TYR 0.091 0.043 TYR A 141 PHE 0.105 0.045 PHE A 162 HIS 0.081 0.050 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= 0.2785 r_free= 0.1814 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.419065 | | target function (ml) not normalized (work): 71778.875276 | | target function (ml) not normalized (free): 3258.400495 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3396 percent. r_work = 0.2919 r_free = 0.1972 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2865 0.2919 0.1972 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2865 0.2919 0.1972 n_refl.: 17050 remove outliers: r(all,work,free)=0.2154 0.2165 0.1972 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2126 0.2137 0.1954 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1608 0.1607 0.1638 n_refl.: 17045 remove outliers: r(all,work,free)=0.1607 0.1606 0.1638 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 0.4012 394.875 365.787 0.649 1.013 0.397 11.894-9.307 99.02 97 4 0.1854 633.785 614.619 0.933 1.013 0.380 9.237-7.194 100.00 213 7 0.2222 518.373 508.233 0.958 1.013 0.350 7.162-5.571 100.00 427 22 0.2348 389.039 376.155 0.921 1.012 0.299 5.546-4.326 100.00 867 58 0.1410 534.088 528.051 0.960 1.010 0.230 4.315-3.360 100.00 1859 96 0.1269 507.923 503.628 1.018 1.006 0.201 3.356-2.611 100.00 3867 181 0.1637 333.677 329.917 1.013 1.001 0.081 2.608-2.000 99.99 8818 434 0.1646 217.500 213.360 1.029 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4838 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1606 r_free=0.1638 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1606 r_free=0.1638 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.580879 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.915994 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 0.1641 0.0290 0.009 1.0 1.0 0.5 0.0 0 11.790 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.41 2.90 3.013 18.443 0.916 0.023 12.77 16.59 3.82 3.615 18.691 0.916 0.020 Individual atomic B min max mean iso aniso Overall: 6.15 113.88 19.94 4.10 1785 0 Protein: 6.15 112.80 17.17 4.10 1519 0 Water: 8.61 113.88 36.06 N/A 258 0 Other: 21.95 37.24 26.40 N/A 8 0 Chain A: 6.15 113.88 19.94 N/A 1785 0 Histogram: Values Number of atoms 6.15 - 16.92 1088 16.92 - 27.69 338 27.69 - 38.47 185 38.47 - 49.24 98 49.24 - 60.02 49 60.02 - 70.79 12 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=0.1277 r_free=0.1659 r_work=0.1280 r_free=0.1666 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1280 r_free = 0.1666 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): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020107 | | target function (ls_wunit_k1) not normalized (work): 326.483950 | | target function (ls_wunit_k1) not normalized (free): 27.095171 | |-----------------------------------------------------------------------------| =========================== 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 0.1983 n_refl.: 17044 remove outliers: r(all,work,free)=0.1911 0.1910 0.1983 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1882 0.1881 0.1968 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1294 0.1276 0.1655 n_refl.: 17044 remove outliers: r(all,work,free)=0.1292 0.1274 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 0.3603 303.789 279.428 0.620 1.010 0.370 11.894-9.307 99.02 97 4 0.1699 488.596 477.899 0.917 1.011 0.367 9.237-7.194 100.00 213 7 0.1848 399.622 395.358 0.958 1.010 0.351 7.162-5.571 100.00 427 22 0.1862 299.917 294.825 0.930 1.009 0.301 5.546-4.326 100.00 867 58 0.1049 411.738 409.445 0.958 1.008 0.211 4.315-3.360 100.00 1859 96 0.0925 391.567 391.206 1.018 1.005 0.201 3.356-2.611 100.00 3867 181 0.1294 257.237 256.026 1.015 1.000 0.101 2.608-2.000 99.99 8818 434 0.1347 167.674 166.212 1.023 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3922 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1655 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1274 r_free=0.1655 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1655 | n_water=258 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.1278 r_free=0.1645 | n_water=253 | time (s): 19.870 (total time: 20.550) Filter (q & B) r_work=0.1279 r_free=0.1645 | n_water=251 | time (s): 2.100 (total time: 22.650) Compute maps r_work=0.1279 r_free=0.1645 | n_water=251 | time (s): 0.790 (total time: 23.440) Filter (map) r_work=0.1310 r_free=0.1637 | n_water=213 | time (s): 1.980 (total time: 25.420) Find peaks r_work=0.1310 r_free=0.1637 | n_water=213 | time (s): 0.680 (total time: 26.100) Add new water r_work=0.1531 r_free=0.1865 | n_water=371 | time (s): 1.720 (total time: 27.820) Refine new water occ: r_work=0.1328 r_free=0.1570 adp: r_work=0.1268 r_free=0.1564 occ: r_work=0.1275 r_free=0.1539 adp: r_work=0.1241 r_free=0.1544 occ: r_work=0.1243 r_free=0.1534 adp: r_work=0.1232 r_free=0.1533 ADP+occupancy (water only), MIN, final r_work=0.1232 r_free=0.1533 r_work=0.1232 r_free=0.1533 | n_water=371 | time (s): 11.900 (total time: 39.720) Filter (q & B) r_work=0.1234 r_free=0.1540 | n_water=363 | time (s): 1.640 (total time: 41.360) Filter (dist only) r_work=0.1234 r_free=0.1542 | n_water=362 | time (s): 27.610 (total time: 68.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.387520 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.987752 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 0.1207 0.1599 0.0392 0.008 0.9 2.6 0.5 0.0 0 12.194 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 15.99 3.92 4.178 21.012 0.988 0.018 11.96 16.23 4.28 4.183 21.338 0.988 0.018 Individual atomic B min max mean iso aniso Overall: 7.02 107.41 21.40 4.26 1889 0 Protein: 7.02 107.41 17.81 4.26 1519 0 Water: 8.99 65.97 36.23 N/A 362 0 Other: 23.55 42.33 32.28 N/A 8 0 Chain A: 7.02 107.41 19.54 N/A 1740 0 Chain S: 17.21 65.97 43.11 N/A 149 0 Histogram: Values Number of atoms 7.02 - 17.06 1036 17.06 - 27.09 365 27.09 - 37.13 228 37.13 - 47.17 157 47.17 - 57.21 67 57.21 - 67.25 26 67.25 - 77.29 3 77.29 - 87.33 4 87.33 - 97.37 1 97.37 - 107.41 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1623 r_work=0.1197 r_free=0.1624 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1624 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1632 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.19 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= 0.1192 r_free= 0.1632 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016925 | | target function (ls_wunit_k1) not normalized (work): 274.774789 | | target function (ls_wunit_k1) not normalized (free): 24.734679 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1192 0.1632 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1765 0.1756 0.1986 n_refl.: 17042 remove outliers: r(all,work,free)=0.1765 0.1756 0.1986 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1740 0.1730 0.1970 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1187 0.1626 n_refl.: 17042 remove outliers: r(all,work,free)=0.1208 0.1187 0.1626 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 0.3358 303.789 284.120 0.599 1.005 0.350 11.894-9.307 99.02 97 4 0.1526 488.596 486.412 0.915 1.005 0.344 9.237-7.194 100.00 213 7 0.1683 399.622 399.107 0.974 1.005 0.320 7.162-5.571 100.00 427 22 0.1579 299.917 296.084 0.938 1.005 0.261 5.546-4.326 100.00 867 58 0.0859 411.738 408.791 0.958 1.004 0.211 4.315-3.360 100.00 1859 96 0.0820 391.567 390.681 1.016 1.003 0.201 3.356-2.611 100.00 3867 181 0.1188 257.237 256.503 1.011 1.001 0.111 2.608-2.000 99.99 8818 434 0.1333 167.674 166.627 1.018 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3725 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1626 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 97 ASN B Total number of N/Q/H flips: 2 r_work=0.1188 r_free=0.1630 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1630 | n_water=362 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.1189 r_free=0.1630 | n_water=361 | time (s): 29.330 (total time: 29.990) Filter (q & B) r_work=0.1189 r_free=0.1630 | n_water=361 | time (s): 0.750 (total time: 30.740) Compute maps r_work=0.1189 r_free=0.1630 | n_water=361 | time (s): 0.620 (total time: 31.360) Filter (map) r_work=0.1259 r_free=0.1655 | n_water=264 | time (s): 1.580 (total time: 32.940) Find peaks r_work=0.1259 r_free=0.1655 | n_water=264 | time (s): 0.430 (total time: 33.370) Add new water r_work=0.1433 r_free=0.1801 | n_water=410 | time (s): 1.410 (total time: 34.780) Refine new water occ: r_work=0.1244 r_free=0.1559 adp: r_work=0.1235 r_free=0.1566 occ: r_work=0.1218 r_free=0.1534 adp: r_work=0.1206 r_free=0.1539 occ: r_work=0.1200 r_free=0.1524 adp: r_work=0.1189 r_free=0.1526 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1526 r_work=0.1189 r_free=0.1526 | n_water=410 | time (s): 50.710 (total time: 85.490) Filter (q & B) r_work=0.1191 r_free=0.1538 | n_water=400 | time (s): 1.550 (total time: 87.040) Filter (dist only) r_work=0.1191 r_free=0.1539 | n_water=399 | time (s): 33.010 (total time: 120.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.873702 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.140957 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 0.1169 0.1528 0.0359 0.009 1.0 3.8 0.5 0.0 0 0.937 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.69 15.28 3.59 4.332 21.590 0.141 4.989 11.47 15.26 3.79 4.865 21.478 0.141 4.964 Individual atomic B min max mean iso aniso Overall: 6.41 104.69 20.91 4.62 1926 0 Protein: 6.41 104.69 17.07 4.62 1519 0 Water: 8.87 62.43 35.32 N/A 399 0 Other: 24.55 42.07 31.68 N/A 8 0 Chain A: 6.41 104.69 18.85 N/A 1739 0 Chain S: 15.10 62.43 40.04 N/A 187 0 Histogram: Values Number of atoms 6.41 - 16.23 1060 16.23 - 26.06 358 26.06 - 35.89 220 35.89 - 45.72 171 45.72 - 55.55 70 55.55 - 65.37 34 65.37 - 75.20 4 75.20 - 85.03 4 85.03 - 94.86 3 94.86 - 104.69 2 =========================== Idealize ADP of riding H ========================== r_work=0.1147 r_free=0.1526 r_work=0.1147 r_free=0.1526 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1147 r_free = 0.1526 target_work(ml) = 4.963 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1142 r_free = 0.1520 target_work(ml) = 4.958 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1142 r_free= 0.1520 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.957860 | | target function (ml) not normalized (work): 80490.861805 | | target function (ml) not normalized (free): 4172.504284 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1160 0.1142 0.1520 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1679 0.1674 0.1830 n_refl.: 17042 remove outliers: r(all,work,free)=0.1679 0.1674 0.1830 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1652 0.1646 0.1819 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1159 0.1141 0.1519 n_refl.: 17042 remove outliers: r(all,work,free)=0.1158 0.1140 0.1519 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 0.3671 300.293 280.886 0.562 1.005 0.340 11.894-9.307 99.02 97 4 0.1738 488.596 484.145 0.911 1.007 0.334 9.237-7.194 100.00 213 7 0.1788 399.622 400.344 0.982 1.007 0.270 7.162-5.571 100.00 427 22 0.1591 299.917 294.652 0.942 1.006 0.230 5.546-4.326 100.00 867 58 0.0937 411.738 407.973 0.961 1.006 0.206 4.315-3.360 100.00 1859 96 0.0876 391.567 389.053 1.012 1.004 0.201 3.356-2.611 100.00 3867 181 0.1271 257.237 255.022 1.012 1.001 0.142 2.608-2.000 99.99 8818 434 0.1090 167.674 166.334 1.018 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3562 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1140 r_free=0.1519 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=0.1140 r_free=0.1515 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1140 r_free=0.1515 | n_water=399 | time (s): 0.860 (total time: 0.860) Filter (dist) r_work=0.1140 r_free=0.1517 | n_water=398 | time (s): 32.900 (total time: 33.760) Filter (q & B) r_work=0.1140 r_free=0.1517 | n_water=398 | time (s): 1.030 (total time: 34.790) Compute maps r_work=0.1140 r_free=0.1517 | n_water=398 | time (s): 0.640 (total time: 35.430) Filter (map) r_work=0.1196 r_free=0.1577 | n_water=316 | time (s): 1.850 (total time: 37.280) Find peaks r_work=0.1196 r_free=0.1577 | n_water=316 | time (s): 0.450 (total time: 37.730) Add new water r_work=0.1334 r_free=0.1677 | n_water=456 | time (s): 1.600 (total time: 39.330) Refine new water occ: r_work=0.1169 r_free=0.1480 adp: r_work=0.1162 r_free=0.1487 occ: r_work=0.1147 r_free=0.1465 adp: r_work=0.1139 r_free=0.1471 occ: r_work=0.1134 r_free=0.1464 adp: r_work=0.1126 r_free=0.1468 ADP+occupancy (water only), MIN, final r_work=0.1126 r_free=0.1468 r_work=0.1126 r_free=0.1468 | n_water=456 | time (s): 29.440 (total time: 68.770) Filter (q & B) r_work=0.1130 r_free=0.1479 | n_water=443 | time (s): 1.530 (total time: 70.300) Filter (dist only) r_work=0.1132 r_free=0.1477 | n_water=441 | time (s): 36.580 (total time: 106.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.929370 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.163436 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 0.1126 0.1539 0.0413 0.010 1.0 3.8 0.5 0.0 0 0.965 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 15.39 4.13 4.463 21.123 0.163 4.959 11.12 15.38 4.26 4.680 21.128 0.163 4.950 Individual atomic B min max mean iso aniso Overall: 5.76 102.16 20.96 4.83 1968 0 Protein: 5.76 102.16 16.60 4.83 1519 0 Water: 8.57 66.37 35.90 N/A 441 0 Other: 19.17 36.69 26.30 N/A 8 0 Chain A: 5.76 102.16 18.33 N/A 1738 0 Chain S: 17.37 66.37 40.89 N/A 230 0 Histogram: Values Number of atoms 5.76 - 15.40 1032 15.40 - 25.04 384 25.04 - 34.68 214 34.68 - 44.32 176 44.32 - 53.96 113 53.96 - 63.60 33 63.60 - 73.24 7 73.24 - 82.88 4 82.88 - 92.52 2 92.52 - 102.16 3 =========================== Idealize ADP of riding H ========================== r_work=0.1112 r_free=0.1538 r_work=0.1112 r_free=0.1539 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1112 r_free = 0.1539 target_work(ml) = 4.950 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1108 r_free = 0.1549 target_work(ml) = 4.948 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1108 r_free= 0.1549 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.947783 | | target function (ml) not normalized (work): 80322.313603 | | target function (ml) not normalized (free): 4179.486045 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1129 0.1108 0.1549 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1602 0.1593 0.1819 n_refl.: 17041 remove outliers: r(all,work,free)=0.1602 0.1593 0.1819 n_refl.: 17041 overall B=-0.30 to atoms: r(all,work,free)=0.1583 0.1574 0.1810 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1127 0.1106 0.1547 n_refl.: 17041 remove outliers: r(all,work,free)=0.1127 0.1106 0.1547 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 0.3759 300.293 277.118 0.542 1.002 0.332 11.894-9.307 99.02 97 4 0.1811 488.596 482.938 0.911 1.004 0.326 9.237-7.194 100.00 213 7 0.1735 399.622 400.586 0.990 1.004 0.260 7.162-5.571 100.00 427 22 0.1522 299.917 294.717 0.944 1.004 0.230 5.546-4.326 100.00 867 58 0.0907 411.738 408.487 0.963 1.004 0.201 4.315-3.360 100.00 1859 96 0.0856 391.567 389.324 1.009 1.003 0.191 3.356-2.611 100.00 3867 181 0.1237 257.237 255.076 1.005 1.001 0.141 2.608-2.000 99.99 8818 434 0.1047 167.674 166.459 1.004 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.0413 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1106 r_free=0.1547 After: r_work=0.1108 r_free=0.1546 ================================== NQH flips ================================== r_work=0.1108 r_free=0.1546 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1108 r_free=0.1546 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1108 r_free=0.1546 | n_water=441 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.1108 r_free=0.1546 | n_water=441 | time (s): 35.840 (total time: 36.560) Filter (q & B) r_work=0.1109 r_free=0.1546 | n_water=440 | time (s): 2.350 (total time: 38.910) Compute maps r_work=0.1109 r_free=0.1546 | n_water=440 | time (s): 0.840 (total time: 39.750) Filter (map) r_work=0.1178 r_free=0.1553 | n_water=329 | time (s): 1.800 (total time: 41.550) Find peaks r_work=0.1178 r_free=0.1553 | n_water=329 | time (s): 0.430 (total time: 41.980) Add new water r_work=0.1307 r_free=0.1631 | n_water=460 | time (s): 1.510 (total time: 43.490) Refine new water occ: r_work=0.1149 r_free=0.1469 adp: r_work=0.1142 r_free=0.1474 occ: r_work=0.1129 r_free=0.1454 adp: r_work=0.1121 r_free=0.1456 occ: r_work=0.1113 r_free=0.1447 adp: r_work=0.1107 r_free=0.1449 ADP+occupancy (water only), MIN, final r_work=0.1107 r_free=0.1449 r_work=0.1107 r_free=0.1449 | n_water=460 | time (s): 30.830 (total time: 74.320) Filter (q & B) r_work=0.1110 r_free=0.1462 | n_water=451 | time (s): 1.570 (total time: 75.890) Filter (dist only) r_work=0.1110 r_free=0.1464 | n_water=449 | time (s): 38.250 (total time: 114.140) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.874974 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.187941 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 0.1126 0.1479 0.0353 0.010 1.1 4.5 0.5 0.0 0 0.937 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 14.79 3.53 4.540 20.785 0.188 4.944 11.15 14.79 3.64 4.640 20.860 0.188 4.936 Individual atomic B min max mean iso aniso Overall: 5.30 102.01 20.88 5.10 1976 0 Protein: 5.30 102.01 16.35 5.10 1519 0 Water: 8.43 67.12 36.12 N/A 449 0 Other: 19.58 36.49 25.62 N/A 8 0 Chain A: 5.30 102.01 18.06 N/A 1738 0 Chain S: 15.67 67.12 41.50 N/A 238 0 Histogram: Values Number of atoms 5.30 - 14.97 1023 14.97 - 24.64 387 24.64 - 34.31 214 34.31 - 43.98 184 43.98 - 53.65 115 53.65 - 63.32 31 63.32 - 73.00 12 73.00 - 82.67 3 82.67 - 92.34 3 92.34 - 102.01 4 =========================== Idealize ADP of riding H ========================== r_work=0.1115 r_free=0.1479 r_work=0.1115 r_free=0.1478 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1115 r_free = 0.1478 target_work(ml) = 4.936 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1108 r_free = 0.1476 target_work(ml) = 4.933 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1108 r_free= 0.1476 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.932629 | | target function (ml) not normalized (work): 80076.299884 | | target function (ml) not normalized (free): 4154.815036 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1133 0.1345 5.4716 5.625| | 2: 3.63 - 2.88 1.00 2711 122 0.1087 0.1425 5.2092 5.3371| | 3: 2.88 - 2.52 1.00 2681 148 0.1345 0.1719 5.1186 5.2165| | 4: 2.52 - 2.29 1.00 2661 139 0.0943 0.1469 4.624 4.938| | 5: 2.29 - 2.13 1.00 2678 122 0.0958 0.1476 4.5747 4.8735| | 6: 2.13 - 2.00 1.00 2692 117 0.1111 0.1653 4.5671 4.7549| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.75 1.00 0.96 6156.88| | 2: 3.63 - 2.88 2711 122 0.93 12.54 1.01 0.96 6156.88| | 3: 2.88 - 2.52 2681 148 0.88 18.57 0.99 0.96 6156.88| | 4: 2.52 - 2.29 2661 139 0.93 11.90 1.01 0.98 2078.33| | 5: 2.29 - 2.13 2678 122 0.92 13.94 1.00 0.98 2078.33| | 6: 2.13 - 2.00 2692 117 0.90 16.59 0.99 0.98 2078.33| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2078.33 max = 6156.88 mean = 4139.21| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.86 mean = 13.68| |phase err.(test): min = 0.00 max = 88.79 mean = 13.33| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1126 0.1108 0.1476 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1589 0.1580 0.1795 n_refl.: 17041 remove outliers: r(all,work,free)=0.1589 0.1580 0.1795 n_refl.: 17041 overall B=-0.25 to atoms: r(all,work,free)=0.1573 0.1564 0.1787 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1126 0.1108 0.1476 n_refl.: 17041 remove outliers: r(all,work,free)=0.1126 0.1108 0.1476 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 0.3708 300.293 279.512 0.545 1.005 0.340 11.894-9.307 99.02 97 4 0.1757 488.596 483.012 0.908 1.006 0.340 9.237-7.194 100.00 213 7 0.1788 399.622 401.170 0.986 1.006 0.240 7.162-5.571 100.00 427 22 0.1563 299.917 294.407 0.938 1.005 0.220 5.546-4.326 100.00 867 58 0.0931 411.738 408.746 0.962 1.005 0.191 4.315-3.360 100.00 1859 96 0.0880 391.567 389.052 1.005 1.003 0.181 3.356-2.611 100.00 3867 181 0.1229 257.237 255.321 1.002 1.001 0.121 2.608-2.000 99.99 8818 434 0.1036 167.674 166.359 0.997 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8725 ================= 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 : 0.2785 0.1814 0.083 5.285 8.8 119.3 19.9 258 0.000 1_bss: 0.1606 0.1638 0.083 5.285 8.4 118.9 19.5 258 0.000 1_settarget: 0.1606 0.1638 0.083 5.285 8.4 118.9 19.5 258 0.000 1_nqh: 0.1606 0.1638 0.083 5.285 8.4 118.9 19.5 258 0.000 1_weight: 0.1606 0.1638 0.083 5.285 8.4 118.9 19.5 258 0.000 1_xyzrec: 0.1351 0.1641 0.009 0.991 8.4 118.9 19.5 258 0.150 1_adp: 0.1277 0.1659 0.009 0.991 6.1 113.9 19.9 258 0.150 1_regHadp: 0.1280 0.1666 0.009 0.991 6.1 113.9 19.9 258 0.150 1_occ: 0.1274 0.1660 0.009 0.991 6.1 113.9 19.9 258 0.150 2_bss: 0.1274 0.1655 0.009 0.991 5.8 113.5 19.5 258 0.150 2_settarget: 0.1274 0.1655 0.009 0.991 5.8 113.5 19.5 258 0.150 2_updatecdl: 0.1274 0.1655 0.009 0.999 5.8 113.5 19.5 258 0.150 2_nqh: 0.1274 0.1655 0.009 0.999 5.8 113.5 19.5 258 0.150 2_sol: 0.1234 0.1542 0.009 0.999 5.8 112.4 20.8 362 n/a 2_weight: 0.1234 0.1542 0.009 0.999 5.8 112.4 20.8 362 n/a 2_xyzrec: 0.1207 0.1599 0.008 0.933 5.8 112.4 20.8 362 n/a 2_adp: 0.1196 0.1623 0.008 0.933 7.0 107.4 21.4 362 n/a 2_regHadp: 0.1197 0.1624 0.008 0.933 7.0 107.4 21.4 362 n/a 2_occ: 0.1192 0.1632 0.008 0.933 7.0 107.4 21.4 362 n/a 3_bss: 0.1187 0.1626 0.008 0.933 6.6 107.0 21.0 362 n/a 3_settarget: 0.1187 0.1626 0.008 0.933 6.6 107.0 21.0 362 n/a 3_updatecdl: 0.1187 0.1626 0.008 0.932 6.6 107.0 21.0 362 n/a 3_nqh: 0.1188 0.1630 0.008 0.932 6.6 107.0 21.0 362 n/a 3_sol: 0.1191 0.1539 0.008 0.932 6.6 107.0 21.1 399 n/a 3_weight: 0.1191 0.1539 0.008 0.932 6.6 107.0 21.1 399 n/a 3_xyzrec: 0.1169 0.1528 0.009 0.960 6.6 107.0 21.1 399 n/a 3_adp: 0.1147 0.1526 0.009 0.960 6.4 104.7 20.9 399 n/a 3_regHadp: 0.1147 0.1526 0.009 0.960 6.4 104.7 20.9 399 n/a 3_occ: 0.1142 0.1520 0.009 0.960 6.4 104.7 20.9 399 n/a 4_bss: 0.1140 0.1519 0.009 0.960 6.0 104.3 20.5 399 n/a 4_settarget: 0.1140 0.1519 0.009 0.960 6.0 104.3 20.5 399 n/a 4_updatecdl: 0.1140 0.1519 0.009 0.961 6.0 104.3 20.5 399 n/a 4_nqh: 0.1140 0.1515 0.009 0.961 6.0 104.3 20.5 399 n/a 4_sol: 0.1132 0.1477 0.009 0.961 6.0 104.3 21.0 441 n/a 4_weight: 0.1132 0.1477 0.009 0.961 6.0 104.3 21.0 441 n/a 4_xyzrec: 0.1126 0.1539 0.010 0.973 6.0 104.3 21.0 441 n/a 4_adp: 0.1112 0.1538 0.010 0.973 5.8 102.2 21.0 441 n/a 4_regHadp: 0.1112 0.1539 0.010 0.973 5.8 102.2 21.0 441 n/a 4_occ: 0.1108 0.1549 0.010 0.973 5.8 102.2 21.0 441 n/a 5_bss: 0.1106 0.1547 0.010 0.973 5.5 101.9 20.7 441 n/a 5_settarget: 0.1106 0.1547 0.010 0.973 5.5 101.9 20.7 441 n/a 5_updatecdl: 0.1106 0.1547 0.010 0.973 5.5 101.9 20.7 441 n/a 5_setrh: 0.1108 0.1546 0.010 0.973 5.5 101.9 20.7 441 n/a 5_nqh: 0.1108 0.1546 0.010 0.973 5.5 101.9 20.7 441 n/a 5_sol: 0.1110 0.1464 0.010 0.973 5.5 101.9 20.7 449 n/a 5_weight: 0.1110 0.1464 0.010 0.973 5.5 101.9 20.7 449 n/a 5_xyzrec: 0.1126 0.1479 0.010 1.075 5.5 101.9 20.7 449 n/a 5_adp: 0.1115 0.1479 0.010 1.075 5.3 102.0 20.9 449 n/a 5_regHadp: 0.1115 0.1478 0.010 1.075 5.3 102.0 20.9 449 n/a 5_occ: 0.1108 0.1476 0.010 1.075 5.3 102.0 20.9 449 n/a end: 0.1108 0.1476 0.010 1.075 5.0 101.8 20.6 449 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8498250_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8498250_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.7400 Refinement macro-cycles (run) : 945.7900 Write final files (write_after_run_outputs) : 18.5800 Total : 968.1100 Total CPU time: 16.54 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:33 PST -0800 (1735494093.55 s) Start R-work = 0.1606, R-free = 0.1638 Final R-work = 0.1108, R-free = 0.1476 =============================================================================== Job complete usr+sys time: 1011.49 seconds wall clock time: 17 minutes 14.63 seconds (1034.63 seconds total)